<?xml version="1.0" encoding="UTF-8" ?>
<root>
<Q75E28 type="dict">
<id type="str">
1</id>
<phase_id type="str">
1</phase_id>
<common_name type="str">
Whi3</common_name>
<name type="str">
ABL158Cp</name>
<accession type="str">
Q75E28</accession>
<organism type="str">
Ashbya gossypii</organism>
<sequence type="str">
MSLVNSHSSASVENAAYNLHRAFSSSTENVGHMTPSNSSPLHHSTVVAMGAESQGGGASNNNNNPANPGSTANNNSNNVNMNSIGGGASLGAGSGATGSISGTKGMNNSHSPLHIATMLNTLSMNSNPPSQQQSNVQGPYLVRLQNVPKDTTLRECHALFALAHGVLSIELSSFQQYAERSQTSGQESTNYIVAKFDSLHLACQYATILDEKAQIFGPSFPFKTYVEVVDELTQQQIPFQTQMQMHQGSPPAPTHVTAYQQPLLSASGVVSPPQSASSVKRPSLLVQRSRFSFTDPFSSEQTNMGSQQPDLITTPLKGHQDTGKSFLLMESDEINDSIWGNGTGIPSSISGLTTSQPPTPHLEWGTTGRRQSSTFYPSQSNTEIPPMHLTGQVQSSQLATGLQQPLPQPQRQSLSYNLVTPLSSDMNLPPQSSQGGILPHQAPAQTQPQSQALQHHQHLHHQQQQLQQQQHHLQQQQHQQQQQSLSQQPQQQQSQQSQAHSQQHQQQHQQQQQQQQPQQQQPQQHPPQQPQQQNSQQAIVGQSQQQVTSGQQKGSSRNSISKTLQVNGPKNAAAALQNTNGISQVDLSLLAKVPPPANPADQNPPCNTLYVGNLPPDATEQELRQLFSSQKGFRRLSFRNKNNNGNGHGPMCFVEFEDVAHATRALAELYGSQLARTSGTHNNKGGIRLSFSKNPLGVRGPNSRRGGATNNTSNAGTTNYSYAAAFGKS</sequence>
<gene type="str">
AGOS_ABL158C</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
PolyQ tract; RNA recognition motif (RRM)</segment>
<boundaries type="str">
461-553; 606-694</boundaries>
<region_ref type="str">
26474065</region_ref>
<partners type="str">
1) specific RNAs (via RRM, not strictly required)</partners>
<determinants type="str">
1) protein concentration of Whi3; 2) salt concentration; 3) RNA type; 4) RNA concentration; 5) molar ratios of Whi3 and RNA</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
26474065 (research article), 29650703 (research article), 25713414 (research article)</pmids>
<description type="str">
Whi3 is essential for the spatial patterning of cyclin and formin transcripts in the cytosol of Ashbya gossypii, deletion of a polyglutamine stretch in this protein results in random transcript localization (PMID:25713414, PMID:24315096, PMID:23769973). Super-assembly of Whi3 is a slow response to pheromone, driven by polyQ and polyN domains, counteracted by Hsp70, and stable over generations. Unlike prion aggregates, Whi3 super-assemblies are not inherited mitotically but segregate to the mother cell and thus migh be employed as cellular memory devices, termed mnemons, that encode previous environmental conditions (PMID:24315096). Whi3 interacts via multivalent binding sites on its mRNA binding partners, CLN3 and BNI1, in the regulation of nuclear division and polarity, respectively (PMID:23769973, PMID:25713414). The liquid-like super-assemblies of Whi3 are driven by liquid-liquid phase separation in vivo and in vitro (PMID:26474065). Adding the specific mRNA partners promotes phase separation at phisiological salt concentrations, mRNA can alter the viscosity of Whi3 superassembly droplets, their propensity to fuse, and the exchange rates of components with bulk solution. Different mRNAs impart distinct biophysical properties of Whi3 droplets (CLN3 RNA leads to more viscous, slowly fusing droplets, while BNI1 RNA leads to less viscous, faster fusing droplets), indicating mRNA can bring individuality to assemblies (PMID:26474065). Thus Whi3 likely forms assemblies at different locations and for distinct functions in a single cytoplasm based on the specific mRNAs with which it is in complex (PMID:26474065). mRNA secondary structure plays a key role in what molecular fluctuations Whi3 generates. (PMID:29650703). Without RNA, Whi3 droplets mature and old droplets can appear fibrillar.</description>
<experiment_llps type="str">
In vivo, Whi3 appears to form dynamic droplet-like assemblies in the cytoplasm (localization), which can fuse. Whi3 droplets reside in the cytosol where nuclei reside and also in foci at nascent branches where polarity is being established (localization), as would be predicted from previous functional analysis linking Whi3 to nuclear division and cell polarity. At relatively low salt (75 mM) and relatively high protein concentrations (28 μM), recombinantly expressed, full-length Whi3 phase separates to condensed liquid-like droplets (morphology, particle size and count by microscopy). At physiological salt concentration (150 mM) we see no evidence of phase separation of Whi3 even at very high concentrations of pure protein, thus, Whi3 protein is capable of phase separating on its own; however, under physiological salt and protein conditions there must be other factors promoting condensation. Shortly after adding CLN3 mRNA, new droplets consisting of Whi3 and RNA start to form and enlarge, while protein-only droplets shrink (particle size and count by microscopy). Starting at a low protein and high salt concentration, in which Whi3 alone does not condense into droplets, and then adding CLN3 RNA resulted in droplet formation. In contrast, adding the same amount of DNA, yeast total RNA or heparin did not promote Whi3 droplets. When deleting the polyQ domain, Whi3 cannot phase separate by simply lowering the salt concentration indicating a role for polyQ-driven assembly. However, upon addition of CLN3 mRNA, ΔpolyQ can form droplets, suggesting that the polyQ domain is not strictly essential in mRNA-mediated assembly. Deletion of the RRM domain and remaining C terminus abrogates droplet formation with or without mRNA. Direct binding of the RRM domain with CLN3 mRNA is necessary for mRNA-mediated assembly of droplets as implied by the observation that a double point mutant of the RRM showed a marked reduction in mRNA-mediated assembly (PMID:26474065).; </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26474065); rheological traits (PMID:26474065); dynamic movement/reorganization of molecules within the droplet (PMID:26474065)</experiment_state>
<rna_req type="str">
specific RNAs: CLN3 and BNI1</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID:26474065); protein-RNA interaction (PMID:26474065)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Ágnes Tantos</annotator>
<functional_class type="str">
memory device; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q75E28>
<D0PV95 type="dict">
<id type="str">
2</id>
<phase_id type="str">
2</phase_id>
<common_name type="str">
LAF-1</common_name>
<name type="str">
ATP-dependent RNA helicase laf-1</name>
<accession type="str">
D0PV95</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MESNQSNNGGSGNAALNRGGRYVPPHLRGGDGGAAAAASAGGDDRRGGAGGGGYRRGGGNSGGGGGGGYDRGYNDNRDDRDNRGGSGGYGRDRNYEDRGYNGGGGGGGNRGYNNNRGGGGGGYNRQDRGDGGSSNFSRGGYNNRDEGSDNRGSGRSYNNDRRDNGGDGQNTRWNNLDAPPSRGTSKWENRGARDERIEQELFSGQLSGINFDKYEEIPVEATGDDVPQPISLFSDLSLHEWIEENIKTAGYDRPTPVQKYSIPALQGGRDLMSCAQTGSGKTAAFLVPLVNAILQDGPDAVHRSVTSSGGRKKQYPSALVLSPTRELSLQIFNESRKFAYRTPITSALLYGGRENYKDQIHKLRLGCHILIATPGRLIDVMDQGLIGMEGCRYLVLDEADRMLDMGFEPQIRQIVECNRMPSKEERITAMFSATFPKEIQLLAQDFLKENYVFLAVGRVGSTSENIMQKIVWVEEDEKRSYLMDLLDATGDSSLTLVFVETKRGASDLAYYLNRQNYEVVTIHGDLKQFEREKHLDLFRTGTAPILVATAVAARGLDIPNVKHVINYDLPSDVDEYVHRIGRTGRVGNVGLATSFFNDKNRNIARELMDLIVEANQELPDWLEGMSGDMRSGGGYRGRGGRGNGQRFGGRDHRYQGGSGNGGGGNGGGGGFGGGGQRSGGGGGFQSGGGGGRQQQQQQRAQPQQDWWS</sequence>
<gene type="str">
LAF-1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal R/G-rich disordered region</segment>
<boundaries type="str">
1-168</boundaries>
<region_ref type="str">
26015579</region_ref>
<partners type="str">
1) RNA (via N-terminal RGG region, not strictly required)</partners>
<determinants type="str">
1) protein concentration of LAF-1; 2) salt concentration; 3) RNA concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
P granule; </organelles>
<pmids type="str">
26015579 (research article), 29064502 (research article), 30061688 (research article)</pmids>
<description type="str">
LAF-1 is a a DDX3 RNA helicase that promotes liquid-liquid phase separation of P granules, which is a process important for intracellular organization and stress granule assembly. It phase separates into P granule-like droplets in vitro (PMID:26015579). In vivo, RNAi knockdown of LAF-1 results in the dissolution of P granules in the early embryo, with an apparent submicromolar phase boundary comparable to that measured in vitro. The strong dependence of the phase boundary of pure LAF-1 on salt concentration suggests that electric charge plays an important role in the intermolecular LAF-1 interactions underlying droplet assembly. RNA decreases viscosity and increases molecular dynamics within the LAF-1 liquid droplet through highly dynamic RNA-protein interactions that emerge close to the droplet phase boundary (PMID:26015579). The N-terminal RGG-rich disordered domain is responsible for both phase separation and multivalent RNA binding (PMID:26015579). LAF-1 droplets are permeable, low-density (semi-dilute) liquids characterized by an effective mesh size of ∼3-8 nm, which determines the size scale at which droplet properties impact molecular diffusion and permeability (PMID:29064502).</description>
<experiment_llps type="str">
In vivo, RNAi knockdown of LAF-1 results in the dissolution of P granules in the early embryo (microscopy). In vivo, endogenous LAF-1 exhibits a high degree of colocalization with PGL-1, the founding P granule protein. Upon lowering the salt concentration of solutions of purified LAF-1, the solution became cloudy. Solution turbidity is the result of condensed, highly spherical (morphology) droplets of LAF-1 as assessed by microscopy. At 125 mM NaCl, LAF-1 begins condensing at a critical protein concentration of roughly 800 nM, which is in the same order of magnitude as the estimated in vivo cytoplasmic concentration of LAF-1. LAF-1 droplets are homogeneous fluids with salt-dependent viscosity. Using a single-stranded poly-uridine model RNA (polyU 50), LAF-1 binds RNA with high affinity (KD ≈ 10 nM; physical interaction). Addition of 5 μM RNA into in vitro LAF-1 droplets results in a threefold decrease in the viscosity and more than twofold decrease in the FRAP recovery timescale of LAF-1, with an increase in the apparent diffusion coefficient. The C terminus is not required for phase separation, because truncated LAF-1 lacking the C terminus (ΔC) still forms droplets in vitro (particle size and count by microscopy), exhibiting a phase diagram similar to full-length LAF-1. In contrast, deletion of the RGG-rich N terminus (ΔRGG) results in no observable droplets, even up to concentrations as high as 250 μM. The isolated N-terminal RGG domain was alone sufficient for forming droplets (particle size and count by microscopy) (PMID:26015579). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26015579); rheological traits (PMID:26015579); dynamic movement/reorganization of molecules within the droplet (PMID:26015579)</experiment_state>
<rna_req type="str">
model RNA (polyU 50)</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID:30765518); electrostatic (cation-anion) interaction (PMID:30765518); π-π (pi-pi) interactions (PMID:30765518)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Ágnes Tantos</annotator>
<functional_class type="str">
regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</D0PV95>
<Q7ZXV8 type="dict">
<id type="str">
125</id>
<phase_id type="str">
3</phase_id>
<common_name type="str">
BugZ</common_name>
<name type="str">
BUB3-interacting and GLEBS motif-containing protein ZNF207</name>
<accession type="str">
Q7ZXV8</accession>
<organism type="str">
Xenopus laevis</organism>
<sequence type="str">
MGRKKKKQLKPWCWYCNRDFDDEKILIQHQKAKHFKCHICHKKLYTGPGLAIHCMQVHKETIDAVPNAIPGRTDIELEIYGMEGIPEKDMEERRRILEQKTQVDGQKKKTNQDDSDYDDDDDTAPSTSFQQMQTQQAFMPTMGQPGIPGLPGAPGMPPGITSLMPAVPPLISGIPHVMAGMHPHGMMSMGGMMHPHRPGIPPMMAGLPPGVPPPGLRPGIPPVTQAQPALSQAVVSRLPVPSTSAPALQSVPKPLFPSAGQAQAHISGPVGTDFKPLNNIPATTAEHPKPTFPAYTQSTMSTTSTTNSTASKPSTSITSKPATLTTTSATSKLVHPDEDISLEEKRAQLPKYQRNLPRPGQAPISNMGSTAVGPLGAMMAPRPGLPPQQHGMRHPLPPHGQYGAPLQGMAGYHPGTMPPFGQGPPMVPPFQGGPPRPLMGIRPPVMSQGGRY</sequence>
<gene type="str">
ZNF207</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
P/Q-rich low complexity region</segment>
<boundaries type="str">
93-452</boundaries>
<region_ref type="str">
26388440</region_ref>
<partners type="str">
1) microtubules (via N-terminal MT-binding domain)</partners>
<determinants type="str">
1) temperature; 2) length of LC region</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
spindle matrix</organelles>
<pmids type="str">
26388440 (research article), 29074706 (research article)</pmids>
<description type="str">
ZNF207/BuGZ is a kinetochore- and microtubule-binding protein that plays a key role in spindle assembly (PMID:24462186, PMID:24462187, PMID:26388440). BuGZ coacervation and its binding to microtubules and tubulin are required to promote assembly of spindle and spindle matrix in Xenopus egg extract and in mammalian cells. Human BuGZ-depleted cells suffered more severe spindle defects than Bub3 depleted cells, so BuGZ could directly regulate spindle assembly independent of facilitating kinetochore loading of BUB3. BuGZ is mainly composed of disordered low-complexity regions and undergoes phase separation or coacervation to form temperature-dependent liquid droplets in vivo and in vitro. The low complexity (LC) regions outside the N-terminal microtubule-binding domain are rich in conserved aromatic and hydrophobic residues, as well as prolins, out of which aromatic ones proved to be essential for phase separation by mutational studies. BuGZ coacervation promotes microtubule bundling and concentrates tubulin, promoting microtubule polymerization and assembly of spindle and spindle matrix by concentrating its building blocks (PMID:26388440). The two zinc fingers in BuGZ directly bind to the kinase domain of AurA, which allows AurA to incorporate into the coacervates formed by BuGZ in vitro. Importantly, mutant BuGZ that disrupts the coacervation activity in vitro fails to promote AurA phosphorylation in Xenopus laevis egg extracts, suggesting that BuGZ coacervation promotes AurA activation in mitosis (PMID:29074706). </description>
<experiment_llps type="str">
In vivo depletion (RNAi) of human BuGZ (hBuGZ)  in HeLa cells resulted in a more severe disruption of spindle morphology and reduction of MT intensity than depletion of Bub3. YFP-xBuGZ formed bright droplet-like spheres in the cytosol of Sf9 cells, whereas YFP was evenly distributed. In vitro, upon warming, YFP-tagged xBuGZ formed droplets of varying sizes in physiologically relevant buffers and the droplet size increased over time (particle size and count). When the solutions were cooled on ice, the droplets disintegrated. Purified YFP-xBuGZ underwent an abrupt increase in solution turbidity above a critical temperature in vitro, and the process was reversible upon cooling to the same temperature. The truncated YFP-xBuGZΔN exhibited similar coacervation properties as YFP-xBuGZ (particle size and count), especially at higher protein concentrations (change in protein concentration), indicating that the MT-binding sequence is dispensable for phase transition in vitro. 5 F--&gt; S or 13 Y--&gt;S mutantions in the disordered low complexity region of xBuGZ weakened phase separation (particle size and count by microscopy). A 75 residue segments of the LC region did not form droplets on their own, and reduced the size of pre-formed droplets of wild type BuGZ. YFP-xBuGZ (4 μM), but not xBuGZΔN, xBuGZ13S, or YFP, caused prominent MT bundling (other change in phenotype/functional readout) (PMID:26388440). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:26388440); reversibility of formation and dissolution (PMID:26388440)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
simple coacervation of hydrophobic residues (PMID:26388440); π-π (pi-pi) interactions (PMID:26388440)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q7ZXV8>
<P35637 type="dict">
<id type="str">
4</id>
<phase_id type="str">
4</phase_id>
<common_name type="str">
FUS</common_name>
<name type="str">
RNA-binding protein FUS</name>
<accession type="str">
P35637</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGSSSQSSSYGQPQSGSYSQQPSYGGQQQSYGQQQSYNPPQGYGQQNQYNSSSGGGGGGGGGGNYGQDQSSMSSGGGSGGGYGNQDQSGGGGSGGYGQQDRGGRGRGGSGGGGGGGGGGYNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGRGRGGPMGRGGYGGGGSGGGGRGGFPSGGGGGGGQQRAGDWKCPNPTCENMNFSWRNECNQCKAPKPDGPGGGPGGSHMGGNYGDDRRGGRGGYDRGGYRGRGGDRGGFRGGRGGGDRGGFGPGKMDSRGEHRQDRRERPY</sequence>
<gene type="str">
FUS</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: PLD and RNA-binding domains (RRMs and RGGs)</segment>
<boundaries type="str">
1-526</boundaries>
<region_ref type="str">
29961577</region_ref>
<partners type="str">
1) poly(ADP-ribose) (not required, drives LLPS nucleation in cells); 2) RNA (induces/inhibits droplet formation in low/high concentrations); 3) karyopherin-β2 (weakens LLPS); 4) ATP (induces/inhibits droplet formation in low/high concentrations)</partners>
<determinants type="str">
1) protein concentration of FUS; 2) salt concentration; 3) crowding agent concentration; 4) number of Tyr and Arg residues; 5) modification state; 6) RNA concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic stress granule; cytoplasmic ribonucleoprotein granule</organelles>
<pmids type="str">
22579282 (research article), 22579281 (research article), 26412307 (research article), 28942918 (research article), 26455390 (research article), 28790177 (research article), 26317470 (research article), 29547565 (review), 26526393 (research article), 29677513 (research article), 29677514 (research article), 29677515 (research article), 28041848 (research article), 30205960 (research article), 29897835 (research article), 29961577 (research article), 26286827 (research article), 31067465 (research article), 31188823 (research article)</pmids>
<description type="str">
FUS is DNA/RNA-binding protein that plays a role in various cellular processes such as transcription regulation, RNA splicing, RNA transport, DNA repair and damage response. There are about 30 FUS family proteins in the human genome. These include FET proteins (FUS and the related proteins EWSR1 and TAF15), TDP-43, and hnRNPA1. Aberrant phase transitions of many FUS family proteins have been associated with the onset of age-related neurodegenerative diseases. The amino acid sequences of FUS family proteins can be divided into two modules: a low sequence complexity domain also known as a prion-like domain (PLD) and a domain that binds RNA (RNA-binding domain, or RBD). The PLD contains a small subset of amino acids including polar residues, such as glycine, glutamine, and serine, as well as aromatic residues, generally tyrosine, while the RBDs comprise one or more folded RNA recognition modules (RNA recognition motif, RRM), but they also carry regions of significant intrinsic disorder. The intrinsically disordered regions in RBDs are typically enriched in glycine and positively charged residues, such as arginine (PMID:29961577). In vitro, some PLDs will drive condensate formation as autonomous units, as a result, there has been a focus on PLDs as the main determinants of phase transitions in cells (PMID:22579282, PMID:26455390, PMID:26412307, PMID:28942918). However it seems that the PLD itself cannot be regarded as a physiologically relevant module of the protein from the point of view of LLPS, since it has been shown later that the phase separation of full-length FUS is mainly driven by cation-pi interactions between the Arg residues of the RBD and the Tyr residues of the PLD. The PLD itself has only few Arg residues and thus its hydrogel formation is rather dependent on pi-pi interactions between the Tyr residues and prion-like behavior, which are largely supressed in the context of full-length FUS.; Phase separated condensates of FUS and TAF15 PLDs have been found to be able to recruite the C-terminal repetitive tail of RNA polymerase II, which is especially important in light of the existance of oncogenic fusion proteins harboring those PLDs in combination with DNA-binding domains (PMID:26455390, PMID:24267890).; Both phosphorylation and phosphomimetic variants reduce the aggregation-prone/prion-like character of FUS PLD, disrupting FUS phase separation in the presence of RNA or salt and reducing FUS propensity to aggregate. Also, phosphomimetic FUS reduces aggregation in human and yeast cell models, and can ameliorate FUS-associated cytotoxicity (PMID:28790177).; FUS can form pathological protein aggregates, and specific mutations in FUS have been identified in patients suffering from neurodegenerative diseases. Mutations in FUS are associated with amyotrophic lateral sclerosis (ALS) and rare forms of frontotemporal lobar degeneration (FTLD). Patient-derived mutations in or around the prion-like domain of FUS (G156E and R244C) have an increased tendency to form aggregates (PMID:26317470).; FUS facilitates DNA repair through the transient compartmentalization of DNA damage sites. Its recruitment at DNA damage sites happens through its binding to PAR (attached to the DNA as a result of PARP-1 activation), and leads to the assembly of damaged DNA-rich compartments that recruit DNA repair factors (PMID:31067465).; ATP and nucleic acids share a common two-stage effect on LLPS of several RBPs, including FUS: enhancement of LLPS at low concentrations but dissolution at high concentrations. Cation-π interactions between the PLD and RBD act as the major driving force for LLPS of FUS. Both ATP and oligonucleic acids modulate LLPS of FUS and its dissected domains in the same manner, primarily by targeting the cation-π interactions through specific binding to Arg/Lys residues, as revealed by NMR (PMID:31188823).</description>
<experiment_llps type="str">
FUS, EWSR1, and TAF15, which constitute the FET family showed robust phase separation (particle size and count by microscopy) in the absence of crowding agents at a protein concentration of 5 μM. Although the majority of the FUS family of proteins can phase separate, only the FET proteins possess the requisite sequence features to drive phase separation at low protein concentrations and physiologically relevant salt concentrations. The measured saturation concentration of full-length FUS is 2 μM in 75 mM KCl. Surprisingly, the FUS PLD (truncated), expressed and purified from insect cells, does not drive phase separation as an independent module even for protein concentrations that are as high as 120 μM. Therefore, the saturation concentration for the PLD is almost two orders of magnitude higher than the saturation concentration for the full-length protein. The RBD alone did not phase separate. However, when the FUS PLD was mixed with the FUS RBD at a ratio of 1:1, the PLD phase separated at concentrations as low as 15 μM. Mutational studies, where all the Tyr residues of the PLD (Y--&gt;S) and/or all the Arg residues of the RBD (R--&gt;G) have been changed suggested that these residues are the major determinants of LLPS of FUS and that their number governs the saturation concentration of FUS both in vitro and in vivo in cells (PMID:29961577). Further mutagenesis studies implied that the driving forces for phase separation in vitro and in vivo, quantified in terms of measured saturation concentrations, follow the order: tyrosine-arginine &gt; tyrosine-lysine &gt; phenylalanine-arginine &gt; phenylalanine-lysine, which shows that the selective preference for tyrosine-arginine interactions cannot be solely due to generic cation-p interactions. Instead, the specific chemical structures of the tyrosine and the arginine side chains appear to be important determinants of the complementarity of tyrosine-arginine interactions (PMID:29961577).; In vivo expression of the protein in human cells, truncated to residues 1-211 (low complexity N-terminal region) led to assembly into structures with remarkably spherical morphology via liquid demixing, evidenced by GFP-tagging and fluorescence and phase-contrast microscopy. The RGG repeat region was shown to mediate poly(ADP-ribose) (PAR) binding, using in vivo expression of GFP-tagged full length protein with induced mutations in the RGG region. The number of RGG repeats determined the efficiency of PAR binding, co-localization with PAR, and hence, recruitment to sites of DNA damage. While this is not strictly required for LLPS, PAR binding serves as a nucleation event, increasing local protein concentration at sites of DNA damage. Protein localization and co-localization was followed using standard widefield, confocal, high-content microscopy and time-lapse imaging. In a cellular, in vivo context, depletion of FUS with RNA interference, and abrogation of PAR formation both led to the lack of granule formation at sites of DNA damage, observed using time-lapse bright-field and phase-contrast live-cell microscopy. In vitro cell-free measurements recombinant FUS was incubated with and without sub-stoichiometric amounts of PAR, forming spontaneous aggregates, which were consistently larger in the presence of PAR, followed by transmission electron microscopy (TEM). Consistent with in vivo results, these data provide evidence for the intrinsic ability of PAR chains to nucleate aggregation of low complexity domain-containing disordered proteins (PMID:26286827).; In vitro phosphorylation of recombinant, isolated FUS LC reduces its ability to bind hydrogels formed from amyloid‐like fibrils of purified recombinant, unphosphorylated FUS LC (PMID:22579282); Both phosphorylation and phosphomimetic variants reduce the aggregation-prone/prion-like character of FUS PLD, disrupting FUS phase separation in the presence of RNA or salt and reducing FUS propensity to aggregate. Also, phosphomimetic FUS reduces aggregation in human and yeast cell models, and can ameliorate FUS-associated cytotoxicity (PMID:28790177).; BAC transgene has been generated for the in vivo expression of GFP-tagged FUS after introduced into HeLa and embryonic stem (ES) cells to generate stable cell lines. Mass spectrometry was used to determine the physiological concentration of FUS in HeLa cells, that is around 2 μM in the cytoplasm and between 4 and 8 μM in the nucleus. Actinomycin D (a potent inhibitor of RNA polymerase II) treatment of FUS-GFP HeLa cells suggested that under normal conditions, FUS assembles into compartments (particle size and count) that may be associated with transcription or splicing. FUS accumulated in the cytoplasm in heat-stressed cells and coalesced into stress granules (in vivo protein localization). In vivo FUS assemblies have all the hallmarks of a liquid state: they turn over quickly; are spherical; and when they fuse, they relax into one spherical assembly. A 10% solution of either dextran or polyethylene glycol (PEG) induced the in vitro assembly of recombinant GFP-tagged FUS (10 μM) purified from insect cells (but not that of truncated FUSΔPLD) into round micrometer-sized structures (PMID:26317470). Inhibition of PARP1/2 prevented the recruitment of FUS to DNA lesions. After 8 hr, no fusion events could be detected for G156E FUS, while 81% of the wild-type FUS droplets still fused. By 12 hr, wild-type droplets also stopped fusing. This indicates that there is indeed a change in the biophysical properties of FUS droplets with time and that the properties of the G156E FUS droplets are changing more quickly than those of the wild-type FUS droplets. This is consistent with the observation that G156E has a higher propensity to aggregate. Another patient-derived mutant of FUS R244C also accelerated the conversion of FUS droplets to a fibrous state (PMID:26317470). ;  </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic exchange of molecules with surrounding solvent (PMID:26317470); dynamic movement/reorganization of molecules within the droplet (PMID:26317470); morphological traits (PMID:26317470); ; </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
212-526|R|hypermethylation|weakens|PMID:29677514,PMID:29677515|PRMT1|Notes:none; 1-211|S|hyperphosphorylation|weakens|PMID:28790177,PMID:29897835|DNA-PK|Notes: FUS&apos;s prionlike domain gets phosphorylated at multiple sites especifically following DNA-damaging stress, which supresses LLPS and aggregation propensity.</ptm_affect>
<disease type="str">
G156E|None|Amyotrophic lateral sclerosis 6 (ALS6)|OMIM:608030|affects|PMID:26317470, PMID:26526393 |Notes: The mutatant has a higher propensity to aggregate, i.e. to get from the liquid-like to the solid-like state.; S96del|None|Amyotrophic lateral sclerosis 6 (ALS6)|OMIM:608030|affects|PMID:26317470, PMID:26526393|Notes: The mutatant has a higher propensity to aggregate, i.e. to get from the liquid-like to the solid-like state.; R244C|dbSNP:rs1165095258|Amyotrophic lateral sclerosis 6 (ALS6)|OMIM:608030|affects|PMID:26317470|Notes: The mutatant has a higher propensity to aggregate, i.e. to get from the liquid-like to the solid-like state.; P525L|dbSNP:rs886041390|Amyotrophic lateral sclerosis 6 (ALS6)|OMIM:608030|promotes|PMID:29677514|Notes: The P525L mutation renders FUS less sensitive to the chaperone activity of TNPO1 and thus not only impairs nuclear import, but also enhances phase separation and SG accumulation of mutant FUS.; </disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
cation-π (cation-pi) interactions (PMID:29961577); π-π (pi-pi) interactions (PMID:29961577); electrostatic (cation-anion) interaction (PMID:29961577)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P35637>
<Q06787 type="dict">
<id type="str">
5</id>
<phase_id type="str">
5</phase_id>
<common_name type="str">
FMRP</common_name>
<name type="str">
Synaptic functional regulator FMR1</name>
<accession type="str">
Q06787</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENNWQPDRQIPFHDVRFPPPVGYNKDINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKPATKDTFHKIKLDVPEDLRQMCAKEAAHKDFKKAVGAFSVTYDPENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLIMRNEEASKQLESSRQLASRFHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEEIMPPNSLPSNNSRVGPNAPEEKKHLDIKENSTHFSQPNSTKVQRVLVASSVVAGESQKPELKAWQGMVPFVFVGTKDSIANATVLLDYHLNYLKEVDQLRLERLQIDEQLRQIGASSRPPPNRTDKEKSYVTDDGQGMGRGSRPYRNRGHGRRGPGYTSGTNSEASNASETESDHRDELSDWSLAPTEEERESFLRRGDGRRRGGGGRGQGGRGRGGGFKGNDDHSRTDNRPRNPREAKGRTTDGSLQIRVDCNNERSVHTKTLQNTSSEGSRLRTGKDRNQKKEKPDSVDGQQPLVNGVP</sequence>
<gene type="str">
FMR1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal R/G-rich RGG motif-containing LC region</segment>
<boundaries type="str">
445-632</boundaries>
<region_ref type="str">
30765518</region_ref>
<partners type="str">
1) RNA (strictly required)</partners>
<determinants type="str">
1) protein concentration of FMRP; 2) RNA concentration; 3) ionic strength; 4) modification state</determinants>
<forms type="str">
liquid droplets, cytoplasmic foci</forms>
<organelles type="str">
cytoplasmic stress granule; cytoplasmic ribonucleoprotein granule; synaptosome, neuron projection; neuronal ribonucleoprotein granule</organelles>
<pmids type="str">
22579281 (research article), 28377034 (research article), 30765518 (research article)</pmids>
<description type="str">
Local translation at the synaptic region of neurons occurs in response to neuronal activity and is referred to as activity-dependent translation. This process regulates synaptic strength and facilitates synaptic plasticity and long-term memory formation. Neurons control activity-dependent translation by sorting and packaging mRNAs into non-membrane-bound protein assemblies known as neuronal granules. These granules transport mRNAs from the neuronal cell body toward the synaptic terminals; mRNA translation is inhibited during transport and then activated in response to stimuli at the synapse. FMRP is a primary component of neuronal granules. It has a low complexity region (LCR), and the FMRP-LCR-RNA droplets are dynamic and liquid-like.  Translational repressors and miRNAs partition into, and concentrate within these FMRP-LCR-RNA droplets. FMRP-LCR phosphorylation by its in vivo kinase partner increases its phase-separation propensity possibly through increasing negative charge densities of glutamic/aspartic acid-rich clusters (PMID:30765518). Arginine perturbations, either by methylation or reduction in pi character by substitution of arginine for lysine residues, perturb important interactions that facilitate the general phase-separation behavior of FMRP-LCR, as previously found for Ddx4. Thus, methylation represents a posttranslational modification that decreases FMRP phase-separation propensity and thus may be important for facilitating neuronal granule disassembly in cells. FMRP-LCR phase separation in vitro, with posttranslational modifications potentially acting as a switch at near physiological concentrations, represents a distinct mechanism for translation inhibition (PMID:30765518).</description>
<experiment_llps type="str">
When transfecting CHO cells with a CFP fused to FMRP (FMRP-CFP) or CFP alone, overexpressed FMRP-CFP induces the formation of distinct micrometer-sized foci in the cytoplasm in vivo (protein localization, particle size and count by microscopy), whereas transfection of CFP alone results in diffuse fluorescence. Three different constructs have been used for in vitro studies: full-length FMRP, truncated FMRP lacking the low-complexity region (FMRPΔLCR), and the 188-residue C-terminal low-complexity region of FMRP containing the RGG motifs. At low in vitro protein concentrations (50μM), droplet formation was not observed for any construct (particle size and count by microscopy). Upon addition of Cy3-labeled sc1 RNA, droplets were formed with FMRP and FMRP-LCR, but not with FMRPΔLCR. FMRP-LCR alone is necessary and sufficient to drive phase separation with sc1 RNA in vitro, however, FMRP-LCR-RNA phase separation is not sequence-specific and does not require sequences capable of G-quadruplex formation. FMRP-LCR-RNA droplets are dynamic and liquid-like (FRAP, morphology). Translational repressors and miRNAs partition into, and concentrate within, FMRP-LCR-RNA droplets (co-localization). Increasing salt concentrations disfavored FMRP-LCR droplet formation in the presence of sc1 RNA. FMRP-LCR phosphorylation by its in vivo kinase partner CKII increases its phase-separation propensity (particle size and count by microscopy) possibly through increasing negative charge densities of glutamic/aspartic acid-rich clusters. FMRP-LCR methylation by PRMT1 decreases phase-separation propensity without notably altering sc1 RNA-binding affinity. Arginine perturbations, either by methylation or reduction in pi character by substitution of arginine for lysine residues, perturb important interactions that facilitate the general phase-separation behavior of FMRP-LCR, as previously found for Ddx4 (PMID:30765518). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30765518); morphological traits (PMID:30765518); other: NMR (PMID:30765518)</experiment_state>
<rna_req type="str">
different RNA sequences, including sc1 RNA</rna_req>
<ptm_affect type="str">
445-632|S|hyperphosphorylation|promotes|PMID:30765518|CKII|Notes:Phospho-FMRP-LCR (containing 8–10 phosphate groups added) shows increased LLPS propensity compared to FMRP-LCR, suggestive of a role of phosphorylations in promoting FMRP-containing neuronal granule formation in cells.; 445-632|R|hypermethylation|weakens|PMID:30765518|PRMT1|Notes: Arginine methylation by PRMT1, PRMT3 or PRMT4 is required for association with polyribosomes, recruitment into stress granules and translation of FMR1 target mRNAs.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID:30765518); electrostatic (cation-anion) interaction (PMID:30765518); π-π (pi-pi) interactions (PMID:30765518)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q06787>
<Q92804 type="dict">
<id type="str">
6</id>
<phase_id type="str">
6</phase_id>
<common_name type="str">
TAF15</common_name>
<name type="str">
TATA-binding protein-associated factor 2N</name>
<accession type="str">
Q92804</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSDSGSYGQSGGEQQSYSTYGNPGSQGYGQASQSYSGYGQTTDSSYGQNYSGYSSYGQSQSGYSQSYGGYENQKQSSYSQQPYNNQGQQQNMESSGSQGGRAPSYDQPDYGQQDSYDQQSGYDQHQGSYDEQSNYDQQHDSYSQNQQSYHSQRENYSHHTQDDRRDVSRYGEDNRGYGGSQGGGRGRGGYDKDGRGPMTGSSGGDRGGFKNFGGHRDYGPRTDADSESDNSDNNTIFVQGLGEGVSTDQVGEFFKQIGIIKTNKKTGKPMINLYTDKDTGKPKGEATVSFDDPPSAKAAIDWFDGKEFHGNIIKVSFATRRPEFMRGGGSGGGRRGRGGYRGRGGFQGRGGDPKSGDWVCPNPSCGNMNFARRNSCNQCNEPRPEDSRPSGGDFRGRGYGGERGYRGRGGRGGDRGGYGGDRSGGGYGGDRSSGGGYSGDRSGGGYGGDRSGGGYGGDRGGGYGGDRGGGYGGDRGGGYGGDRGGYGGDRGGGYGGDRGGYGGDRGGYGGDRGGYGGDRGGYGGDRSRGGYGGDRGGGSGYGGDRSGGYGGDRSGGGYGGDRGGGYGGDRGGYGGKMGGRNDYRNDQRNRPY</sequence>
<gene type="str">
TAF15</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal S/Y/Q/G-rich disordered domain; disordered RGG repeats; RNA binding region RRM</segment>
<boundaries type="str">
1-180; 181-216; 234-320</boundaries>
<region_ref type="str">
26286827</region_ref>
<partners type="str">
1) poly(ADP-ribose) (drives LLPS nucleation in cells); 2) RNA (induces/inhibits droplet formation in low/high concentrations)</partners>
<determinants type="str">
1) protein concentration of TAF15; 2) concentration of poly(ADP-ribose); 3) RNA concentration</determinants>
<forms type="str">
liquid droplet</forms>
<organelles type="str">
nuclear protein granule; </organelles>
<pmids type="str">
22454397 (research article), 24267890 (research article), 26286827 (research article), 29650702 (research article)</pmids>
<description type="str">
The intracellular environment is organized into membraneless compartments that have been termed biomolecular condensates because they form by liquid-liquid phase separation. These condensates often contain RNA binding proteins (RBPs) with distinctive domains, so-called prion-like domains, which are structurally disordered and contain polar amino acids. Interactions between prion-like domains and additional interactions between RNAs and RNA binding domains drive the assembly of prion-like RBPs by phase separation. Many of these phase separated granules are found inside the nucleus, and while their exact roles are not fully understood, many such organelles – for example those that are formed by EWS or TAF15 – are associated with genotoxic stress and can form in response to DNA damage (PMID:29650702 PMID:26286827).</description>
<experiment_llps type="str">
FUS, EWSR1, and TAF15, which constitute the FET family showed robust phase separation in the absence of crowding agents at a protein concentration of 5 μM (PMID:29961577).; In vivo expression of the protein in human cells, truncated to residues 1-216 (low complexity N-terminal region) led to assembly into structures with remarkably spherical morphology via liquid demixing, evidenced by GFP-tagging and fluorescence and phase-contrast microscopy. The RGG repeat region was shown to mediate poly(ADP-ribose) (PAR) binding, using in vivo expression of GFP-tagged full length protein with induced mutations in the RGG region. The number of RGG repeats determined the efficiency of PAR binding, co-localization with PAR, and hence, recruitment to sites of DNA damage. While this is not strictly required for LLPS, PAR binding serves as a nucleation event, increasing local protein concentration at sites of DNA damage. Protein localization and co-localization was followed using standard widefield, confocal, high-content microscopy and time-lapse imaging. In a cellular, in vivo context, depletion of TAF15 with RNA interference, and abrogation of PAR formation both led to the lack of granule formation at sites of DNA damage, observed using time-lapse bright-field and phase-contrast live-cell microscopy.; In vitro cell-free measurements recombinant TAF15 was incubated with and without sub-stoichiometric amounts of PAR, forming spontaneous aggregates, which were consistently larger in the presence of PAR, followed by transmission electron microscopy (TEM). Consistent with in vivo results, these data provide evidence for the intrinsic ability of PAR chains to nucleate aggregation of low complexity domain-containing disordered proteins (PMID:26286827).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26286827); reversibility of formation and dissolution (PMID:26286827)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
complex coacervation (PMID:26286827); prion-like aggregation (PMID:29961577); cation-π (cation-pi) interactions (PMID:29961577) ; π-π (pi-pi) interactions (PMID:29961577)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q92804>
<Q13148 type="dict">
<id type="str">
7</id>
<phase_id type="str">
7</phase_id>
<common_name type="str">
TDP-43, TDP43</common_name>
<name type="str">
TAR DNA-binding protein 43</name>
<accession type="str">
Q13148</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLGNNQGSNMGGGMNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSSMDSKSSGWGM</sequence>
<gene type="str">
TARDBP</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal region (ubiquitin-like domain+disordered region); C-terminal region (prion-like domain, low complexity, G-rich IDR); </segment>
<boundaries type="str">
1-102; 263-414; </boundaries>
<region_ref type="str">
29555476</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) RNA concentration; 2) concentration of poly(ADP-ribose) (PAR); 3) DNA concentration; </determinants>
<forms type="str">
cellular granules, dynamic liquid droplets; </forms>
<organelles type="str">
cytoplasmic stress granule; cytoplasmic ribonucleoprotein granule; </organelles>
<pmids type="str">
22579281 (research article), 22454397 (research article), 27545621 (research article), 28112502 (review), 28988034 (research article), 29511089 (research article), 29438978 (research article), 28265061 (research article), 30814253 (research article), 30728452 (research article), 30826182 (research article), 30853299 (research article), 30100264 (research article), 29555476 (research article); </pmids>
<description type="str">
The TAR-DNA-binding protein-43 (TDP-43) was initially identified to be a host-cell protein capable of binding the TAR DNA of HIV and repressing transcription. TDP-43 belongs to a group of human RNA-binding proteins with prion-like domains incorporating low complexity sequences. The RNA-binding ability of TDP-43 is conferred by two RNA recognition motifs, while the C-terminal prion-like glycine-rich region mediates protein-protein interactions. One key feature of TDP-43 is its functional involvement in forming cellular granules containing both RNA-binding proteins (RBPs) and nucleic acids. TDP-43 is recruited to these cytoplasmic RNA granules (stress granules, SGs) following exposure to various environmental stresses (oxidative, osmotic, heat shock, viral infection). SGs follow a linear dynamic featuring an initial nucleation/formation followed by assembly into larger structures, and eventual disassembly as the cell recovers. In transformed cell lines, depletion of TDP-43 has a negative impact on each of these steps, indicating a key role for TDP-43 in the regulation of this essential cell survival mechanism (PMID:29765078, PMID:29555476).; </description>
<experiment_llps type="str">
The C-terminal domain (CTD) of TDP-43 was knocked-in and were expressein in bacterial cells, to show in vitro using differential interference contrast microscopy that this protein region is enough to form liquid droplets. The particle size and count of CTD droplets showed that single stranded DNA (ssDNA) enhances the LLPS, leading to the formation of an increased number of larger droplets. The extent of this enhancement follows the change in DNA concentration, and this effect is largely independent of the DNA sequence and length. In addition, ssDNA also induced the LLPS of the similarly expressed N-terminal domain fragment (NTD) of TDP-43 in vitro, also followed by differential interference contrast microscopy. The ability of NTD to undergo LLPS is heavily modulated by changes in the protein concentration and changes in the DNA concertraion (or the ratio of these two concentrations). The transition of NTD to the liquid phase is largely independent of the actual DNA sequence, and instead depends mostly on DNA length and concentration. NMR studies also show that at low protein concentrations, NTD exists as a folded entity, while at increasing ssDNA concentrations, the DNA forms aspecific interactions with NTD and induces LLPS (PMID:29555476).; In another study, it has been shown that in vitro TDP-43 interacts with poly(ADP-ribose) (PAR) through its nuclear localization signal (NLS) in the NTD (residues 80-100). In vivo analysis of TDP-43 localization in transgenic drosophila nerve cells using co-immunoprecipitation showed, that PAR and TDP-43 coexist in the same protein complex. The TDP-43:PAR binding was confirmed in vitro, using a PAR-binding dot-blot, where a GST-tagged TDP-43 was spotted onto a membrane, and was incubated with PAR polymer followed by immunoblotting with an antibody directed to PAR. TDP-43 undergoes LLPS, as evidenced by in vitro studies, using a change in salt concentration and the concentration of a crowding agent (dextran), showing that TDP-43 alone pontaneously formed dynamic spherical droplets that fused and increased in size, indicating liquid-like properties, followed using microscopy (PMID:30100264).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:29555476); dynamic movement/reorganization of molecules within the droplet (PMID:30826182); sensitivity to 1,6-hexanediol (PMID:28265061); other: NMR (PMID:29555476)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Q331K|dbSNP:rs80356727|Amyotrophic lateral sclerosis|OMIM:612069|weakens|PMID:30100264|Notes: The Q331K mutation did not completely prevent TDP-43 from forming protein droplets; however, the droplets were fewer in number, and, at lower NaCl concentrations, the droplets coexisted with irregular solid structure.; G348C|dbSNP:rs80356733|Amyotrophic lateral sclerosis|OMIM:612069|affects|PMID:21173160|Notes: Mutant TDP-43 localizes to progressively larger stress granules during stress.; R361S|dbSNP:rs80356735|Amyotrophic lateral sclerosis|OMIM:612069|abolishes|PMID:21257637|Notes: There was a 2-fold reduction in the number of cells forming stress granules in cells expressing the mutation.; M337V|dbSNP:rs80356730|Myotrophic lateral sclerosis|OMIM:612069|weakens|PMID:28265061|Notes:The mutant granules display subprocessive motility.; G298S|dbSNP:rs4884357|Myotrophic lateral sclerosis|OMIM:612069|weakens|PMID:28265061|Notes:The mutant granules display subprocessive motility.; S2_M85del|None|Amyotrophic lateral sclerosis|OMIM:612069|weakens|PMID:30100264|Notes:The truncated form of TDP-43 formed small, spherical structures that did not fuse.; M1_C175del|None|Amyotrophic lateral sclerosis|OMIM:612069|abolishes|PMID:30100264|Notes:The truncated form of TDP-43 formed filamentous aggregates.; </disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-DNA interaction (PMID:29555476); helix-helix interaction driven oligomerization (PMID:28988034); simple coacervation of hydrophobic residues (PMID:29511089); linear oligomerization (PMID:30826182)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; protective storage/reservoir; sensor</functional_class>
<date type="str">
2019-09-11</date>
</Q13148>
<Q8SWR8 type="dict">
<id type="str">
9</id>
<phase_id type="str">
9</phase_id>
<common_name type="str">
Ataxin-2</common_name>
<name type="str">
Ataxin-2 homolog</name>
<accession type="str">
Q8SWR8</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MNNNSKRKTRPTGGGASGGISRYNSNDNSLRPTNNKAGAGGGNGGAAVRPSAQGVYNNTFFMHSATALVGSVVEVRLRSGNIYEGVFRTFSGNFDIALELPACIKSKNLPEEGKVPKHIIFPADTVVTIVAKDFDSQYATAGAFQTDGAISDKCNGARPDEKELEPWDSGANGDIDIELDSAANGWDPNEMFRKNENTFGVTSTFDDSLASYTVPLDKGDSLEFKEAEAKAEKLAAEIENNPTCRDRLDLENGDEEALFAAVERPSTEQDQRGDRGDRERNDRDREREERDRDRDRDRGNKPRGAGDFQLRETMSSDRYITKQTRSITGPQLSHVGMSSQGSGRDRDTRGDGSMMMQSGGGSGQGGSTQSTAALMLAGGLKGVGPAPSANASADSSSKYSGGSMVKRKTVPQGGKVMRNNVPTGGSNVSVSQGGNGNSVGQNKGGYQPSMGMPSQYSYQGNSQIMHGSSQYRNQSHMGGANKLNGDSNANTNKPLPQRQMRQYQGSQSNSSLNYGGEPQSLGKPVHGSHGGHPGQNSNSPPLQTAGPQQQQQQQQQQQQQQQQQQPPQQQQHQNIQPQGQNTQPARQVRTRDNQMQELRQFGQDFQLAPSNTSPPQQQQQQQQQQQQHQVQQQQQRALQQSASPPQQQQQQQQQQQHVVLHQVPQTHLHQAALSQPHYVPQQQPQQAPLPQQQHVPHHMQQKAQQQQLVETQHQHVQKQHQSQPQVQQPPPQLLQDPSQQPLPIYHTMPPPQTSPVVVTSPVLLEQPPPQPMPVVQQQQTQQLATPKPEVSPAPPSSNTTTPTGIASTPTAGVIASAGSEKTTPAAPTPTSNSATVPTGTAATAGGATGTTPVVKKHVLNPSAKPFTPRGPSTPNPSRPHTPQTPVPMTNIYTTTGGHVPPAANQPIYVMQPQHPFPPQTHPQAGQPPRLRRSNYPPMAASQMHVSASAATGQPLITAGPIPQFIQYGHAPHQQQFQSHTYAPMQMRVYPDQPQQLQFMTQTPQSTTPSPGQPHQQFHPPPQPSPAGGGPQPAFTPPTQAATYQLMCVHPQSLLANHYFPPPTPQHPQQNQQQYQIVMQQHQPQ</sequence>
<gene type="str">
ATX2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Middle mIDR: prion-like and poly-Q regions; cIDR: Q/P-rich region</segment>
<boundaries type="str">
351-750; 900-1084</boundaries>
<region_ref type="str">
29772202</region_ref>
<partners type="str">
1) AU-rich RNA (mIDR requires AU-rich RNA for LLPS while cIDR does not)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
neuronal ribonucleoprotein granule; cytoplasmic stress granule</organelles>
<pmids type="str">
29772202 (research article)</pmids>
<description type="str">
Drosophila Ataxin-2 (Atx2) is essential, it is required for multiple functions including animal survival, cell growth, and behavioral plasticity. Both the mIDR and cIDR domains of the Atx2 protein are essential for the normal formation of RNP granules observed in neurons in vivo. However, the efficient formation of Atx2-dependent RNP granules, at least in these neurons, is not necessary for animal survival. In contrast, and critically, loss of either the mIDR or cIDR from Atx2 greatly reduced long term habituation (LTH), arguing that Atx2 contributes to LTH through its IDRs by facilitating the assembly of RNP granules (PMID:29772202). This fits previous observations that mRNP assemblies are thought to function in both the transport of mRNAs to synapses and in maintaining a pool of translationally repressed mRNAs available for activity-induced translation that is required for long-term synaptic plasticity and long-term memory. Importantly, mammalian ATXN2 has been proposed as a target for ALS therapeutics because silencing of Atx2/ATXN2 in neurons can slow down the progression of ALS phenotypes observed in mouse and/or Drosophila models of TDP-43 or C9ORF72 dipeptide toxicity. Strikingly, both GR50 dipeptide repeat and dFUS failed to assemble into granules in S2 cells that expressed Atx2ΔcIDR. Thus, the Atx2 cIDR contributes to and promotes the formation of granules to which GR50 and dFUS are localized in S2 cells (PMID:29772202).</description>
<experiment_llps type="str">
Transgenes (genetic transformation) lacking the mIDR or cIDR (mutants) rescued atx2X1/atx206490 flies (knock-out) to full viability in vivo, therefore, the functions of these IDRs are non-essential. In unstressed cells, endogenous Atx2 is most frequently seen diffusely in the cytoplasm (protein localization) or in very small puncta, however, exposure to arsenite, which mediates oxidative stress, causes Atx2 to accumulate in stress granules (protein localization, co-localization). Loss of the mIDR (mutation) did not cause any visible change in the number or brightness of Atx2-GFP granules (particle size and count) in transfected S2 cells in vivo. In contrast, loss of the cIDR (mutation) results in drastic reduction in the number of cells that formed granules (particle size and count), as well as in a dramatically altered granule morphology, indicating that the cIDR is required for normal assembly of Atx2 into RNP granules. Deleting both the mIDR and cIDR from Atx2 almost completely removes Atx2 granules in S2 cells. Purified mIDR (residues 351–750) of Atx2 protein did not show LLPSs at 10 μM concentration (300 mM NaCl and 10% PEG3350) (paticle size and count by microscopy), however addition of 2 μM AU-rich RNA induced robust phase separation (paticle size and count by microscopy). The cIDR polypeptide (residues 900-1084) showed robust RNA-independent LLPS (paticle size and count by microscopy) in vitro. In vivo imaging of cells expressing GFP-fused IDR-deleted mutants confirmed that both mIDR and cIDR domains of the Atx2 protein are essential for the normal formation of RNP granules observed in neurons in vivo (paticle size and count, morphology). Atx2 IDRs are required for protein synthesis-dependent long-term habituation (LTH), as loss of either the mIDR or cIDR (mutation) from Atx2 greatly reduced LTH (other change in phenotype/functional readout) (PMID:29772202).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29772202)</experiment_state>
<rna_req type="str">
AU-rich RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID:29772202); cation-π (cation-pi) interactions (PMID:29772202) ; π-π (pi-pi) interactions (PMID:29772202)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q8SWR8>
<Q01844 type="dict">
<id type="str">
10</id>
<phase_id type="str">
10</phase_id>
<common_name type="str">
EWS</common_name>
<name type="str">
RNA-binding protein EWS</name>
<accession type="str">
Q01844</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MASTDYSTYSQAAAQQGYSAYTAQPTQGYAQTTQAYGQQSYGTYGQPTDVSYTQAQTTATYGQTAYATSYGQPPTGYTTPTAPQAYSQPVQGYGTGAYDTTTATVTTTQASYAAQSAYGTQPAYPAYGQQPAATAPTRPQDGNKPTETSQPQSSTGGYNQPSLGYGQSNYSYPQVPGSYPMQPVTAPPSYPPTSYSSTQPTSYDQSSYSQQNTYGQPSSYGQQSSYGQQSSYGQQPPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSMRGGLPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGPGGMFRGGRGGDRGGFRGGRGMDRGGFGGGRRGGPGGPPGPLMEQMGGRRGGRGGPGKMDKGEHRQERRDRPY</sequence>
<gene type="str">
EWSR1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal S/Y/Q/G-rich disordered domain; disordered RGG repeats; RNA binding region RRM</segment>
<boundaries type="str">
1-285; 286-360; 361-447</boundaries>
<region_ref type="str">
26286827</region_ref>
<partners type="str">
1) poly(ADP-ribose) (drives LLPS nucleation in cells); 2) RNA (induces/inhibits droplet formation in low/high concentrations)</partners>
<determinants type="str">
1) protein concentration of EWS; 2) concentration of poly(ADP-ribose); 3) RNA concentration</determinants>
<forms type="str">
liquid droplet; ; </forms>
<organelles type="str">
nuclear protein granule; </organelles>
<pmids type="str">
22454397 (research article), 24267890 (research article), 26286827 (research article), 29650702 (research article); </pmids>
<description type="str">
The intracellular environment is organized into membraneless compartments that have been termed biomolecular condensates because they form by liquid-liquid phase separation. These condensates often contain RNA binding proteins (RBPs) with distinctive domains, so-called prion-like domains, which are structurally disordered and contain polar amino acids. Interactions between prion-like domains and additional interactions between RNAs and RNA binding domains drive the assembly of prion-like RBPs by phase separation. Many of these phase separated granules are found inside the nucleus, and while their exact roles are not fully understood, many such organelles – for example those that are formed by EWS or TAF15 – are associated with genotoxic stress and can form in response to DNA damage (PMID:29650702 PMID:26286827).</description>
<experiment_llps type="str">
FUS, EWSR1, and TAF15, which constitute the FET family showed robust phase separation in the absence of crowding agents at a protein concentration of 5 μM (PMID:29961577). In vivo expression of the protein in human cells, truncated to residues 1-285 (low complexity N-terminal region) led to assembly into structures with remarkably spherical morphology via liquid demixing, evidenced by GFP-tagging, fluorescence microscopy and phase-contrast microscopy. The RGG repeat region was shown to mediate poly(ADP-ribose) (PAR) binding (physical interaction), using in vivo expression of GFP-tagged full length protein with mutations in the RGG region. The number of RGG repeats determined the efficiency of PAR binding, co-localization with PAR, and hence, recruitment to sites of DNA damage. While this is not strictly required for LLPS, PAR binding serves as a nucleation event, increasing local protein concentration at sites of DNA damage. Protein localization and co-localization was followed using standard widefield, confocal, high-content microscopy and time-lapse imaging. In a cellular, in vivo context, depletion of EWS with RNA interference, and abrogation of PAR formation both led to the lack of granule formation at sites of DNA damage, observed using time-lapse bright-field and phase-contrast live-cell microscopy.; In vitro cell-free measurements recombinant EWS was incubated with and without sub-stoichiometric amounts of PAR, forming spontaneous aggregates, which were consistently larger in the presence of PAR, followed by transmission electron microscopy (TEM). Consistent with in vivo results, these data provide evidence for the intrinsic ability of PAR chains to nucleate aggregation of low complexity domain-containing disordered proteins (PMID:26286827).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26286827); reversibility of formation and dissolution (PMID:26286827)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
complex coacervation (PMID:26286827); prion-like aggregation (PMID:29961577); cation-π (cation-pi) interactions (PMID:29961577) ; π-π (pi-pi) interactions (PMID:29961577)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q01844>
<P09651 type="dict">
<id type="str">
12</id>
<phase_id type="str">
12</phase_id>
<common_name type="str">
HNRNPA1, HNRPA1</common_name>
<name type="str">
Heterogeneous nuclear ribonucleoprotein A1</name>
<accession type="str">
P09651</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF</sequence>
<gene type="str">
HNRNPA1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal G-rich prion-like LC region</segment>
<boundaries type="str">
186-372</boundaries>
<region_ref type="str">
26406374</region_ref>
<partners type="str">
1) RNA (not strictly required, but reduces critical hnRNPA1 concentration)</partners>
<determinants type="str">
1) crowding agent concentration; 2) salt concantration; 3) temperature; 4) protein concentration of hnRNPA1</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
26406374 (research article), 22579281 (research article), 23455423 (research article), 26412307 (research article), 28041848 (research article), 27768896 (research article), 29425497 (research article), 30728452 (research article), 31043593 (research article)</pmids>
<description type="str">
hnRNPA1 in stress granules is in dynamic equilibrium with the surrounding cytosol. LLPS by hnRNPA1 occurs spontaneously in a temperature- and protein-concentration-dependent manner in the absence of a crowding agent. Liquid-liquid phase separation by hnRNPA1 is mediated by the C-terminal low complexity domain (LCD) and is distinct from fibrillization. Its LLPS is enthalpy driven and aromatic and electrostatic interactions are its major driving forces. hnRNPA1 amino acid residues 259–264 correspond to a steric zipper motif centered in the LCD and are essential to hnRNPA1’s intrinsic tendency to fibrillize (PMID:23455423). Importantly, the corresponding deletion mutant (A1-Dhexa), which does not fibrillize, readily underwent LLPS, demonstrating that LLPS and fibrillization are two mechanistically distinct processes (PMID:23455423). Molecular crowding, electrostatic and hydrophobic interactions, and increased cytoplasmic concentration of hnRNPs contribute to liquid-liquid phase separation of hnRNPA1. RNA facilitates liquid-liquid phase separation of hnRNPA1 by binding to RRMs and LCD. hnRNPA1 is also able to assemble into hydrogels composed of uniformly polymerized amyloid-like fibers (PMID:22579281), however, hnRNPA1 is more rigidly incorporated into hydrogels than into liquid droplets. Missense mutations in the LCD of hnRNPA1 cause ALS and multisystem proteinopathy (MSP), a pleiotropic degenerative disorder affecting muscle and brain (PMID:26406374, PMID:26412307, PMID:23455423). </description>
<experiment_llps type="str">
The His-SUMO-hnRNPA1 solution exhibited spontaneous temperature-dependent reversible turbidity in the absence of a crowding agent in vitro, which was revealed by differential interference contrast microscopy to reflect the presence of numerous droplets (protein localization, particle size and count). Deletion studies indicate that liquid-liquid phase separation by hnRNPA1 is mediated by the C-terminal low complexity domain (LCD). Using His-SUMO fusion constructs of truncated hnRNPA1 containing either the folded N-terminal RNA recognition motifs (A1-RRM) or the C-terminal disordered LCD (A1-LCD), the A1-LCD alone had the ability to form liquid droplets, whereas A1-RRM failed to undergo LLPS under comparable conditions to full-length hnRNPA1 (A1-FL) and all other conditions tested. Both GFP-tagged A1-LCD and a version with deletion of aa259–264 constituting the steric zipper (GFP-LCD Δhexa) efficiently incorporated into stress granules in HeLa cells in vivo. Ficoll and polyethylene glycol (PEG) were both able to promote hnRNPA1 LLPS. Lowering the NaCl concentration led to LLPS at lower A1-FL concentrations, suggesting that electrostatic interactions contributed to LLPS (PMID:26406374). After cooling down the hnRNPA1 solution from 25 °C to 4 °C negative-staining TEM showed bunches of amyloid fibrils within hnRNPA1 droplets (morphology), which was confirmed by monitoring Thioflavin T (ThT) fluorescence. As temperature was reverted back to 25 °C, the hnRNPA1 solution became clear again, and neither droplets nor amyloid fibrils was observed, indicating that the fibrils are reversible. Based on the ThT intensity, &lt;10% of the total proteins in droplets formed reversible fibrils. However, when keeping the cloudy hnRNPA1 solution at 4 °C for several hours, the solution spontaneously became clear and the amount of reversible fibrils decreased, while a significant amount of irreversible amyloid fibrils emerged which are stable as temperature increased to 25 °C for elongated time. Segment 209-GFGGNDNFG-217, called hnRNPA1 reversible amyloid core, hnRAC1, but not the others, formed hydrogel at 4 °C. The hydrogel was composed of amyloid fibrils observed by TEM. As temperature increased to 25 °C, the fibrils disassociated spontaneously, resembling the behavior of full-length hnRNPA1. In addition to hnRAC1, another two candidates, 246-GFGNDGSNF-254 (named hnRAC2) and 260-YNDFGNY-266 (named hnRAC3) have also been identified. X-ray fibril diffraction showed that reversible hnRAC1, hnRAC2 and hnRAC3 fibrils also feature a typical cross-β architecture as seen in irreversible amyloid fibrils (PMID:31043593).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26406374); dynamic exchange of molecules with surrounding solvent (PMID:26406374); temperature-dependence (PMID:26406374); reversibility of formation and dissolution (PMID:26406374)</experiment_state>
<rna_req type="str">
N-terminally fluorescently labeled RNA fl-RNA44</rna_req>
<ptm_affect type="str">
298|K|poly ADP-ribosylation|promotes|PMID:30728452||Notes: PAR not only dramatically enhances the liquid-liquid phase separation of hnRNP A1, but also promotes the co-phase separation of hnRNP A1 and TDP-43 in vitro and their interaction in vivo.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:23455423); cation-π (cation-pi) interactions (PMID:23455423) ; π-π (pi-pi) interactions (PMID:23455423); formation of amyloid-like/cross-beta/kinked/stacked beta-sheet structures (PMID:31043593)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P09651>
<P22626-2 type="dict">
<id type="str">
88</id>
<phase_id type="str">
13</phase_id>
<common_name type="str">
HNRNPA2B1, HNRPA2B1 </common_name>
<name type="str">
Isoform A2 of Heterogeneous nuclear ribonucleoproteins A2/B1</name>
<accession type="str">
P22626-2</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTINGHNAEVRKALSRQEMQEVQSSRSGRGGNFGFGDSRGGGGNFGPGPGSNFRGGSDGYGSGRGFGDGYNGYGGGPGGGNFGGSPGYGGGRGGYGGGGPGYGNQGGGYGGGYDNYGGGNYGSGNYNDFGNYNQQPSNYGPMKSGNFGGSRNMGGPYGGGNYGPGGSGGSGGYGGRSRY</sequence>
<gene type="str">
HNRNPA2B1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: N-terminal RRMs, C-terminal prion-like LCD</segment>
<boundaries type="str">
1-341</boundaries>
<region_ref type="str">
26544936</region_ref>
<partners type="str">
1) mRNA; 2) TDP-43; 3) tyrosine protein kinase Fyn (not strictly requiered, but induces LLPS)</partners>
<determinants type="str">
1) salt concentration; 2) temperature</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic stress granule; cytoplasmic ribonucleoprotein granule</organelles>
<pmids type="str">
26544936 (research article), 22579281 (research article), 29358076 (research article), 30397184 (research article), 26412307 (research article)</pmids>
<description type="str">
The low complexity (LC) region of hnRNPAB2 is intrinsically disordered. When incubated at high concentration, it is able to polymerize into labile, amyloid-like fibers and form cross-beta polymerization structures, probably driving the formation of hydrogels. In contrast to irreversible, pathogenic amyloids, the fibers polymerized from LC regions disassemble upon dilution. A number of evidence suggest that formation of cross-beta structures by LC regions mediate the formation of RNA granules, liquid-like droplets, and hydrogels. LC domain is collapsed and undergoes LLPS, which readily converts to aggregates for disease mutations. The LC of hnRNPA2 is necessary and sufficient for LLPS and aggregation. The LC domain and the C-terminal domain of TDP-43 interact and co-phase-separate via transient interactions, while hnRNPA2 LC domain methylation by PRMT1 reduces phase separation (PMID:26544936, PMID:29358076). Tyrosine protein kinase Fyn is not strictly required for LLPS, but promotes it and delays aggregation of the P298L mutant (PMID:30397184, PMID:18490510).</description>
<experiment_llps type="str">
U2OS cells were grown on coverslips, heat shocked at 44°C for 45 min, fixed and co-stained with DAPI (blue color), and antibodies to TIA1 (red color) and PPIA (green color). In vivo, TIA1 showed a punctate localization to stress granules and co-localization with the PPIA enzyme (PMID:26544936). ; In vitro differential interference contrast (DIC) microscopy experiments: Full-length WT hnRNPA2 undergoes LLPS after cleavage of a solubility tag (N-terminal maltose-binding protein). At the same conditions, D290V mutant quickly forms aggregates (morphology). Over time, WT droplets fuse and grow (morphology, particle size and count) while D290V aggregates grow larger. P298L forms droplets initially but aggregates over time. Truncation of LC domain (residues 1–189, DLC) prevents both LLPS and aggregation, suggesting that the LC domain is necessary for both phase separation and aggregation.; In vitro NMR experiments: NMR spectrum of phase-separated (apparent concentration 30 mM) hnRNPA2 LC domain (181-341) is highly similar to the spectrum of the monomeric peptide in dispersed phase (65 μM), indicating that the conformations that give rise to the observed LLPS resonances remain disordered. Overlay of 15N-edited one-dimensional spectra of 65 μM monomer and phase-separated state: The monomeric signals are so weak compared to the phase-separated state, they appear as a straight line. The monomeric spectrum is visible at much lower intensity than the phase-separated state, about 470 times less intense than the condensed phase signals, providing an estimated concentration in the condensed phase. NMR spin relaxation parameters R2, R1, and NOE sensitive to local motions at observable resonances of phase-separated and monomer hnRNPA2 LC domains are consistent with structural disorder but slowed motions after LLPS. Slightly lower values of R2 for dispersed-phase reference sample at lower pH suggest some contribution from water exchange to measured R2. (PMID:26544936, PMID:29358076)</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:26544936); reversibility of formation and dissolution (PMID:26544936)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
191|R|methylation|weakens|PMID:23455423|PRMD1|Notes: Effect was tested on LC domain, not on the full-length protein.; 201|R|methylation|weakens|PMID:23455423|PRMD1|Notes:none; 216|R|methylation|weakens|PMID:23455423|PRMD1|Notes:none; 254|R|methylation|weakens|PMID:23455423|PRMD1|Notes:none; 181-341|Y|phosphorylation|promotes|PMID:30397184|Fyn|Notes:none</ptm_affect>
<disease type="str">
D290V|dbSNP:rs397515326|Multisystem proteinopathy 2|OMIM:615422| weakens|PMID:23455423|Notes:none; P298L|None|Paget disease of bone 2, early-onset|OMIM:602080|affects|PMID:23455423|Notes: Increases aggregation propensity.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID:29961577); cation-π (cation-pi) interactions (PMID:29961577) ; π-π (pi-pi) interactions (PMID:29961577)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Beáta Szabó</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P22626-2>
<P31483 type="dict">
<id type="str">
13</id>
<phase_id type="str">
15</phase_id>
<common_name type="str">
TIA1</common_name>
<name type="str">
Nucleolysin TIA-1 isoform p40</name>
<accession type="str">
P31483</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEDEMPKTLYVGNLSRDVTEALILQLFSQIGPCKNCKMIMDTAGNDPYCFVEFHEHRHAAAALAAMNGRKIMGKEVKVNWATTPSSQKKDTSSSTVVSTQRSQDHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQLSYDEVVNQSSPSNCTVYCGGVTSGLTEQLMRQTFSPFGQIMEIRVFPDKGYSFVRFNSHESAAHAIVSVNGTTIEGHVVKCYWGKETLDMINPVQQQNQIGYPQPYGQWGQWYGNAQQIGQYMPNGWQVPAYGMYGQAWNQQGFNQTQSSAPWMGPNYGVQPPQGQNGSMLPNQPSGYRVAGYETQ</sequence>
<gene type="str">
TIA1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: 3 RRM domains and IDR</segment>
<boundaries type="str">
1-386</boundaries>
<region_ref type="str">
29298433</region_ref>
<partners type="str">
1) RNA</partners>
<determinants type="str">
1) presence of Zn²⁺ (upregulator of TIA-1 multimerization); 2) salt concentration</determinants>
<forms type="str">
droplets</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
15371533 (research article), 22579281 (research article), 26412307 (research article), 27768896 (research article), 28817800 (research article), 29298433 (research article), 29457785 (research article)</pmids>
<description type="str">
Tia1 is a well-known stress granule protein. The IDR of Tia1 alone (without RNA binding regions) was not able to phase separate in vitro even in the presence of RNA (tested at low and phisiological salt concentration) (PMID:26412307). Zn²⁺ is rapidly released during arsenite treatment and is necessary for efficient recruitmentof TIA-1 into stress granules, as well as retention. Both in vitro data and cell culture studies are consistent with the idea that Zn²⁺ promotes homomeric multimerization and phase separation of TIA-1, which in turn drives the assembly of TIA-1-positive stress granules (PMID:29298433).; ; </description>
<experiment_llps type="str">
SG dynamics were monitored in HeLa in vivo cells expressing N-terminal GFP-tagged TIA1 wild-type, P362L, A381T, or E384K mutants. GFP-tagged TIA1 showed the identical punctate subcellular distribution as endogenous or untagged TIA1 proteins (protein localization), and the frequency and size of SGs containing these proteins were not altered by introduction of exogenous TIA1 at this modest expression level. We observed no significant impact of the P362L, A381T, or E384K TIA1 mutations on the rates of SG assembly. By contrast, each of these disease-associated mutations resulted in significantly protracted SG disassembly, as assessed by both blinded manual counting and automated image analysis (particle size and count) (PMID:28817800).; Fluorescently tagged, recombinant TIA1-EYFP was shown to self-multimerize in the presence of ZnCl₂ detected by a FRET-based assay in vitro. Using Confocal and Differential interference contrast (DIC) microscopy the droplet formation of the same fluorescently labeled protein was observed in a Zn²⁺ concentration dependent manner at physiological salt concentration. Both low and high salt (50 and 500 mM NaCl, respectively) caused a reduction in droplet size, droplet number, and rate of droplet formation emphasizing the importance of optimal electrostatic interactions to drive the formation of higher-order TIA-1 condensates. The solutions of TIA-1-EYFP developed visible turbidity that varied positively with protein concentration, zinc addition, and molecular crowding by poly-ethylene glycol (PEG) addition. Addition of DTT to simulate the reducing environment of the cell prevented the formation of TIA-1 droplets normaly induced by ZnCl₂ and eliminated the zinc dose response in the FRET assay, consistent with the idea that TIA-1 multimerization is responsive to both zinc and reduction-oxidation (redox) environment (PMID:29298433).; In vitro full-length TIA1 spontaneously phase separated in the absence of any cosolute, at physiological ionic strength of 150 mM, and pH 7.5 on a temperature-sensitive way observed by DIC microscopy. The three disease related mutant of Tia1 (P362L, A381T, E384K) underwent spontaneous temperature- and concentration-dependent LLPS to create liquid droplets that at early time points were morphologically indistinguishable from liquid droplets formed by wild-type protein. In all cases a significant leftward shift in the co-existence line to a lower protein concentration was observed, indicating an increased propensity of mutant TIA1 to phase separate, due to stronger intermolecular protein-protein interactions. Using a quantitative ThT fluorescence assay it has been confirmed that disease-associated mutations in TIA1 significantly accelerated fibrillization. Fluorescence recovery after photobleaching (FRAP) measurements showed that disease-associated mutations significantly altered the dynamic exchange of TIA1 between the dense droplet phase and the light mono-disperse phase, with increased half-recovery times and a smaller overall mobile fraction. These results suggest that the mutations changed the material properties of mutant TIA1 droplets by enhancing transient, nonspecific intermolecular interactions that reduce protein mobility. This observation raises the possibility that material properties of membrane-less organelles composed of TIA1 protein in live cells, such as SGs, could be adversely affected by the disease-associated mutations (PMID:28817800). The same results were obtained in the case of the N357S mutant (PMID:29457785).; The intact protein and the IDR alone precipitates by the b-isox chemical treatment. (PMID:22579281)</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29298433); dynamic exchange of molecules with surrounding solvent (PMID:29298433)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
P362L|dbSNP:rs757332023|Amyotrophic lateral sclerosis (ALS)|OMIM:612069|promotes|PMID:28817800|Notes: Significantly increases the propensity towards phase separation, delaying SG disassembly, and promoting the accumulation of non-dynamic SGs.; A381T|dbSNP:rs768554955|Amyotrophic lateral sclerosis (ALS)|OMIM:612069|promotes|PMID:28817800; E384K|dbSNP:rs747068278|Welander distal myopathy (WDM)|OMIM:604454|promotes|PMID:28817800; N357S|dbSNP:rs116621885|Welander distal myopathy (WDM)|OMIM:604454|promotes|PMID:29457785 </disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
linear oligomerization/self-association (PMID:29298433); prion-like aggregation (PMID:29961577); cation-π (cation-pi) interactions (PMID:29961577) ; π-π (pi-pi) interactions (PMID:29961577)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Beáta Szabó; Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P31483>
<O60500 type="dict">
<id type="str">
16</id>
<phase_id type="str">
18</phase_id>
<common_name type="str">
Nephrin</common_name>
<name type="str">
Nephrin</name>
<accession type="str">
O60500</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MALGTTLRASLLLLGLLTEGLAQLAIPASVPRGFWALPENLTVVEGASVELRCGVSTPGSAVQWAKDGLLLGPDPRIPGFPRYRLEGDPARGEFHLHIEACDLSDDAEYECQVGRSEMGPELVSPRVILSILVPPKLLLLTPEAGTMVTWVAGQEYVVNCVSGDAKPAPDITILLSGQTISDISANVNEGSQQKLFTVEATARVTPRSSDNRQLLVCEASSPALEAPIKASFTVNVLFPPGPPVIEWPGLDEGHVRAGQSLELPCVARGGNPLATLQWLKNGQPVSTAWGTEHTQAVARSVLVMTVRPEDHGAQLSCEAHNSVSAGTQEHGITLQVTFPPSAIIILGSASQTENKNVTLSCVSKSSRPRVLLRWWLGWRQLLPMEETVMDGLHGGHISMSNLTFLARREDNGLTLTCEAFSEAFTKETFKKSLILNVKYPAQKLWIEGPPEGQKLRAGTRVRLVCLAIGGNPEPSLMWYKDSRTVTESRLPQESRRVHLGSVEKSGSTFSRELVLVTGPSDNQAKFTCKAGQLSASTQLAVQFPPTNVTILANASALRPGDALNLTCVSVSSNPPVNLSWDKEGERLEGVAAPPRRAPFKGSAAARSVLLQVSSRDHGQRVTCRAHSAELRETVSSFYRLNVLYRPEFLGEQVLVVTAVEQGEALLPVSVSANPAPEAFNWTFRGYRLSPAGGPRHRILSSGALHLWNVTRADDGLYQLHCQNSEGTAEARLRLDVHYAPTIRALQDPTEVNVGGSVDIVCTVDANPILPGMFNWERLGEDEEDQSLDDMEKISRGPTGRLRIHHAKLAQAGAYQCIVDNGVAPPARRLLRLVVRFAPQVEHPTPLTKVAAAGDSTSSATLHCRARGVPNIVFTWTKNGVPLDLQDPRYTEHTYHQGGVHSSLLTIANVSAAQDYALFTCTATNALGSDQTNIQLVSISRPDPPSGLKVVSLTPHSVGLEWKPGFDGGLPQRFCIRYEALGTPGFHYVDVVPPQATTFTLTGLQPSTRYRVWLLASNALGDSGLADKGTQLPITTPGLHQPSGEPEDQLPTEPPSGPSGLPLLPVLFALGGLLLLSNASCVGGVLWQRRLRRLAEGISEKTEAGSEEDRVRNEYEESQWTGERDTQSSTVSTTEAEPYYRSLRDFSPQLPPTQEEVSYSRGFTGEDEDMAFPGHLYDEVERTYPPSGAWGPLYDEVQMGPWDLHWPEDTYQDPRGIYDQVAGDLDTLEPDSLPFELRGHLV</sequence>
<gene type="str">
NPHS1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Negatively charged intracellular domain (NICD), blocks of high negative charge density with distributed aromatic hydrophobic residues and phosphorylated tyrosines</segment>
<boundaries type="str">
1077-1241</boundaries>
<region_ref type="str">
26553976</region_ref>
<partners type="str">
1) N-WASP (strictly required); 2) Nck1 (strictly required)</partners>
<determinants type="str">
1) phosphorylation state; 2) valency of Nck1; 3) valency of N-WASP; 4) molecular affinities between the components; 5) stoichiometry of the components</determinants>
<forms type="str">
protein-rich dense liquid droplets</forms>
<organelles type="str">
membrane cluster; actin cortical patch; Arp2/3 protein complex</organelles>
<pmids type="str">
22398450 (research article), 25321392 (research article), 26553976 (research article), 27392146 (research article), 30846599 (research article)</pmids>
<description type="str">
In kidney podocytes, the transmembrane protein nephrin plays a central role in forming the glomerular filtration barrier, functioning partly through assembling cortical actin. The cytoplasmic tail of nephrin contains three tyrosine phosphorylation (pTyr) sites, which can each bind the SH2 domain of Nck1. Nck contains three SH3 domains, which can bind the six PRMs in the proline-rich region of N-WASP. N-WASP, in turn, stimulates the nucleation of actin filaments by the Arp2/3 complex. The multivalency of nephrin or NCK is necessary for proper actin assembly and, together with the multivalency of N-WASP, has the potential to cause phase transitions (PMID:22398450, PMID:25321392). With nephrin attached to the bilayer, multivalent interactions enable these proteins to polymerize on the membrane surface and undergo two-dimensional phase separation, producing micrometer-sized clusters. Phosphorylated tyrosines of nephrin cytoplasmic domain get bound by the SH2 domain of Nck1 (PMID:22398450, PMID:25321392), but the NICD of nephrin is also able to form micron-scale nuclear bodies/liquid droplets on its own by complex coacervation helped by positively charged partners as well, even when the Ys are replaced by Fs, so no phosphorylation can happen (PMID:27392146). Also, the 50-residue linker between the first two SH3 domains of Nck enhances phase separation of Nck/N-WASP/nephrin assemblies (PMID:26553976). In the presence of the Arp2/3 complex, the clusters assemble actin filaments, suggesting that clustering of regulatory factors could promote local actin assembly at membranes (PMID:25321392). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. This increase occurs because LLPS of the Nephrin-Nck-N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent (PMID:30846599).</description>
<experiment_llps type="str">
In vitro experiments with engineered proteins: one composed of repeats of a single SH3 domain (SH3m, where m = 1–5), and the other composed of repeats of a PRM ligand (PRMn, where n = 1–5) showed change in optical properties (turbidity) due to the formation liquid droplets by phase separation as assessed by microscopy at high protein concentrations (change in protein concentration). The proteins were concentrated by about 100-fold in the droplets relative to the bulk phase. Higher valency (mutation) allowed for the formation of larger species (particle size and count) at a lower fractional saturation of the binding modules. The phase transition could be blocked by a high-affinity monovalent ligand. The multivalent proteins formed large polymers within the droplets (DLS, SAXS), such that the phase transition probably coincides with a sol–gel transition. The photobleaching recovery rate (FRAP) correlated inversely with the monomer–monomer affinity and valency, suggesting that recovery represents reorganization of a polymer matrix. The coexpression of mCherry–SH35 and eGFP–PRM5 fusion proteins in HeLa cells resulted in the formation of approximately 0.5–2-µm diameter (particle size and count) cytoplasmic (protein localization) puncta containing both fluorophores (protein co-localization) in vivo. The puncta did not stain with a large range of vesicle markers or a lipid dye, suggesting that they are phase-separated bodies rather than vesicular structures (morphology). The addition of NCK to an N-WASP construct caused droplet formation, as occurred in the model systems described above. The addition of a diphosphorylated (2pTyr) nephrin tail peptide dropped the phase boundary for both proteins by more than or equal to twofold (protein phosphorylation). This effect was even more pronounced when nephrin–3pTyr peptide (protein phosphorylation) was added (to the same total pTyr concentration), showing the importance of valency of the components and that the whole system could be regulated by kinases and phosphatases in vivo (PMID:22398450). Fluorescently tagged p-Nephrin, Nck and N-WASP co-localized to clusters formed on fluid supported lipid bilayers. Addition of 10 µM of a monovalent pTyr peptide derived from TIR (with KD of 40 nM for the Nck SH2 domain) to clusters formed from p-Nephrin /(SH3)3/N-WASP dissolved the clusters (particle size and count). Fluorescently tagged p-Nephrin (2200 molecules/µm²) was clustered by addition of 2 μM N-WASP and 1 μM Nck, addition of 10 nM Arp2/3 complex and 1 µM actin (10% rhodamine labeled) showed that actin specifically assembles on p-Nephrin/Nck/N-WASP clusters in an Arp2/3 dependent manner (protein co-localization) (PMID:25321392).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:22398450, PMID:25321392); dynamic movement/reorganization of molecules within the droplet (PMID:22398450, PMID:25321392); dynamic exchange of molecules with surrounding solvent (PMID:22398450)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
1176|Y|phosphorylation|promotes|PMID:16525419|FYN|Notes:none; 1193|Y|phosphorylation|promotes|PMID:16525419|FYN|Notes:none; 1217|Y|phosphorylation|promotes|PMID:16525419|FYN|Notes: Phosphorylation of human nephrin at Y1176, 1193, and 1217 results in the recruitment of the adaptor protein, Nck, leading to a localized actin polymerization.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:22398450, PMID:25321392); multivalent domain-PTM interactions (PMID:22398450, PMID:25321392); complex coacervation (PMID:27392146)</interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</O60500>
<O00401 type="dict">
<id type="str">
17</id>
<phase_id type="str">
18</phase_id>
<common_name type="str">
N-WASP</common_name>
<name type="str">
Neural Wiskott-Aldrich syndrome protein</name>
<accession type="str">
O00401</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSSVQQQPPPPRRVTNVGSLLLTPQENESLFTFLGKKCVTMSSAVVQLYAADRNCMWSKKCSGVACLVKDNPQRSYFLRIFDIKDGKLLWEQELYNNFVYNSPRGYFHTFAGDTCQVALNFANEEEAKKFRKAVTDLLGRRQRKSEKRRDPPNGPNLPMATVDIKNPEITTNRFYGPQVNNISHTKEKKKGKAKKKRLTKADIGTPSNFQHIGHVGWDPNTGFDLNNLDPELKNLFDMCGISEAQLKDRETSKVIYDFIEKTGGVEAVKNELRRQAPPPPPPSRGGPPPPPPPPHNSGPPPPPARGRGAPPPPPSRAPTAAPPPPPPSRPSVAVPPPPPNRMYPPPPPALPSSAPSGPPPPPPSVLGVGPVAPPPPPPPPPPPGPPPPPGLPSDGDHQVPTTAGNKAALLDQIREGAQLKKVEQNSRPVSCSGRDALLDQIRQGIQLKSVADGQESTPPTPAPTSGIVGALMEVMQKRSKAIHSSDEDEDEDDEEDFEDDDEWED</sequence>
<gene type="str">
WASL</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
P-rich motifs</segment>
<boundaries type="str">
277-392</boundaries>
<region_ref type="str">
26553976</region_ref>
<partners type="str">
1) Nephrin (strictly required); 2) Nck1 (strictly required)</partners>
<determinants type="str">
1) phosphorylation state; 2) valency of Nck1; 3) valency of N-WASP; 4) molecular affinities between the components; 5) stoichiometry of the components</determinants>
<forms type="str">
protein-rich dense liquid droplets</forms>
<organelles type="str">
membrane cluster; actin cortical patch; Arp2/3 protein complex</organelles>
<pmids type="str">
22398450 (research article), 25321392 (research article), 26553976 (research article), 27392146 (research article), 30846599 (research article)</pmids>
<description type="str">
In kidney podocytes, the transmembrane protein nephrin plays a central role in forming the glomerular filtration barrier, functioning partly through assembling cortical actin. The cytoplasmic tail of nephrin contains three tyrosine phosphorylation (pTyr) sites, which can each bind the SH2 domain of Nck1. Nck contains three SH3 domains, which can bind the six PRMs in the proline-rich region of N-WASP. N-WASP, in turn, stimulates the nucleation of actin filaments by the Arp2/3 complex. The multivalency of nephrin or NCK is necessary for proper actin assembly and, together with the multivalency of N-WASP, has the potential to cause phase transitions (PMID:22398450, PMID:25321392). With nephrin attached to the bilayer, multivalent interactions enable these proteins to polymerize on the membrane surface and undergo two-dimensional phase separation, producing micrometer-sized clusters. Phosphorylated tyrosines of nephrin cytoplasmic domain get bound by the SH2 domain of Nck1 (PMID:22398450, PMID:25321392), but the NICD of nephrin is also able to form micron-scale nuclear bodies/liquid droplets on its own by complex coacervation helped by positively charged partners as well, even when the Ys are replaced by Fs, so no phosphorylation can happen (PMID:27392146). Also, the 50-residue linker between the first two SH3 domains of Nck enhances phase separation of Nck/N-WASP/nephrin assemblies (PMID:26553976). In the presence of the Arp2/3 complex, the clusters assemble actin filaments, suggesting that clustering of regulatory factors could promote local actin assembly at membranes (PMID:25321392). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. This increase occurs because LLPS of the Nephrin-Nck-N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent (PMID:30846599).</description>
<experiment_llps type="str">
In vitro experiments with engineered proteins: one composed of repeats of a single SH3 domain (SH3m, where m = 1–5), and the other composed of repeats of a PRM ligand (PRMn, where n = 1–5) showed change in optical properties (turbidity) due to the formation liquid droplets by phase separation as assessed by microscopy at high protein concentrations (change in protein concentration). The proteins were concentrated by about 100-fold in the droplets relative to the bulk phase. Higher valency (mutation) allowed for the formation of larger species (particle size and count) at a lower fractional saturation of the binding modules. The phase transition could be blocked by a high-affinity monovalent ligand. The multivalent proteins formed large polymers within the droplets (DLS, SAXS), such that the phase transition probably coincides with a sol–gel transition. The photobleaching recovery rate (FRAP) correlated inversely with the monomer–monomer affinity and valency, suggesting that recovery represents reorganization of a polymer matrix. The coexpression of mCherry–SH35 and eGFP–PRM5 fusion proteins in HeLa cells resulted in the formation of approximately 0.5–2-µm diameter (particle size and count) cytoplasmic (protein localization) puncta containing both fluorophores (protein co-localization) in vivo. The puncta did not stain with a large range of vesicle markers or a lipid dye, suggesting that they are phase-separated bodies rather than vesicular structures (morphology). The addition of NCK to an N-WASP construct caused droplet formation, as occurred in the model systems described above. The addition of a diphosphorylated (2pTyr) nephrin tail peptide dropped the phase boundary for both proteins by more than or equal to twofold (protein phosphorylation). This effect was even more pronounced when nephrin–3pTyr peptide (protein phosphorylation) was added (to the same total pTyr concentration), showing the importance of valency of the components and that the whole system could be regulated by kinases and phosphatases in vivo (PMID:22398450). Fluorescently tagged p-Nephrin, Nck and N-WASP co-localized to clusters formed on fluid supported lipid bilayers. Addition of 10 µM of a monovalent pTyr peptide derived from TIR (with KD of 40 nM for the Nck SH2 domain) to clusters formed from p-Nephrin /(SH3)3/N-WASP dissolved the clusters (particle size and count). Fluorescently tagged p-Nephrin (2200 molecules/µm²) was clustered by addition of 2 μM N-WASP and 1 μM Nck, addition of 10 nM Arp2/3 complex and 1 µM actin (10% rhodamine labeled) showed that actin specifically assembles on p-Nephrin/Nck/N-WASP clusters in an Arp2/3 dependent manner (protein co-localization) (PMID:25321392).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:22398450, PMID:25321392); dynamic movement/reorganization of molecules within the droplet (PMID:22398450, PMID:25321392); dynamic exchange of molecules with surrounding solvent (PMID:22398450)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:22398450, PMID:25321392); multivalent domain-PTM interactions (PMID:22398450, PMID:25321392); complex coacervation (PMID:27392146)</interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</O00401>
<P16333 type="dict">
<id type="str">
18</id>
<phase_id type="str">
18</phase_id>
<common_name type="str">
NCK1, Nck</common_name>
<name type="str">
Cytoplasmic protein NCK1</name>
<accession type="str">
P16333</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDDSKSWWRVRNSMNKTGFVPSNYVERKNSARKASIVKNLKDTLGIGKVKRKPSVPDSASPADDSFVDPGERLYDLNMPAYVKFNYMAEREDELSLIKGTKVIVMEKCSDGWWRGSYNGQVGWFPSNYVTEEGDSPLGDHVGSLSEKLAAVVNNLNTGQVLHVVQALYPFSSSNDEELNFEKGDVMDVIEKPENDPEWWKCRKINGMVGLVPKNYVTVMQNNPLTSGLEPSPPQCDYIRPSLTGKFAGNPWYYGKVTRHQAEMALNERGHEGDFLIRDSESSPNDFSVSLKAQGKNKHFKVQLKETVYCIGQRKFSTMEELVEHYKKAPIFTSEQGEKLYLVKHLS</sequence>
<gene type="str">
NCK1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: SH3-SH3-SH3-SH2 domains with 50 residue conserved linker between SH3_1 and SH3_2</segment>
<boundaries type="str">
1-377</boundaries>
<region_ref type="str">
26553976</region_ref>
<partners type="str">
1) Nephrin (strictly required); 2) N-WASP (strictly required)</partners>
<determinants type="str">
1) phosphorylation state; 2) valency of Nck1; 3) valency of N-WASP; 4) molecular affinities between the components; 5) stoichiometry of the components</determinants>
<forms type="str">
protein-rich dense liquid droplets</forms>
<organelles type="str">
membrane cluster; actin cortical patch; Arp2/3 protein complex</organelles>
<pmids type="str">
22398450 (research article), 25321392 (research article), 26553976 (research article), 27392146 (research article), 30846599 (research article)</pmids>
<description type="str">
In kidney podocytes, the transmembrane protein nephrin plays a central role in forming the glomerular filtration barrier, functioning partly through assembling cortical actin. The cytoplasmic tail of nephrin contains three tyrosine phosphorylation (pTyr) sites, which can each bind the SH2 domain of Nck1. Nck contains three SH3 domains, which can bind the six PRMs in the proline-rich region of N-WASP. N-WASP, in turn, stimulates the nucleation of actin filaments by the Arp2/3 complex. The multivalency of nephrin or NCK is necessary for proper actin assembly and, together with the multivalency of N-WASP, has the potential to cause phase transitions (PMID:22398450, PMID:25321392). With nephrin attached to the bilayer, multivalent interactions enable these proteins to polymerize on the membrane surface and undergo two-dimensional phase separation, producing micrometer-sized clusters. Phosphorylated tyrosines of nephrin cytoplasmic domain get bound by the SH2 domain of Nck1 (PMID:22398450, PMID:25321392), but the NICD of nephrin is also able to form micron-scale nuclear bodies/liquid droplets on its own by complex coacervation helped by positively charged partners as well, even when the Ys are replaced by Fs, so no phosphorylation can happen (PMID:27392146). Also, the 50-residue linker between the first two SH3 domains of Nck enhances phase separation of Nck/N-WASP/nephrin assemblies (PMID:26553976). In the presence of the Arp2/3 complex, the clusters assemble actin filaments, suggesting that clustering of regulatory factors could promote local actin assembly at membranes (PMID:25321392). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. This increase occurs because LLPS of the Nephrin-Nck-N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent (PMID:30846599).</description>
<experiment_llps type="str">
In vitro experiments with engineered proteins: one composed of repeats of a single SH3 domain (SH3m, where m = 1–5), and the other composed of repeats of a PRM ligand (PRMn, where n = 1–5) showed change in optical properties (turbidity) due to the formation liquid droplets by phase separation as assessed by microscopy at high protein concentrations (change in protein concentration). The proteins were concentrated by about 100-fold in the droplets relative to the bulk phase. Higher valency (mutation) allowed for the formation of larger species (particle size and count) at a lower fractional saturation of the binding modules. The phase transition could be blocked by a high-affinity monovalent ligand. The multivalent proteins formed large polymers within the droplets (DLS, SAXS), such that the phase transition probably coincides with a sol–gel transition. The photobleaching recovery rate (FRAP) correlated inversely with the monomer–monomer affinity and valency, suggesting that recovery represents reorganization of a polymer matrix. The coexpression of mCherry–SH35 and eGFP–PRM5 fusion proteins in HeLa cells resulted in the formation of approximately 0.5–2-µm diameter (particle size and count) cytoplasmic (protein localization) puncta containing both fluorophores (protein co-localization) in vivo. The puncta did not stain with a large range of vesicle markers or a lipid dye, suggesting that they are phase-separated bodies rather than vesicular structures (morphology). The addition of NCK to an N-WASP construct caused droplet formation, as occurred in the model systems described above. The addition of a diphosphorylated (2pTyr) nephrin tail peptide dropped the phase boundary for both proteins by more than or equal to twofold (protein phosphorylation). This effect was even more pronounced when nephrin–3pTyr peptide (protein phosphorylation) was added (to the same total pTyr concentration), showing the importance of valency of the components and that the whole system could be regulated by kinases and phosphatases in vivo (PMID:22398450). Fluorescently tagged p-Nephrin, Nck and N-WASP co-localized to clusters formed on fluid supported lipid bilayers. Addition of 10 µM of a monovalent pTyr peptide derived from TIR (with KD of 40 nM for the Nck SH2 domain) to clusters formed from p-Nephrin /(SH3)3/N-WASP dissolved the clusters (particle size and count). Fluorescently tagged p-Nephrin (2200 molecules/µm²) was clustered by addition of 2 μM N-WASP and 1 μM Nck, addition of 10 nM Arp2/3 complex and 1 µM actin (10% rhodamine labeled) showed that actin specifically assembles on p-Nephrin/Nck/N-WASP clusters in an Arp2/3 dependent manner (protein co-localization) (PMID:25321392).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:22398450, PMID:25321392); dynamic movement/reorganization of molecules within the droplet (PMID:22398450, PMID:25321392); dynamic exchange of molecules with surrounding solvent (PMID:22398450)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:22398450, PMID:25321392); multivalent domain-PTM interactions (PMID:22398450, PMID:25321392); complex coacervation (PMID:27392146)</interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</P16333>
<Q9NQI0 type="dict">
<id type="str">
19</id>
<phase_id type="str">
19</phase_id>
<common_name type="str">
DDX4</common_name>
<name type="str">
Probable ATP-dependent RNA helicase DDX4</name>
<accession type="str">
Q9NQI0</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MGDEDWEAEINPHMSSYVPIFEKDRYSGENGDNFNRTPASSSEMDDGPSRRDHFMKSGFASGRNFGNRDAGECNKRDNTSTMGGFGVGKSFGNRGFSNSRFEDGDSSGFWRESSNDCEDNPTRNRGFSKRGGYRDGNNSEASGPYRRGGRGSFRGCRGGFGLGSPNNDLDPDECMQRTGGLFGSRRPVLSGTGNGDTSQSRSGSGSERGGYKGLNEEVITGSGKNSWKSEAEGGESSDTQGPKVTYIPPPPPEDEDSIFAHYQTGINFDKYDTILVEVSGHDAPPAILTFEEANLCQTLNNNIAKAGYTKLTPVQKYSIPIILAGRDLMACAQTGSGKTAAFLLPILAHMMHDGITASRFKELQEPECIIVAPTRELVNQIYLEARKFSFGTCVRAVVIYGGTQLGHSIRQIVQGCNILCATPGRLMDIIGKEKIGLKQIKYLVLDEADRMLDMGFGPEMKKLISCPGMPSKEQRQTLMFSATFPEEIQRLAAEFLKSNYLFVAVGQVGGACRDVQQTVLQVGQFSKREKLVEILRNIGDERTMVFVETKKKADFIATFLCQEKISTTSIHGDREQREREQALGDFRFGKCPVLVATSVAARGLDIENVQHVINFDLPSTIDEYVHRIGRTGRCGNTGRAISFFDLESDNHLAQPLVKVLTDAQQDVPAWLEEIAFSTYIPGFSGSTRGNVFASVDTRKGKSTLNTAGFSSSQAPNPVDDESWD</sequence>
<gene type="str">
DDX4</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
IDR with alternating clusters of opposing charge, FG and RG motifs</segment>
<boundaries type="str">
1-236</boundaries>
<region_ref type="str">
25747659</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of DDX4; 2) salt concentration; 3) modification state; 4) alternative splicing</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
P granule; pi-body</organelles>
<pmids type="str">
25747659 (research article), 27824447 (review), 28894006 (research article), 28041848 (research article)</pmids>
<description type="str">
The disordered tails of Ddx4, a primary constituent of nuage or germ granules, form phase-separated organelles both in live cells and in vitro. These bodies are stabilized by patterned electrostatic interactions that are highly sensitive to temperature, ionic strength, arginine methylation, and splicing. The bodies provide an alternative solvent environment that can concentrate single-stranded DNA but largely exclude double-stranded DNA. This epigenetically crucial nuage/chromatoid body (CB) family of membraneless organelles hosts components of an RNAi pathway, guarding spermatocytes and spermatids against the deleterious activity of transposable elements. Human Ddx4 and its isolated disordered N terminus (residues 1-236) spontaneously self-associate both in cells and in vitro into structures that are indistinguishable from the cellular Ddx4-organelles (PMID:25747659).; </description>
<experiment_llps type="str">
Under near-physiological conditions solutions of 100 μM Ddx4-N1 (mutation, truncation) and Ddx4-YFP (fusion protein) rapidly became turbid (change in optical properties). Under identical conditions, the splicing variant Ddx4-N2 (mutation) remained soluble, revealing that alternative splicing can regulate the formation of organelles. When droplets in the turbid phase were imaged by microscopy, their morphologies and (qualitatively) their distribution of particle size (particle size and count) and time dependence mirrored that seen within cells. Using bright-field microscopy and a thermal stage,a fully dispersed solution of Ddx4N1 (pH 8.0) at 50°C was cooled at 4°C to 22°C. At 36°C, the solution became turbid and droplets were observed to condense with the change in temperature. At all ionic strengths examined, TP increased with increasing Ddx4N1 concentration (change in protein concentration) in a manner that is well predicted by Flory-Huggins theory. The Ddx4-N1-YFP fusion protein was transfected into HeLa cells, and both its expression and protein localization were monitored using fluorescence microscopy in vivo. As the intra-cellular concentration increased over time, dense micron-sized spherical bodies (morphology) were observed to form in the nucleus. A detailed analysis suggested that the number of in vivo formed droplets and their sizes (particle size and count) were limited by the quantity of free monomers. Ddx4-N1 is posttranslationally modified at multiple sites by PRMT1 in vivo and contains six predicted methylation sites. Remarkably, a few methylations per protein of this type significantly destabilized the droplets, lowering the transition temperature by 25°C. The charge clusters of DDX4 persist for approximately 8–10 residues in length and tend to contain 3–8 similarly charged residues. To determine the physical importance of this charge patterning, a Ddx4 variant was produced, Ddx4N1CS (mutation), with the same overall net charge, but in which the blocks were scrambled. In Ddx4N1CS, the regions of opposing charge are removed while simultaneously maintaining the same overall isoelectric point (PI), amino acid composition, and positions of all other residues; this construct was unable to form organelles in vitro under near-physiological conditions or in vivo. To test the physical significance of the distributed phenylalanine residues to droplet formation, a construct was produced where these nine residues were mutated to alanine (Ddx4-N1-FtoA), which was unable to induce droplet formation either in cells (in vivo) or in vitro. While double-stranded DNA was largely excluded from the droplets, the single-stranded DNA was concentrated significantly in the interior of the droplets (protein co-localization). PMID:25747659. The protein within the concentrated phase of phase-separated Ddx4 diffuses as a particle of 600-nm hydrodynamic radius dissolved in water as studied in vitro by NMR. However, NMR spectra reveal sharp resonances with chemical shifts showing Ddx4 to be intrinsically disordered. Spin relaxation measurements indicate that the backbone amides of Ddx4 have significant mobility, explaining why high-resolution spectra are observed, but motion is reduced compared with an equivalently concentrated nonphase-separating control. PMID:28894006.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:25747659, PMID:28894006); temperature-dependence (PMID:25747659); reversibility of formation and dissolution (PMID:25747659)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
1-236|R|hypermethylation|abolishes|PMID:25747659|PRMT1|Notes: The methylation of arginines within the N-terminal disordered region resulting in asymmetric dimethyl arginines (aDMAs) dissolves the DDX4 droplets.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Isoform Q9NQI0-2|affected|PMID:25747659; Isoform Q9NQI0-3|affected|PMID:25747659; </splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:28894006, PMID:25747659); cation-π (cation-pi) interactions (PMID:28894006, PMID:25747659)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
regulator of spatial patterns; inactivation/separation/molecular shield; biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</Q9NQI0>
<O00571 type="dict">
<id type="str">
22</id>
<phase_id type="str">
22</phase_id>
<common_name type="str">
DDX3</common_name>
<name type="str">
ATP-dependent RNA helicase DDX3X</name>
<accession type="str">
O00571</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSHVAVENALGLDQQFAGLDLNSSDNQSGGSTASKGRYIPPHLRNREATKGFYDKDSSGWSSSKDKDAYSSFGSRSDSRGKSSFFSDRGSGSRGRFDDRGRSDYDGIGSRGDRSGFGKFERGGNSRWCDKSDEDDWSKPLPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSSSRASSSRSGGGGHGSSRGFGGGGYGGFYNSDGYGGNYNSQGVDWWGN</sequence>
<gene type="str">
DDX3X</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal S/K-rich LC IDR containing RG motifs and the EIF4E-binding motif</segment>
<boundaries type="str">
1-168</boundaries>
<region_ref type="str">
30531905</region_ref>
<partners type="str">
1) eIF4E (required for in vivo SG formation but not for LLPS)</partners>
<determinants type="str">
1) temperature; 2) salt concentration; 3) concentration of crowding agent; 4) modification state</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
21883093 (research article), 30531905 (research article)</pmids>
<description type="str">
DDX3 is a stress granule (SG)-nucleating factor. It has an active role in stimulating SG formation and maintaining SG integrity independent of its ATPase and helicase activities. It is the N-terminus harbouring the eIF4E-binding motif that is responsible for SG-induction and the recruitement of PABP1 to SGs (PMID:21883093). The spatiotemporal acetylation of DDX3X-IDR1, regulated by CBP and HDAC6, is important for controlling SG formation. Both IDR1 and the helicase core interacting with RNAs contribute to SG localization. The N-terminal IDR of DDX3X (IDR1) can undergo LLPS in vitro, and its acetylation at multiple lysine residues impairs the formation of liquid droplets. Enhanced LLPS propensity through deacetylation of DDX3X-IDR1 by HDAC6 is necessary for SG maturation, but not initiation (PMID:30531905).; </description>
<experiment_llps type="str">
DDX3 functions as an eIF4E-inhibitory protein to specifically repress cap-dependent translation, utilizing an N-terminal eIF4E-binding consensus YIPPHLR motif to interact with eIF4E (physical interaction), thereby blocking the formation of pre-initiation complex eIF4F and translation initiation by trapping eIF4E in a translationally inactive complex. DDX3 has been reported to localize into cytoplasmic SGs while overexpressed or after arsenite treatment stress (protein localization). A GST pull-down was conducted with bacterially expressed fusion proteins, indicating a direct physical interaction between DDX3 and PABP1. ShRNA-specific knockdown of endogenous DDX3 (RNAi) in HeLa cells in vivo led to the formation of much fewer eIF4E-positive SG foci on sorbitol treatment (particle size and count by microscopy). Overexpression of FLAG–DDX3 alone could induce the assembly of PABP1-containing SGs without stress stimuli. Overexpression of FLAG–DDX3_DQAD (impaired ATPase and helicase activity) and FLAG–DDX3_AAA (oss of RNA-unwinding activity) mutants induced PABP1- and eIF4E-containing SG assembly without stress treatment (particle size and count by microscopy), and neither affected the ratio of the cells harbouring PABP1-positive SGs nor had any significant effect on the number of PABP1-positive SGs, indicating that enzymatic activities have no critical role in the SG-inducing ability of DDX3. In vivo mutagenesis /truncation studies indicated that, under resting conditions, the SG-induction ability of DDX3 is mapped to its N-terminal region of amino acids 1–100 and that the DDX3–eIF4E interaction is critical. DDX3-silenced cells (RNAi) lost viability significantly after osmotic stress release, indicating that DDX3 down-regulation reduces cell viability (other change in phenotype/functional readout) after osmotic stress. Overexpression of the EIF4E-binding-defective DDX3_L43A mutant failed to rescue cell survival following oxidative stress, as cell viability decreased from 88% (wild-type DDX3) to 53% (DDX3L43A) (PMID:21883093).; Both CBP and p300, but not PCAF or Tip60, led to acetylation (other PTMs) of endogenous or overexpressed DDX3X in vivo when expressed in HEK293T cells. Five acetylation sites were detected in the IDR1 of DDX3 (K50, K64, K66, K81 and K118). Presence of DDX3X-K118Ac (immunodetection assay) increased upon treatment of cells with HDAC6-specific inhibitors, but not with other HDAC inhibitors. Acetylation assays (other PTMs) confirmed that stress induces (perturbation of the cell environment to induce phenotypic changes) acetylation of DDX3X and other proteins. Oxidative stress inducers including arsenite, puromycin and sorbitol all significantly increased acetylation of DDX3X-K118, while other stresses did not. When adding polyethylene glycol (PEG) to the in vitro expressed and purified DDX3X IDR1 sample, it became turbid (change in optical properties), and micron-sized droplets (particle size and count) were observed by differential interference contrast (DIC) microscopy. The turbidity (OD600) of unacetylated and acetylated IDR1 during LLPS was quantified. Incubation of purified IDR1 with CBP and acetyl-CoA (other PTMs) led to acetylation of all of its ten lysine residues, including K118 and the turbidity (change in optical properties) of this acetylated IDR1 solution was much lower compared to the solution of unacetylated IDR1. The turbidity was restored upon co-incubation of acetylated IDR1 with the purified catalytic domains of HDAC6 (other PTMs) indicating that lysine acetylation impairs the LLPS of IDR1 and that this effect is reversible. The total area of G3BP foci were quantified in vivo, and in DDX3X KO cells clear defects in G3BP granule formation were observed (morphology, particle size and count by microscopy) under oxidative stress, energy depletion and translation inhibition, indicating that DDX3X is important for SG assembly under these specific stress conditions. The reduced total area of G3BP foci in cells lacking DDX3X is restored to WT levels by re-expression of WT or del-IDR2 DDX3X, an observation indicating the critical role of IDR1 for SGs. Granule growth of the acetyl-mimic mutants starts as for the WT protein, but becomes impaired during the process due to low LLPS efficiency; deacetylation by HDAC6 is then required for SG maturation (PMID:30531905). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30531905); temperature-dependence (PMID:30531905); reversibility of formation and dissolution (PMID:30531905)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
118|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes: CBP or p300 acetylates DDX3X on multiple lysines on oxidative stresses. Deacetylation of DDX3X-IDR1 by HDAC6 within stress granules is required for SG maturation.; 35|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes:none; 50|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes:none; 55|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes:none; 64|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes:none; 66|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes:none; 81|K|acetylation|weakens|PMID:30531905|CBP/p300|Notes:none; </ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:30531905)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</O00571>
<P52948 type="dict">
<id type="str">
24</id>
<phase_id type="str">
24</phase_id>
<common_name type="str">
NUP98 </common_name>
<name type="str">
Nuclear pore complex protein Nup98-Nup96</name>
<accession type="str">
P52948</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MFNKSFGTPFGGGTGGFGTTSTFGQNTGFGTTSGGAFGTSAFGSSNNTGGLFGNSQTKPGGLFGTSSFSQPATSTSTGFGFGTSTGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTSTSSGGLFGTTNTTSNPFGSTSGSLFGPSSFTAAPTGTTIKFNPPTGTDTMVKAGVSTNISTKHQCITAMKEYESKSLEELRLEDYQANRKGPQNQVGAGTTTGLFGSSPATSSATGLFSSSTTNSGFAYGQNKTAFGTSTTGFGTNPGGLFGQQNQQTTSLFSKPFGQATTTQNTGFSFGNTSTIGQPSTNTMGLFGVTQASQPGGLFGTATNTSTGTAFGTGTGLFGQTNTGFGAVGSTLFGNNKLTTFGSSTTSAPSFGTTSGGLFGNKPTLTLGTNTNTSNFGFGTNTSGNSIFGSKPAPGTLGTGLGAGFGTALGAGQASLFGNNQPKIGGPLGTGAFGAPGFNTTTATLGFGAPQAPVALTDPNASAAQQAVLQQHINSLTYSPFGDSPLFRNPMSDPKKKEERLKPTNPAAQKALTTPTHYKLTPRPATRVRPKALQTTGTAKSHLFDGLDDDEPSLANGAFMPKKSIKKLVLKNLNNSNLFSPVNRDSENLASPSEYPENGERFSFLSKPVDENHQQDGDEDSLVSHFYTNPIAKPIPQTPESAGNKHSNSNSVDDTIVALNMRAALRNGLEGSSEETSFHDESLQDDREEIENNSYHMHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHFSKYGLQDSDEEEEEHPSKTSTKKLKTAPLPPASQTTPLQMALNGKPAPPPQSQSPEVEQLGRVVELDSDMVDITQEPVLDTMLEESMPEDQEPVSASTHIASSLGINPHVLQIMKASLLTDEEDVDMALDQRFSRLPSKADTSQEICSPRLPISASHSSKTRSLVGGLLQSKFTSGAFLSPSVSVQECRTPRAASLMNIPSTSSWSVPPPLTSVFTMPSPAPEVPLKTVGTRRQLGLVPREKSVTYGKGKLLMDMALFMGRSFRVGWGPNWTLANSGEQLNGSHELENHQIADSMEFGFLPNPVAVKPLTESPFKVHLEKLSLRQRKPDEDMKLYQTPLELKLKHSTVHVDELCPLIVPNLGVAVIHDYADWVKEASGDLPEAQIVKHWSLTWTLCEALWGHLKELDSQLNEPREYIQILERRRAFSRWLSCTATPQIEEEVSLTQKNSPVEAVFSYLTGKRISEACSLAQQSGDHRLALLLSQFVGSQSVRELLTMQLVDWHQLQADSFIQDERLRIFALLAGKPVWQLSEKKQINVCSQLDWKRSLAIHLWYLLPPTASISRALSMYEEAFQNTSDSDRYACSPLPSYLEGSGCVIAEEQNSQTPLRDVCFHLLKLYSDRHYDLNQLLEPRSITADPLDYRLSWHLWEVLRALNYTHLSAQCEGVLQASYAGQLESEGLWEWAIFVLLHIDNSGIREKAVRELLTRHCQLLETPESWAKETFLTQKLRVPAKWIHEAKAVRAHMESDKHLEALCLFKAEHWNRCHKLIIRHLASDAIINENYDYLKGFLEDLAPPERSSLIQDWETSGLVYLDYIRVIEMLRHIQQVDCSGNDLEQLHIKVTSLCSRIEQIQCYSAKDRLAQSDMAKRVANLLRVVLSLHHPPDRTSDSTPDPQRVPLRLLAPHIGRLPMPEDYAMDELRSLTQSYLRELAVGSL</sequence>
<gene type="str">
NUP98</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
FG-rich repeats </segment>
<boundaries type="str">
1-500</boundaries>
<region_ref type="str">
25562883</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of Nup98</determinants>
<forms type="str">
3D meshwork with hydrogel-like properties</forms>
<organelles type="str">
nuclear pore central transport channel; selective hydrogel-like meshwork formed by FG-nucleoporins in nuclear pore central channel</organelles>
<pmids type="str">
25562883 (research article), 27198189 (research article), 23427268 (research article)</pmids>
<description type="str">
The permeability barrier of nuclear pore complexes (NPCs) controls the exchange between nucleus and cytoplasm. It suppresses the flux of inert macromolecules &gt;30 kDa but allows rapid passage of even very large cargoes, provided these are bound to appropriate nuclear transport receptors (facilitated translocation). FG-rich nucleoporin repeats constitute the permeability barrier (PMID:17082456). Nup98 FG domains of mammals, lancelets, insects, nematodes, fungi, plants, amoebas, ciliates, and excavates spontaneously and rapidly phase-separate from dilute (submicromolar) aqueous solutions into characteristic ‘FG particles’ (PMID:25562883). Nup98 FG domain also formed characteristic intra-cellular foci in HeLa cells (PMID:23427268).</description>
<experiment_llps type="str">
Overexpression of GFP-fused Nup98 FG domain in HeLa cells in vivo resulted in characteristic intra-cellular foci (particle size and count) (PMID:23427268). Recombinantly expressed, purified, and immobilized Nup98 domains of diverse species, including human, bound to (physical interaction) human Importin β specifically in vitro. They have also self-assembled into highly selective FG particles. Strikingly, Nup98 FG particles from all ten tested Nup98 FG domains efficiently excluded not only the rather large MBP-mCherry fusion protein (≈75 kDa) but also rejected the far smaller mCherry (≈25 kDa) (other change in phenotype/functional readout). At the same time, these FG phases allowed a high or very high accumulation of NTF2 (other change in phenotype/functional readout, co-localization). In each case, the partition coefficient of NTF2 was at least 1000 times higher than that of mCherry (PMID:25562883).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
sensitivity to 1,6-hexanediol (PMID:25562883); other: FG NUPs form hydrogels rather than liquids through phase separation (PMID:17082456, PMID:25562883)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
gelation (PMID:17082456); π-π (pi-pi) interactions (PMID:17082456)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</P52948>
<P14907 type="dict">
<id type="str">
25</id>
<phase_id type="str">
25</phase_id>
<common_name type="str">
Nsp1, Nsp1p</common_name>
<name type="str">
Nucleoporin NSP1</name>
<accession type="str">
P14907</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MNFNTPQQNKTPFSFGTANNNSNTTNQNSSTGAGAFGTGQSTFGFNNSAPNNTNNANSSITPAFGSNNTGNTAFGNSNPTSNVFGSNNSTTNTFGSNSAGTSLFGSSSAQQTKSNGTAGGNTFGSSSLFNNSTNSNTTKPAFGGLNFGGGNNTTPSSTGNANTSNNLFGATANANKPAFSFGATTNDDKKTEPDKPAFSFNSSVGNKTDAQAPTTGFSFGSQLGGNKTVNEAAKPSLSFGSGSAGANPAGASQPEPTTNEPAKPALSFGTATSDNKTTNTTPSFSFGAKSDENKAGATSKPAFSFGAKPEEKKDDNSSKPAFSFGAKSNEDKQDGTAKPAFSFGAKPAEKNNNETSKPAFSFGAKSDEKKDGDASKPAFSFGAKPDENKASATSKPAFSFGAKPEEKKDDNSSKPAFSFGAKSNEDKQDGTAKPAFSFGAKPAEKNNNETSKPAFSFGAKSDEKKDGDASKPAFSFGAKSDEKKDSDSSKPAFSFGTKSNEKKDSGSSKPAFSFGAKPDEKKNDEVSKPAFSFGAKANEKKESDESKSAFSFGSKPTGKEEGDGAKAAISFGAKPEEQKSSDTSKPAFTFGAQKDNEKKTEESSTGKSTADVKSSDSLKLNSKPVELKPVSLDNKTLDDLVTKWTNQLTESASHFEQYTKKINSWDQVLVKGGEQISQLYSDAVMAEHSQNKIDQSLQYIERQQDELENFLDNFETKTEALLSDVVSTSSGAAANNNDQKRQQAYKTAQTLDENLNSLSSNLSSLIVEINNVSNTFNKTTNIDINNEDENIQLIKILNSHFDALRSLDDNSTSLEKQINSIKK</sequence>
<gene type="str">
NSP1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
FG-rich repeats with N-rich inter-FG spacers</segment>
<boundaries type="str">
2-601</boundaries>
<region_ref type="str">
20304795</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of Nsp1</determinants>
<forms type="str">
hydrogel with amyloid-like; properties</forms>
<organelles type="str">
nuclear pore central transport channel; selective hydrogel-like meshwork formed by FG-nucleoporins in nuclear pore central channel</organelles>
<pmids type="str">
17082456 (research article), 17693259 (research article), 20304795 (research article), 25562883 (research article)</pmids>
<description type="str">
The permeability barrier of nuclear pore complexes (NPCs) controls the exchange between nucleus and cytoplasm. It suppresses the flux of inert macromolecules &gt;30 kDa but allows rapid passage of even very large cargoes, provided these are bound to appropriate nuclear transport receptors (facilitated translocation). FG-rich nucleoporin repeats constitute the permeability barrier, they are essential for viability and engage in two known kinds of interactions: binding of NTRs and hydrogel formation that arises through inter-repeat contact. The F→S mutated Nsp1 repeats failed to form a hydrogel (PMID:17082456). A saturated hydrogel formed by a single nucleoporin FG-repeat domain is sufficient to reproduce the permeability properties of NPCs. Importin beta and related nuclear transport receptors entered such hydrogel &gt;1000x faster than a similarly sized inert macromolecule (PMID:17693259). The NQTS-rich sequences of nucleoporins connect FG motifs in a repeat domain. In contrast to previous belief, they are, however, not just functionless spacers. Instead, they engage in amyloid-like protein-protein contacts that presumably tighten the FG hydrogel-based permeability barrier of NPCs. The cohesiveness of the NQTS-rich FG repeats appears to be so akin to that of the NQ-rich prion domain of Sup35p that the two modules interact with each other. However, while NQ-rich amyloids are very dense, tightly packed structures, where side chain stacking generates an additional anhydrous peptide interface between the β-sheets, FG hydrogel formation apparently stops before a complete collapse of the structure. Consequently, FG hydrogels include water and allow passive entry of small molecules and facilitated entry of NTRs. Too strong inter-FG repeat interactions might be counteracted by the presence of residues that form weaker β-sheets than Gln, such as Ser or Gly. Likewise, while the N-terminal segment of Nsp1p (residues 2-277) alone forms more strong hydrogels, presence of the charged C-terminal FxFG repeats of Nsp1p (residues 274-601) apparently modulate the gel strength such that NTRs can move ≈3-fold faster through the gel. Therefore, in contrast to pathological amyloids, inter-FG repeat contacts do not result in irreversible aggregates (PMID:20304795).</description>
<experiment_llps type="str">
The FG repeats of NUPs can form an elastic hydrogel (morphology) in aqueous solution in vitro as demonstrated by gelling of 26 mg/ml wild-type fsFG-repeat domain from Nsp1 (400 μM). The F→S mutated repeat domain showed no signs of gelling and remained liquid in aqueous solution even at high concentrations (morphology). Thus, inter-repeat contacts between phenylalanines caused the gelling of the wild-type Nsp1 fsFG-repeat domain. FRAP measurement indicated that the fluorescently labeled wild-type Nsp1 fsFG-repeat domain was nearly immobile within the wild-type fsFG-repeat hydrogel. A fluorescently labeled F→S mutated repeat domain showed no interaction and diffused freely within the wild-type gel. The F→Y mutated Nsp1-repeat domains formed a homotypic hydrogel, but failed to bind NTRs (physical interaction), probably because the additional OH group at the phenyl ring cannot be accommodated into the FXFG binding pockets of the NTRs. Remarkably, nsp1 with F→Y mutated repeats fully complemented the removal of NSP1 in a wild-type background in vivo, while Nsp1 F→S could not (other change in phenotype/functional readout). These results indicate that not only the NTR binding but inter-repeat contacts and, hence, hydrogel formation is also required for NPC function and viability (PMID:17082456).; The permeability properties of NUP FG repeat hydrogels have been studied using the N-terminal region the Nsp1 protein. Permeability properties of saturated FG-hydrogels resembled those of NPCs, but unsaturated FG-hydrogels did not (morphology, other change in phenotype/functional readout). The saturated FG-hydrogel (change in protein concentration) became an efficient barrier that firmly excluded the acRedStar protein (inert probe macromolecule). The specific NTR probe, importin β rapidly dissolved within the gel, reaching a partition coefficient of &gt;100. The FG-hydrogel thus behaved as a selective phase constituting an excellent solvent for importin β (PMID:17693259).; The N-terminal segment of Nsp1p (residues 2-277) alone forms more strong hydrogels (morphology), presence of the charged C-terminal FxFG repeats of Nsp1p (residues 274-601) apparently modulate the gel strength such that NTRs can move ≈3-fold faster through the gel in vitro. Therefore, in contrast to pathological amyloids, inter-FG repeat contacts do not result in irreversible aggregates (PMID:20304795). The regular and highly charged part of Nsp1 FG domain (residues 274–601) failed to form particles (particle size and count by microscopy) at 10 µM domain concentration on its own (PMID:25562883).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
other: FG NUPs form hydrogels through phase separation (PMID:17082456, PMID:25562883)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
gelation (PMID:17082456); π-π (pi-pi) interactions (PMID:17082456)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</P14907>
<Q02629 type="dict">
<id type="str">
26</id>
<phase_id type="str">
26</phase_id>
<common_name type="str">
Nup100</common_name>
<name type="str">
Nucleoporin NUP100/NSP100</name>
<accession type="str">
Q02629</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MFGNNRPMFGGSNLSFGSNTSSFGGQQSQQPNSLFGNSNNNNNSTSNNAQSGFGGFTSAAGSNSNSLFGNNNTQNNGAFGQSMGATQNSPFGSLNSSNASNGNTFGGSSSMGSFGGNTNNAFNNNSNSTNSPFGFNKPNTGGTLFGSQNNNSAGTSSLFGGQSTSTTGTFGNTGSSFGTGLNGNGSNIFGAGNNSQSNTTGSLFGNQQSSAFGTNNQQGSLFGQQSQNTNNAFGNQNQLGGSSFGSKPVGSGSLFGQSNNTLGNTTNNRNGLFGQMNSSNQGSSNSGLFGQNSMNSSTQGVFGQNNNQMQINGNNNNSLFGKANTFSNSASGGLFGQNNQQQGSGLFGQNSQTSGSSGLFGQNNQKQPNTFTQSNTGIGLFGQNNNQQQQSTGLFGAKPAGTTGSLFGGNSSTQPNSLFGTTNVPTSNTQSQQGNSLFGATKLTNMPFGGNPTANQSGSGNSLFGTKPASTTGSLFGNNTASTTVPSTNGLFGNNANNSTSTTNTGLFGAKPDSQSKPALGGGLFGNSNSNSSTIGQNKPVFGGTTQNTGLFGATGTNSSAVGSTGKLFGQNNNTLNVGTQNVPPVNNTTQNALLGTTAVPSLQQAPVTNEQLFSKISIPNSITNPVKATTSKVNADMKRNSSLTSAYRLAPKPLFAPSSNGDAKFQKWGKTLERSDRGSSTSNSITDPESSYLNSNDLLFDPDRRYLKHLVIKNNKNLNVINHNDDEASKVKLVTFTTESASKDDQASSSIAASKLTEKAHSPQTDLKDDHDESTPDPQSKSPNGSTSIPMIENEKISSKVPGLLSNDVTFFKNNYYISPSIETLGNKSLIELRKINNLVIGHRNYGKVEFLEPVDLLNTPLDTLCGDLVTFGPKSCSIYENCSIKPEKGEGINVRCRVTLYSCFPIDKETRKPIKNITHPLLKRSIAKLKENPVYKFESYDPVTGTYSYTIDHPVLT</sequence>
<gene type="str">
NUP100</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
FG-rich repeats with N/S-rich inter-FG spacers</segment>
<boundaries type="str">
1-959</boundaries>
<region_ref type="str">
25562883</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of Nup100</determinants>
<forms type="str">
3D meshwork with hydrogel-like properties</forms>
<organelles type="str">
nuclear pore central transport channel; selective hydrogel-like meshwork formed by FG-nucleoporins in nuclear pore central channel</organelles>
<pmids type="str">
25562883 (research article), 17082456 (research article), 17418788 (research article)</pmids>
<description type="str">
The permeability barrier of nuclear pore complexes (NPCs) controls the exchange between nucleus and cytoplasm. It suppresses the flux of inert macromolecules &gt;30 kDa but allows rapid passage of even very large cargoes, provided these are bound to appropriate nuclear transport receptors (facilitated translocation). FG-rich nucleoporin repeats constitute the permeability barrier. S. cerevisiae Nup100 is a well-studied Nup98 homolog that can restore a functional permeability barrier in FG Nup-depleted Xenopus NPCs (PMID:25562883). </description>
<experiment_llps type="str">
A 1000 µM Nup100 FG domain stock solution supplemented by 2 M guanidinium hydrochloride (used in order to initially keep the domain molecules in a non-interacting state) was rapidly diluted in 100 volumes of a neutral Tris/NaCl buffer, which reduced the protein concentration to 10 µM (change in protein concentration) and the guanidinium ion concentration to negligible levels. Remarkably, the Nup100 FG domain solution turned instantaneously turbid (change in optical properties), pointing to a very rapid in vitro phase-separation and formation of small particles or liquid droplets, which can be easily recovered by centrifugation. Dynamic light scattering (DLS) on the 10 µM Nup100 FG domain sample showed a very prominent particle population with diameters ranging mostly between 2 and 8 µm (particle size and count). At a lower concentration (0.625 µM, change in protein concentration), a broader main peak with 0.4–4 µm particles was observed (accounting for ≈60% by mass), another peak with 25 nm assembly intermediates (10%) and residual monomers (30%) (particle size and count). Confocal laser-scanning microscopy (CLSM) of Nup100 FG particles, formed in the presence of 5% (vol/vol) Atto390-labeled FG domain tracers, indicated that the particle size (particle size and count) increased with higher initial concentration (change in protein concentration). Regarding their morphology, particles were of nearly spherical shape, whereby the evident deviations from perfect spheres indicated that the phase-separated objects represent solids rather than liquids. After FRAP bleaching the Atto390 fluorophore of labelled FG domains, bleached patterns within the Nup100 FG particles remained stable for some minutes at least. This indicates a solid state of the particles and stable interactions between FG domains. The simultaneously bleached NTR-signal was, however, far more dynamic. Following recombinant expression (after modest induction) FG domains from Nup100 and Nup116 had formed rather large structures (PMID:25562883). Overexpressing YFP-Nup100 FG repeat fusion in S. cerevisiae in vivo also resulted in characteristic intra-cellular foci (PMID:17418788).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
other: FG NUPs form hydrogels rather than liquids through phase separation (PMID:17082456, PMID:25562883)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
gelation (PMID:17082456); π-π (pi-pi) interactions (PMID:17082456)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</Q02629>
<P15502 type="dict">
<id type="str">
27</id>
<phase_id type="str">
27</phase_id>
<common_name type="str">
Elastin</common_name>
<name type="str">
Elastin</name>
<accession type="str">
P15502</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MAGLTAAAPRPGVLLLLLSILHPSRPGGVPGAIPGGVPGGVFYPGAGLGALGGGALGPGGKPLKPVPGGLAGAGLGAGLGAFPAVTFPGALVPGGVADAAAAYKAAKAGAGLGGVPGVGGLGVSAGAVVPQPGAGVKPGKVPGVGLPGVYPGGVLPGARFPGVGVLPGVPTGAGVKPKAPGVGGAFAGIPGVGPFGGPQPGVPLGYPIKAPKLPGGYGLPYTTGKLPYGYGPGGVAGAAGKAGYPTGTGVGPQAAAAAAAKAAAKFGAGAAGVLPGVGGAGVPGVPGAIPGIGGIAGVGTPAAAAAAAAAAKAAKYGAAAGLVPGGPGFGPGVVGVPGAGVPGVGVPGAGIPVVPGAGIPGAAVPGVVSPEAAAKAAAKAAKYGARPGVGVGGIPTYGVGAGGFPGFGVGVGGIPGVAGVPGVGGVPGVGGVPGVGISPEAQAAAAAKAAKYGAAGAGVLGGLVPGPQAAVPGVPGTGGVPGVGTPAAAAAKAAAKAAQFGLVPGVGVAPGVGVAPGVGVAPGVGLAPGVGVAPGVGVAPGVGVAPGIGPGGVAAAAKSAAKVAAKAQLRAAAGLGAGIPGLGVGVGVPGLGVGAGVPGLGVGAGVPGFGAGADEGVRRSLSPELREGDPSSSQHLPSTPSSPRVPGALAAAKAAKYGAAVPGVLGGLGALGGVGIPGGVVGAGPAAAAAAAKAAAKAAQFGLVGAAGLGGLGVGGLGVPGVGGLGGIPPAAAAKAAKYGAAGLGGVLGGAGQFPLGGVAARPGFGLSPIFPGGACLGKACGRKRK</sequence>
<gene type="str">
ELN</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Repeats of GVPGV of hydrophobic domains, KA- and KP-type cross-linking domains</segment>
<boundaries type="str">
27-786</boundaries>
<region_ref type="str">
24727034</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) ionic strength; 2) pH; 3) temperature</determinants>
<forms type="str">
extracellular matrix of elastic fibres</forms>
<organelles type="str">
extracellular matrix; collagen-containing extracellular matrix</organelles>
<pmids type="str">
14500713 (research article), 21081222 (review article), 24727034 (research article), 28507126 (research article), 29120326 (research article), 29886015 (review article), 29738068 (research article), 16906757 (research article), 9431995 (research article)</pmids>
<description type="str">
Elastin is an extracellular matrix (ECM) protein that imparts the elastic properties of stretch and reversible recoil to vertebrate tissues including major blood vessels, lung and skin. Elastin self-assembles from monomers into polymer networks that display elasticity and resilience. The first major step in assembly is a liquid–liquid phase separation known as coacervation. This process represents a continuum of stages from initial phase separation to early growth of droplets by coalescence and later “maturation” leading to fiber formation (PMID:24727034).</description>
<experiment_llps type="str">
Coacervation of tropoelastin was assayed by monitoring turbidity in vitro through light scattering at 300 nm (PMID:9431995) Light scattering and microscopy in vitro measurements reveal that the droplets are 2-6 ím in diameter. Scanning electron microscopy confirms that the droplets are spherical. Three dimensional confocal image stacks based on the autofluorescence of tropoelastin reveal that droplets are loaded with hydrated tropoelastin. In the presence of lysine crosslinking reagents, fibrous and clustered aggregates of droplets are produced visualized after stained with orcein. (PMID:16906757). Phase separation, growth and maturation (particle size and count, morphology) of the coacervates were monitored in real time using light microscopy. The surface properties of a stabilized coacervate droplet of tropoelastin were probed qualitatively using indentation by an atomic force microscopy AFM cantilever tip. (PMID:24727034). Elastin-like polypeptides (ELPs) derived from the tropoelastin sequence have been shown to undergo a similar phase separation, allowing formation of biomaterials that closely mimic the material properties of native elastin. Combination of in vitro solution and solid-state NMR spectroscopy was used to obtain site-specific structure and dynamics of a self-assembling elastin-like polypeptide along its entire self-assembly pathway, from monomer through coacervation and into a cross-linked elastic material. These measurements provide direct evidence for an entropy-driven mechanism of simple coacervation of a protein in which transient and nonspecific intermolecular hydrophobic contacts are formed by disordered chains, whereas bulk water and salt are excluded (PMID:28507126).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
rheological traits (PMID:9431995); temperature-dependence (PMID:9431995); morphological traits (PMID:16906757, PMID:24727034); dynamic movement/reorganization of molecules within the droplet (PMID:28507126)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
simple coacervation of hydrophobic residues (PMID:9431995, PMID:24727034, PMID:28507126); linear oligomerization/self-association (PMID:16906757, PMID:24727034, PMID:28507126)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Éva Schád</annotator>
<functional_class type="str">
mechanical property exploitation</functional_class>
<date type="str">
2019-09-11</date>
</P15502>
<G5EBV6 type="dict">
<id type="str">
28</id>
<phase_id type="str">
28</phase_id>
<common_name type="str">
PGL-3</common_name>
<name type="str">
Guanyl-specific ribonuclease pgl-3</name>
<accession type="str">
G5EBV6</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MEANKRQIVEVDGIKSYFFPHLAHYLASNDELLVNNIAQANKLAAFVLGATDKRPSNEEIAEMILPNDSSAYVLAAGMDVCLILGDDFRPKFDSGAEKLSQLGQAHDLAPIIDDEKKISMLARKTKLKKSNDAKILQVLLKVLGAEEAEEKFVELSELSSALDLDFDVYVLAKLLGFASEELQEEIEIIRDNVTDAFEACKPLLKKLMIEGPKIDSVDPFTQLLLTPQEESIEKAVSHIVARFEEASAVEDDESLVLKSQLGYQLIFLVVRSLADGKRDASRTIQSLMPSSVRAEVFPGLQRSVFKSAVFLASHIIQVFLGSMKSFEDWAFVGLAEDLESTWRRRAIAELLKKFRISVLEQCFSQPIPLLPQSELNNETVIENVNNALQFALWITEFYGSESEKKSLNQLQFLSPKSKNLLVDSFKKFAQGLDSKDHVNRIIESLEKSSSSEPSATAKQTTTSNGPTTVSTAAQVVTVEKMPFSRQTIPCEGTDLANVLNSAKIIGESVTVAAHDVIPEKLNAEKNDNTPSTASPVQFSSDGWDSPTKSVALPPKISTLEEEQEEDTTITKVSPQPQERTGTAWGSGDATPVPLATPVNEYKVSGFGAAPVASGFGQFASSNGTSGRGSYGGGRGGDRGGRGAYGGDRGRGGSGDGSRGYRGGDRGGRGSYGEGSRGYQGGRAGFFGGSRGGS</sequence>
<gene type="str">
PGL-3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Self-interaction domain; RGG domain</segment>
<boundaries type="str">
160-320; 633-693</boundaries>
<region_ref type="str">
21402787</region_ref>
<partners type="str">
1) mRNA (not strictly required, dependant on RGG region 633-693); 2) MEX-5 (negative regulator, compeptitor for mRNA)</partners>
<determinants type="str">
1) salt concentration; 2) protein concentration of PGL-3</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
P granule</organelles>
<pmids type="str">
21402787 (research article), 27594427 (research article), 30173914 (research article), 30608810 (research article), 30833787 (research article)</pmids>
<description type="str">
P granules are non-membrane-bound RNA-protein compartments that are involved in germline development in C. elegans. They are liquids that condense at one end of the embryo by localized phase separation, driven by gradients of polarity proteins such as the mRNA-binding protein MEX-5. The protein PGL-3 can phase separate into P-granule-like droplets in vitro (PMID:27594427). PGL proteins self-aggregate through direct interaction between self-interaction domains. Assembly of PGL-3 droplets at physiological concentration requires mRNA-binding to PGL-3. RGG box of PGL-3 is dispensable for the formation of globular granules but necessary to capture and incorporate RNA and RNA-binding proteins into the granules (PMID:21402787). MEX-5 inhibits mRNA-dependent droplet assembly by competing with PGL-3 for binding mRNA. Competition among MEX-5 and PGL-3 for mRNA can regulate the formation of PGL-3 droplets. It is concluded that gradients of polarity proteins can position RNP granules during development by using RNA competition to regulate local phase separation. In other words, competition for RNA between different proteins can be used to organize the distribution of non-membrane-bound compartments, therefore to spatially organize the cytoplasm (PMID:27594427).</description>
<experiment_llps type="str">
In vivo GST-tagged PGL-1 and PGL-3 formed globular granules—either spherical or ellipsoidal shape with clear boundaries, reminiscent of P granules—in the cytoplasm of CHO cells (protein localization). Granules were detected in 92% (46/50) and 100% (50/50) of the GST::PGL-1– and GST::PGL-3–positive cells, respectively (particle size and count). Granule formation by PGL-3 was confirmed in four other mammalian cell lines (NIH3T3, HeLa, MDCK, and HEK293) (PMID:21402787). Purified PGL-3 fused to monomeric enhanced green fluorescent protein (mEGFP) phase separates into two phases in vitro: one containing PGL-3 at ∼50-fold higher concentration compared to the bulk phase in physiological buffer. When measured in vitro, PGL-3 drops are rare below 0.5 μM (physiological concentration), and the number of drops and the extent of phase separation increases rapidly in the 0.5- to 10-μM range (change in protein concentration, particle size and count by microscopy). Total RNA purified from C. elegans (200 ng/μl) promoted PGL-3 drop assembly (particle size and count by microscopy), while rRNA did not. Addition of total mRNA significantly increased both the number of PGL-3 drops and fraction of total PGL-3 that concentrated within these drops (particle size and count by microscopy). Total mRNA failed to promote the in vitro assembly of drops (particle size and count by microscopy) at physiological protein concentrations of a PGL-3 construct where the arginines in all the six RGG repeats have been mutated to glycine or leucine (RGG_mut). mRNA concentrated within PGL-3 drops (co-localization). Physiological concentration of mRNA can promote assembly of drops at physiological concentrations of PGL-3. Presence of MEX-5 (region 236–350) significantly inhibits mRNA-dependent assembly of PGL-3 drops (particle size and count by microscopy) over a broad range of mRNA concentrations (PMID:27594427). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:27594427); dynamic movement/reorganization of molecules within the droplet (PMID:27594427); dynamic exchange of molecules with surrounding solvent (PMID:27594427); rheological traits (PMID:27594427, PMID:30608810)</experiment_state>
<rna_req type="str">
PolyA cellular mRNA</rna_req>
<ptm_affect type="str">
633-693|R|methylation|weakens|PMID:30173914|PRMT1|Notes: Methylation at arginine residues in the RNA-binding RGG-box by prmt-1 promotes P-granule degradation by autophagy; </ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID:27594427, PMID:21402787); discrete oligomerization (PMID:21402787)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</G5EBV6>
<Q9TXM1 type="dict">
<id type="str">
29</id>
<phase_id type="str">
29</phase_id>
<common_name type="str">
MEG-3</common_name>
<name type="str">
Uncharacterized protein</name>
<accession type="str">
Q9TXM1</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MSSSKPYPSGLPNSRRKRGGRRSSSRSNQESASNNMEHQITLDELFNPIAKQDSAQSTSREYGAKSGISHHGSVSFNGNTFMNGQQLNHSMTRHGRVFNQSMHAAQGNGSNAFNSIPPTAPVFSADFRRNLQTRNSSSWYERRFPVSTDQDDVQQSNTRRSRSRQNGQHGLSFSDGSNNYGHAGNKSFSVSSVPVGFQKQENNSKKLRQTNVHQQCLGNKSFNAQAGVHGHAFKKGHKDNKNASGKEVINSSLVQKHDAIKSRNLNQSFSGFPTHETSSMKNQQQKSRNDRKKSRGSSNFQDRTYFNTNDDELTDDVFIDDSMDAARGRRSRSVTKKLQQSTYSKQNAGSKQLTEKCKSSEEAAKRNLVSNVFSKDGTELSIEQLLEIVSMKIGQQIHLPSSSHGECSNLNRTLPASDLNCSIGEDFDSSFVDANNQTLPVSLPKKTSLSIKRRGSSRSASRLASLDVTLETVEEDEEPTPSPQPSSPPKISRRKWTGTFDANVEEMRRLLHGDPEMPKSANRASSSKDQINRNNVDVKRTPSSSIIPTPKALIGERCLTSSSKSSKLNKSLGVVDSKATKSPMYSVTVSGKETASGKRIAQKLTPKVVALESSYITGIPVSTDCNGCPTPKRSGINCEIRAAEVYNQAGKWPFEITSDPAPLPCESADRIEYPSQDCTQDPASTSPPPRISESLTAFLEAQQDFNDYIDTNYKEKTQLLKVNLNIHGMSPERWLYLNYFCTETIPRLDGPYADDPRVPPVRNMFRKWFLRFAEACLGNPHQLAVMQEIAATFVQARLDDTSSSTDSTNMLYMLWKECIGQKNIIAIADACLLAHLRKSDPIKYLNVKRDWLESIFDPPRDQ</sequence>
<gene type="str">
MEG-3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal Q/N/S-rich IDR</segment>
<boundaries type="str">
1-544</boundaries>
<region_ref type="str">
27914198</region_ref>
<partners type="str">
1) mRNA (stimulates LLPS but not required); 2) MEX-5 (negative regulator, probably competes for mRNA)</partners>
<determinants type="str">
1) protein concentration; 2) salt concentration</determinants>
<forms type="str">
condensates, liquid droplets, hydrogels</forms>
<organelles type="str">
P granule</organelles>
<pmids type="str">
27914198 (research article), 25535836 (research article), 30833787 (research article)</pmids>
<description type="str">
RNA granules are ubiquitous cytoplasmic organelles that contain RNA and RNA-binding proteins. A group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos. The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility. MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2APPTR-1/2. Phosphorylation of the MEGs by MBK-2/DYRK promotes granule disassembly and dephosphorylation promotes granule assembly. The process is detailed as it follows. PPTR-1 functions redundantly with PPTR-2 to stabilize P granules and is antagonized by MBK-2. MEG-3 and MEG-1 are MBK-2 and PPTR-1 substrates. MEG-3 and MEG-4 are required for granule assembly in embryos. MEG-1 contributes to granule assembly and disassembly and is required redundantly with MEG-3 and MEG-4 for fertility. The MEGs function downstream of MBK-2 and PPTR-1 to regulate P granule dynamics. MEG-3 and MEG-4 localize to embryonic P granules and stabilize them. It is concluded that, despite their liquid-like behaviour, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation (PMID:25535836). The MEG3 N-terminal disordered region is responsible for phase separation and RNA-binding (PMID:27914198).; Theoretical studies have suggested that spontaneous LLPS of the RNA-binding protein PGL-3 with RNA drives the assembly of P granules. PGL-3 phase is intrinsically labile and requires a second phase for stabilization in embryos. The second phase is formed by gel-like assemblies of the disordered protein MEG-3 that associate with liquid PGL-3 droplets in the embryo posterior. Co-assembly of gel phases and liquid phases confers local stability and long-range dynamics, both of which contribute to localized assembly of P granules. These findings suggest that condensation of RNA granules can be regulated spatially by gel-like polymers that stimulate LLPS locally in the cytoplasm (PMID:30833787).</description>
<experiment_llps type="str">
MEG-3 contains a long N-terminal IDR but no recognizable RNA-binding domain. Electrophoretic mobility shift assay (EMSA) and fluorescent polarization (FP) assay showed that MEG-3 binds RNA (poly-U30) with nanomolar affinity in vitro. The IDR of MEG-3 is essential for binding, but on its own binds with lower affinity. MEG-3 readily formed condensates in vitro (particle size and count) within minutes of dilution from urea (and high salt) to an aqueous buffer (150 mM NaCl) as observed by Confocal and Differential interference contrast (DIC) microscopy. MEG-3 phase separation could be stimulated by RNA: addition of poly-U30 to the phase separation buffer increased the number of MEG-3 condensates (particle size and count) and they became larger and more abundant with increasing protein concentrations. The IDR of MEG-3 behaved similarly to full-length MEG-3, except that MEG-3 IDR required higher concentrations of RNA to phase separate at low protein concentrations. MEG-3 and the IDR of MEG-3 have an intrinsic propensity to phase separate that can be stimulated by RNA. (PMID:27914198). These observations could be recapitulated in vivo, before the polarization of the cell MEG-3 was distributed evenly throughout the cytoplasm, both diffusely and enriched in many small (&lt;1 micron diameter) foci. During polarization MEX-5 and MEG-3 began to redistribute into opposing cytoplasmic gradients along the long axis of the zygote (anterior-posterior axis) with MEG-3 beginning to form large (~1 micron) granules in the posterior. To examine the behavior of MEG-3-IDR in vivo, the C-terminus of MEG-3 was deleted by CRISPR/Cas9 genome editing to generate a meg-3 allele that only expresses MEG-3-IDR. Like full-length MEG-3, MEG-3-IDR is a cytoplasmic protein that redistributes into a posterior-rich gradient during polarization of the zygote. Unlike MEG-3, however, MEG-3IDR did not coalesce into prominent, micron-sized granules in zygotes. Distinct MEG-3-IDR granules were only observed starting in the 2-cell stage as MEG-3-IDR segregates into the progressively smaller P blastomeres. However, MEG-3-IDR formed numerous micron-sized granules in let-711(RNAi) zygotes, which had a surpluss of maternal mRNA. (PMID:27914198).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:25535836)</experiment_state>
<rna_req type="str">
poly-U30</rna_req>
<ptm_affect type="str">
1-862|ST|hyperphosphorylation|weakens|PMID:25535836|MBK-2, PPTR-1|Notes: hyperphosphorylation of MEG-3 promote granule disassembly (its intrinsic negative charge increased further by phosphorylation).</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID:27914198); protein-RNA interaction (PMID:27914198)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács; Beáta Szabó</annotator>
<functional_class type="str">
regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</Q9TXM1>
<P32588 type="dict">
<id type="str">
30</id>
<phase_id type="str">
30</phase_id>
<common_name type="str">
Pub1</common_name>
<name type="str">
Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1</name>
<accession type="str">
P32588</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MSENNEEQHQQQQQQQPVAVETPSAVEAPASADPSSEQSVAVEGNSEQAEDNQGENDPSVVPANAITGGRETSDRVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKRDNNNNNNYQQRRNYGNNNRGGFRQYNSNNNNNMNMGMNMNMNMNMNNSRGMPPSSMGMPIGAMPLPSQGQPQQSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKERSNFMPQQQQQGGQPLIMNDQQQPVMSEQQQQQQQQQQQQ</sequence>
<gene type="str">
PUB1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: 3 RRM domains and a prion-like N/Q-rich LC domain with RGG motif</segment>
<boundaries type="str">
1-453</boundaries>
<region_ref type="str">
29898402</region_ref>
<partners type="str">
1) RNA (inhibits phase separation)</partners>
<determinants type="str">
1) pH; 2) temperature</determinants>
<forms type="str">
biomolecular condensates</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
26412307 (research article), 29898402 (research article)</pmids>
<description type="str">
There is a stress-adaptive system that involves changes in the physical state of the cytoplasm. In energy-depleted budding yeast and bacteria, stress causes a transition of the cytoplasm from a fluid to a protective, solid-like state. In budding yeast, the RNA-binding and stress granule protein Pub1 has an intrinsic property to form condensates upon starvation (that induces the loss of ATP and the subsequent acidification of the cytosole) or heat stress. Condensate formation is associated with cell-cycle arrest. pH- and heat-induced Pub1 condensates have different material properties. Starvation-induced Pub1 condensates form by liquid-liquid demixing and subsequently convert into reversible gel-like particles, while heat-induced condensates are more solid-like and require chaperones for disaggregation. Pub1 phase separation is primarily driven by the folded RRM domains, while the LC domain acts as a modifier that modulates the LLPS of the RRMs and ensures its responsiveness/ reversibility. Thus Pub1 is a phase-separating biosensor that can sense specific changes of the environment. Its solubility is tuned to the conditions relevant in the cytoplasm of growing yeast cells and acts as a potent stress sensor (PMID:29898402). </description>
<experiment_llps type="str">
In unstressed transgenic yeast cells overexpressing GFP-fused Pub1 it showed a diffue distribution in the cytoplasm (microscopy). On a pH drop in the cytoplasm, for instance as a result of starvation, Pub1 forms liquid condensates in vivo (particle size and count by microscopy). Purified GFP-fused Pub1 shows diffuse distribution among physiological conditions in vitro, however when changing the pH to 6.2 Pub1 coalesced into small foci (particle size and count by microscopy). In vitro Pub1 assemblies were sensitive to changes in salt concentration (particle size and count by microscopy). Addition of RNA reduced the number and size of Pub1 condensates in vitro (particle size and count by microscopy). The Pub1 truncation mutant comprised of only the 3 RRM domains showed more intensive condensate formation among stress in vivo (particle size and count by microscopy) than the wild type Pub1. Purified only-RRM truncated variants also showed pH- and temperature-dependent phase separation in vitro, but with a reduced reversibily than the wild type Pub1. Heat-induced Pub1 condensates are larger, more irregular, solid-like (morphology) and they require chaperones for dissolution (PMID:29898402).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
reversibility of formation and dissolution (PMID:29898402)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
weak electrostatic or hydrophobic interactions between folded domains (PMID:29898402)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
sensor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P32588>
<P39936 type="dict">
<id type="str">
31</id>
<phase_id type="str">
31</phase_id>
<common_name type="str">
eIF4GII</common_name>
<name type="str">
Eukaryotic initiation factor 4F subunit p130</name>
<accession type="str">
P39936</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MTDQRGPPPPHPQQANGYKKFPPHDNQYSGANNSQPNNHYNENLYSAREPHNNKQYQSKNGKYGTNKYNNRNNSQGNAQYYNNRFNNGYRLNNNDYNPAMLPGMQWPANYYAPQMYYIPQQMVPVASPPYTHQPLNTNPEPPSTPKTTKIEITTKTGERLNLKKFHEEKKASKGEEKNDGVEQKSKSGTPFEKEATPVLPANEAVKDTLTETSNEKSTSEAENTKRLFLEQVRLRKAAMERKKNGLISETEKKQETSNHDNTDTTKPNSVIESEPIKEAPKPTGEANEVVIDGKSGASVKTPQHVTGSVTKSVTFNEPENESSSQDVDELVKDDDTTEISDTTGGKTVNKSDDETINSVITTEENTVKETEPSTSDIEMPTVSQLLETLGKAQPISDIYEFAYPENVERPDIKYKKPSVKYTYGPTFLLQFKDKLKFRPDPAWVEAVSSKIVIPPHIARNKPKDSGRFGGDFRSPSMRGMDHTSSSRVSSKRRSKRMGDDRRSNRGYTSRKDREKAAEKAEEQAPKEEIAPLVPSANRWIPKSRVKKTEKKLAPDGKTELFDKEEVERKMKSLLNKLTLEMFDSISSEILDIANQSKWEDDGETLKIVIEQIFHKACDEPHWSSMYAQLCGKVVKDLDPNIKDKENEGKNGPKLVLHYLVARCHEEFEKGWADKLPAGEDGNPLEPEMMSDEYYIAAAAKRRGLGLVRFIGYLYCLNLLTGKMMFECFRRLMKDLNNDPSEETLESVIELLNTVGEQFEHDKFVTPQATLEGSVLLDNLFMLLQHIIDGGTISNRIKFKLIDVKELREIKHWNSAKKDAGPKTIQQIHQEEEQLRQKKNSQRSNSRFNNHNQSNSNRYSSNRRNMQNTQRDSFASTKTGSFRNNQRNARKVEEVSQAPRANMFDALMNNDGDSD</sequence>
<gene type="str">
TIF4632</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal N/Q-rich IDR</segment>
<boundaries type="str">
13-97</boundaries>
<region_ref type="str">
26412307</region_ref>
<partners type="str">
1) RNA (promotes phase separation); 2) competitor proteins (negative regulator)</partners>
<determinants type="str">
1) protein concentration; 2) salt concentration; 3) temperature</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
26412307 (research article), 29425497 (research article)</pmids>
<description type="str">
The N-terminal N-rich IDR of EIF4G2 undergoes LLPS in a salt-concentration dependant manner. RNA promotes its LLPS (PMID:26412307). It interacts nonspecifically with generic proteins, and those proteins and yeast lysates disrupt its ability to undergo LLPS in isolation (PMID:29425497). </description>
<experiment_llps type="str">
The SNAP-tagged IDR (with N-terminal SNAP tag coupled to the SNAP-Surface 488 or SNAP-Surface 649 fluorophores, fluorescent tagging) showed phase separation in vitro in low salt concentration (change in optical properties, particle size and count by fluorescent microscopy). The SNAP-tagged IDR phase separated upon addition of RNA. The selective recruitment of GFP-IDR into PTB+RNA droplets (protein co-localization by microscopy) could be explained by weak interactions of the IDR with RNA, as according to electrophoretic mobility shift assays eIF4GII-IDR formed stable interactions with RNA. The selective recruitment of GFP-IDR into phase-separated droplets of hnRNPA1 (protein co-localization by microscopy) indicates that the heterotypic recruitment of IDR proteins into droplets can occur in a protein-dependent manner (PMID:26412307). LLPS of the SNAP-tagged IDR was inhibited by the presence of BSA, lysozyme, or RNase A (PMID:29425497).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26412307); reversibility (PMID:26412307); dynamic movement/reorganization of molecules within the droplet (PMID:26412307)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known (PMID:26412307)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P39936>
<Q96PK6 type="dict">
<id type="str">
34</id>
<phase_id type="str">
34</phase_id>
<common_name type="str">
RBM14 </common_name>
<name type="str">
RNA-binding protein 14</name>
<accession type="str">
Q96PK6</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MKIFVGNVDGADTTPEELAALFAPYGTVMSCAVMKQFAFVHMRENAGALRAIEALHGHELRPGRALVVEMSRPRPLNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKGPGLAVQSGDKTKKPGAGDTAFPGTGGFSATFDYQQAFGNSTGGFDGQARQPTPPFFGRDRSPLRRSPPRASYVAPLTAQPATYRAQPSVSLGAAYRAQPSASLGVGYRTQPMTAQAASYRAQPSVSLGAPYRGQLASPSSQSAAASSLGPYGGAQPSASALSSYGGQAAAASSLNSYGAQGSSLASYGNQPSSYGAQAASSYGVRAAASSYNTQGAASSLGSYGAQAASYGAQSAASSLAYGAQAASYNAQPSASYNAQSAPYAAQQAASYSSQPAAYVAQPATAAAYASQPAAYAAQATTPMAGSYGAQPVVQTQLNSYGAQASMGLSGSYGAQSAAAATGSYGAAAAYGAQPSATLAAPYRTQSSASLAASYAAQQHPQAAASYRGQPGNAYDGAGQPSAAYLSMSQGAVANANSTPPPYERTRLSPPRASYDDPYKKAVAMSKRYGSDRRLAELSDYRRLSESQLSFRRSPTKSSLDYRRLPDAHSDYARYSGSYNDYLRAAQMHSGYQRRM</sequence>
<gene type="str">
RBM14</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Prion-like domain with 21 Y[G/N/A/S]AQ or [S/G]YG motifs</segment>
<boundaries type="str">
350-669</boundaries>
<region_ref type="str">
26283796</region_ref>
<partners type="str">
1) Long noncoding RNA NEAT1 (not required for LLPS but for paraspeckles); 2) NONO</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
hydrogel with amyloid-like; properties</forms>
<organelles type="str">
paraspeckle</organelles>
<pmids type="str">
26283796 (research article)</pmids>
<description type="str">
The protein RBM14 connects key paraspeckle subcomplexes via interactions mediated by its PLD. These subcomplexes are NONO (Non-POU domain-containing octamer-binding protein) and SFPQ (Splicing factor, proline- and glutamine- rich). RBM14 PLD, as well as the PLD of another essential paraspeckle protein, FUS, is required to rescue paraspeckle formation in cells in which their endogenous counterpart has been knocked down. Similar to FUS, the RBM14-PLD also forms hydrogels with amyloid-like properties in itself. These results suggest a role for PLD-mediated liquid-phase transitions in paraspeckle formation (PMID:26283796).</description>
<experiment_llps type="str">
Superresolution microscopy was used to confirm enrichment of NONO and RBM14 in paraspeckles (protein localization). Overexpression of YFP-fused fragments of RBM14, combined with FISH to detect endogenous NEAT1, showed that the the PLD and full-length RBM14 both co-localize with NEAT1 at paraspeckles (protein co-localization), but the amino-terminal fragment that contains only the RRMs (residues 1–176) does not. Thus the PLD domain is sufficient for paraspeckle targeting. RBM14 PLD mutants with partial Y→S showed significantly diminished paraspeckle targeting and YFP-RBM14-PLD all Y→S failed to target to paraspeckles (protein localization). The RBM14 PLD can also promote aggregation independent of paraspeckles, as seen with numerous, additional, non-NEAT1–containing foci (protein localization, morphology) in cells overexpressing YFP-RBM14 PLD in vivo. The ability of wild-type and mutant constructs of FUS and RBM14 to rescue the ablation of parasepeckles by siRNA (RNAi) knockdown of endogenous FUS, or RBM14 was tested. Knockdown (RNAi) of the endogenous proteins results in significantly diminished paraspeckle numbers in HeLa cells in vivo, as determined by counting NEAT1 foci (particle size and count by microscopy). Wild-type FUS, or RBM14, but not the vector control, could rescue paraspeckle formation (particle size and count by microscopy), but the Y→S PLD mutants could not. Purified GFP-tagged RBM14-PLD and PLD mutants were concentrated and cooled and all of them formed hydrogels (morphology) in vitro with the exception of GFP-RBM14-PLD all Y→S. Examination of their biophysical attributes confirmed similarities of RBM14 to FUS hydrogels, with scanning electron microscopy, revealing the fibril mesh networks characteristic of amyloids (morphology) and X-ray diffraction showing the typical amyloid signature of diffraction rings at ∼4.6 and 10 Å (morphology). Unlike pathological amyloids, however, hydrogels are relatively soluble in SDS (morphology) (PMID:26283796). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26283796)</experiment_state>
<rna_req type="str">
other specific RNA: NEAT1 architectural lncRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
gelation (PMID:26283796); π-π (pi-pi) (PMID:26283796); formation of amyloid-like/cross-beta/kinked/stacked beta-sheet structures (PMID:26283796)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q96PK6>
<P45973 type="dict">
<id type="str">
36</id>
<phase_id type="str">
36</phase_id>
<common_name type="str">
HP1α </common_name>
<name type="str">
Chromobox protein homolog 5</name>
<accession type="str">
P45973</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MGKKTKRTADSSSSEDEEEYVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNLDCPELISEFMKKYKKMKEGENNKPREKSESNKRKSNFSNSADDIKSKKKREQSNDIARGFERGLEPEKIIGATDSCGDLMFLMKWKDTDEADLVLAKEANVKCPQIVIAFYEERLTWHAYPEDAENKEKETAKS</sequence>
<gene type="str">
CBX5</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full length protein without the C-terminal extension</segment>
<boundaries type="str">
1-177</boundaries>
<region_ref type="str">
28636604</region_ref>
<partners type="str">
1) DNA (promotes LLPS)</partners>
<determinants type="str">
1) protein concentration; 2) phosphorylation state</determinants>
<forms type="str">
puncta</forms>
<organelles type="str">
heterochromatin</organelles>
<pmids type="str">
28636604 (research article), 30845353 (research article), 30471698 (research article)</pmids>
<description type="str">
Constitutive heterochromatin is an important component of eukaryotic genomest hat has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension (NTA) or DNA-binding promotes the formation of phase-separated droplets. The LLPs-compatible forms are capable of higher order oligomerisation, while others only form dimers. The phosphorylated residues of NTE in one dimer probably make electrostatic interactions with basic residues in the hinge of another dimer to generate higher-order oligomers. Depending on nuclear context, heterochromatin could exist in a more permissive soluble state or a less permissive phase-separated state. DNA-binding and NTE-phosphorylation could provide qualitatively different means of regulating heterochromatin. Phase-separated HP1α droplets allow the means to physically sequester and compact chromatin while enabling recruitment of repressive factors (PMID:28636604). Solid-state NMR spectroscopy was used to track the conformational dynamics of phosphorylated HP1α during its transformation from the liquid to the gel state. Experiments designed to probe distinct dynamic modes identified regions with varying mobilities within HP1α molecules and show that specific serine residues uniquely contribute to gel formation (PMID:30845353).</description>
<experiment_llps type="str">
Two different phosphorylated versions of HP1α nPhos-HP1α and hPhos-HP1α have been generated in vitro by respectively phosphorylating (protein phosphorylation) HP1α proteins that have their hinge or NTE serine residues mutated to alanine. nPhos-HP1α solution became turbid upon cooling, and revealed liquid droplets (morphology) when investigated by microscopy. The turbid solution became clear upon raising the temperature or upon treatment with alkaline phosphatase (protein dephosphorylation) suggesting reversibility. Wild-type HP1α did not phase-separate upon cooling only in the presence of DNA. nPhos-HP1α forms higher-order oligomers beyond a dimer (physical interaction), so phase separation probably depends on inter-dimer contacts. When mutating a conserved basic patch in the hinge to alanines (residues 89–91, basic patch mutant) phos-HP1α(BPM) was defective for both phosphorylation-driven oligomerization (physical interaction) and phase separation (particle size and count by microscopy). Sequence features of both the hinge and NTE that are specific to HP1α are required for oligomerization. There are several putative inter-HP1α cross-links between the CTE and the hinge, deleting the 14-amino-acid CTE (truncation) in the context of NTE phosphorylation (nPhos-HP1α(ΔCTE) lowers the saturation concentration by approximately tenfold compared to nPhos-HP1α, suggesting that interactions between the CTE and the hinge stabilize the HP1αdimer in a compact auto-inhibited state that cannot make multivalent interactions. Mutating the basic patch in the wild-type HP1α hinge that is proposed to interact with DNA eliminated droplet formation (particle size and count by microscopy). DNA compaction (other change in phenotype/functional readout) appears to be driven largely by electrostatic interactions, as increasing the level of monovalent salts reverses compaction. Results imply that macromolecules that interact with HP1α can remain solvated in the HP1α dominated phase, while others are either excluded or partitioned according to volume. In vivo, in NIH3T3 cells transduced with Cy3-labelled HP1 proteins HP1 formed puncta (PMID:28636604).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28636604); reversibility of formation and dissolution (PMID:28636604)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
11-14|S|phosphorylation|promotes|PMID:28636604||Notes: phosphorylation of the N-terminal extension allows for phase separation of HP1α even in the absence of DNA.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
linear oligomerization/self-association (PMID:28636604); protein-DNA interaction (PMID:28636604); electrostatic (cation-anion) interaction (PMID:28636604)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P45973>
<P05205 type="dict">
<id type="str">
37</id>
<phase_id type="str">
37</phase_id>
<common_name type="str">
HP1a</common_name>
<name type="str">
Heterochromatin protein 1</name>
<accession type="str">
P05205</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MGKKIDNPESSAKVSDAEEEEEEYAVEKIIDRRVRKGKVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKDEEKSAASKKDRPSSSAKAKETQGRASSSTSTASKRKSEEPTAPSGNKSKRTTDAEQDTIPVSGSTGFDRGLEAEKILGASDNNGRLTFLIQFKGVDQAEMVPSSVANEKIPRMVIHFYEERLSWYSDNED</sequence>
<gene type="str">
SU(VAR)205</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-206</boundaries>
<region_ref type="str">
28636597</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) temperature; 2) salt concentration; 3) protein concentration of HP1a</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
heterochromatin</organelles>
<pmids type="str">
28636597 (research article)</pmids>
<description type="str">
Constitutive heterochromatin is an important component of eukaryotic genomest hat has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. The formation of heterochromatin domains is mediated by phase separation. Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid proprties during the first stages of heterochromatin domain formation in early Drosophila embryos. HP1a is required for heterochromatin domain integrity and compartmentalization. In D. melanogaster post-fertilization nuclear cycles 11-14 HP1a droplets appear in early interphase and dissolve at the onset of mitotic prophase. The integrity of mature heterochromatin domains relies on weak hydrophobic interactions (responsible for LLPS) and also, dimerization and interactions with non-histone binding partners contribute to HP1a immobilization. Thus mature chromatin domains consist of both immobile (static) and mobile(liquid) HP1a compartments (PMID:28636597). </description>
<experiment_llps type="str">
Among high protein concentrations and low levels of salt purified Drosophila HP1a protein solutions spontaneously demixed to form droplets at 22 °C in vitro (particle size and count by microscopy) that reversibly dissolved at 37 °C with change in temperature. High-resolution 4D analysis using lattice light-sheet microscopy revealed that GFP-HP1a (fusion protein) is initially diffuse, then forms highly spherical foci (protein localization) that grow, frequently fuse together, and dissolve (morphology) at the onset of mitotic prophase in vivo. HP1a is needed for compartmentalization of heterochromatin in vivo, since after depleting (RNAi) it from cultured Drosophila S2 cells GFP–HP4 lost coordinated movement and became dispersed throughout the nucleus (protein localization) (PMID:28636597). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28636597); reversibility of formation and dissolution (PMID:28636597); morphological traits (PMID:28636597); dynamic movement/reorganization of molecules within the droplet (PMID:28636597); sensitivity to 1,6-hexanediol (PMID:28636597)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:28636597)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P05205>
<P04147 type="dict">
<id type="str">
38</id>
<phase_id type="str">
38</phase_id>
<common_name type="str">
PAB1</common_name>
<name type="str">
Polyadenylate-binding protein, cytoplasmic and nuclear</name>
<accession type="str">
P04147</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MADITDKTAEQLENLNIQDDQKQAATGSESQSVENSSASLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAITKTSLGYAYVNFNDHEAGRKAIEQLNYTPIKGRLCRIMWSQRDPSLRKKGSGNIFIKNLHPDIDNKALYDTFSVFGDILSSKIATDENGKSKGFGFVHFEEEGAAKEAIDALNGMLLNGQEIYVAPHLSRKERDSQLEETKAHYTNLYVKNINSETTDEQFQELFAKFGPIVSASLEKDADGKLKGFGFVNYEKHEDAVKAVEALNDSELNGEKLYVGRAQKKNERMHVLKKQYEAYRLEKMAKYQGVNLFVKNLDDSVDDEKLEEEFAPYGTITSAKVMRTENGKSKGFGFVCFSTPEEATKAITEKNQQIVAGKPLYVAIAQRKDVRRSQLAQQIQARNQMRYQQATAAAAAAAAGMPGQFMPPMFYGVMPPRGVPFNGPNPQQMNPMGGMPKNGMPPQFRNGPVYGVPPQGGFPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQEQQTEQA</sequence>
<gene type="str">
PAB1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
4 RRMs; P-rich LCR</segment>
<boundaries type="str">
38-400; 419-502</boundaries>
<region_ref type="str">
28283059</region_ref>
<partners type="str">
1) RNA (inhibitor of LLPS)</partners>
<determinants type="str">
1) temperature; 2) pH; 3) ionic strength</determinants>
<forms type="str">
quinary assembly</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
28283059 (research article), 20368989 (research article), 28873979 (research article), 30877200 (review)</pmids>
<description type="str">
In eukaryotic cells, diverse stresses trigger coalescence of RNA-binding proteins into stress granules. In vitro, stress-granule-associated proteins can demix to form liquids, hydrogels, and other assemblies lacking fixed stochiometry. Poly(A)-binding protein (Pab1 in yeast), a defining marker of stress granules, phase separates and forms hydrogels in vitro upon explosure to physiological stress conditions (physiological thermal and pH changes). Unlike other RNA-binding proteins’, Pab1’s P-rich LCR is not required for demixing only modulates it. LLPS is mediated by its RRMs, and RNA inhibits phase separation. Pab1 acts as a physiological stress sensor, exploiting phase separation to precisely mark stress onset, a broadly generizable mechanism. Phase separation is mediated by electrostatic interactions between four RNA-recognition motifs (RRMs) and promoted by hydrophobic residues in Pab1’s LCR (low- complexity region) that modulates temperature sensitivity. RRM1-3 in itself is also able to phase separate (PMID:28283059). Pab1’s phase separation is tuned to occur at the organism’s heat shock temperature by modulatory hydrophobic residues in its proline-rich domain. Phase separation is mediated by its RNA binding domains, and Pab1 releases RNA during phase separation. The ability of Pab1 to autonomously sense a mere 3% change in absolute temperature, from robust growth (30°C/303K) to stress (40°C/313K), makes Pab1’s phase separation one of the most thermosensitive biomolecular processes yet found (PMID:30877200).; </description>
<experiment_llps type="str">
Pab1 shows diffuse localization under favorable growth conditions, and localizes to stress granules—large cytosolic foci—within minutes of a shift to 46°C in vivo (change in temperature, protein localization). Purified recombinant yeast Pab1 was soluble at 30°C in vitro but demixed to form large particles after a 30 min treatment on 46°C (change in temperature, protein localization). After incubating Pab1 with a small excess of 19-mer polyadenylate RNA (A19), shifting to 46°C for 30 min caused Pab1:RNA complexes to partially dissociate (change in temperature, protein co-localization, particle size and count), with the free protein demixing into large particles and the released A19 returning to the free pool. These results indicate that upon heat stress Pab1 releases RNA and demixes, forming particles stabilized by protein-protein interactions. Rapid particle growth in a narrow temperature window indicated the onset of demixing (change in temperature, particle size and count) by DLS. Adding RNA (change in RNA concentration) increasingly inhibited Pab1 demixing (particle size and count) by DLS. At higher salt concentrations (change in salt concentration) or above physiological pH values (change in pH), demixing was almost completely inhibited at 46°C (particle size and count). Pab1 was split into its N- and C-terminal halves, RRM1-3 and RRM4-P-C (RPC) mutation. RRM1-3 demixed,whereas RPC did not up to 50°C. Pab1deltaP mutant assemblies largely retained the droplet-cluster morphology of full-length Pab1 quinary assemblies. Mutational studies imply that Pab1 phase separates in vivo during heat shock, with temperature sensitivity modulated by its low-complexity region. Strikingly, only the three variants whose phase separation occurs at temperatures substantially above that of the WT (MV/A, MVFY/AGPNQ, and DP) showed reduced fitness under heat-shock conditions in vivo. Altered in vivo stress tolerance correlates with altered quinary assembly formation in vivo, phase separation in vitro, P domain hydrophobicity, and P domain compaction in the monomer, revealing connections between each phenomenon (PMID:28283059).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28283059); morphological traits (PMID:28283059)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
weak electrostatic or hydrophobic interactions between folded domains (PMID:28283059)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir; sensor</functional_class>
<date type="str">
2019-09-11</date>
</P04147>
<Q22053 type="dict">
<id type="str">
39</id>
<phase_id type="str">
39</phase_id>
<common_name type="str">
Fibrillarin, fib-1 </common_name>
<name type="str">
rRNA 2-O-methyltransferase fibrillarin</name>
<accession type="str">
Q22053</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MGRPEFNRGGGGGGFRGGRGGDRGGSRGGFGGGGRGGYGGGDRGSFGGGDRGGFRGGRGGGDRGGFRGGRGGGDRGGFGGRGSPRGGFGGRGSPRGGRGSPRGGRGGAGGMRGGKTVVVEPHRLGGVFIVKGKEDALATKNMVVGESVYGEKRVSVDDGAGSIEYRVWNPFRSKLAASIMGGLENTHIKPGTKLLYLGAASGTTVSHCSDVVGPEGIVYAVEFSHRSGRDLLGVAKKRPNVVPIVEDARHPHKYRMLVGMVDVIFSDVAQPDQARIVALNAQNFLRNGGHAVISIKANCIDSTAEPEAVFAGEVNKLKEEKFKPLEQVTLEPYERDHAVVVAVYRPVKGKKV</sequence>
<gene type="str">
FIB-1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
RGG-rich region, methyltransferase domain</segment>
<boundaries type="str">
1-352</boundaries>
<region_ref type="str">
27212236</region_ref>
<partners type="str">
1) RNA (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration; 2) salt concentration</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
nucleolus; dense fibrillar component; nuclear body</organelles>
<pmids type="str">
26351690 (research article), 27212236 (research article)</pmids>
<description type="str">
Nuclear bodies are RNA and protein-rich, membraneless organelles that play important roles in gene regulation. They condense from the nucleoplasm by concentration-dependent phase separation. FIB1 and NPM1 form immiscible droplets in vitro and in vivo. FIB1 can phase separate in vitro under near physiological protein and salt concentrations, giving rise to condensed liquid-phase droplets that are ∼50-fold more concentrated with protein than the surrounding dilute phase (PMID:26351690,  PMID:27212236). The N-terminal R/G domain of FIB1 is sufficient for droplet formation, but does not encode for a separate liquid-like DFC subcompartment; instead, the C-terminal MD of FIB1, which alone is not sufficient for droplet formation, confers immiscibility with proteins in the GC (PMID:27212236).</description>
<experiment_llps type="str">
In vivo, in C. elegans embryo cells FIB1::GFP forms large puncta that co-localize with rRNA (PMID:26351690). In vitro, in the presence of 5 μg/ml rRNA and 150 mM NaCl, FIB1 condenses into droplets at a protein concentration of ∼600 nM. FIB1 droplet microrheology reveals that they are not simple viscous liquid droplets, but are instead viscoelastic. The C-terminal methyltransferase domain (MD) of FIB1 plays a key role in promoting viscoelastic maturation of FIB1 droplets in vitro. The R/G domain (FIB1ΔC) is sufficient to form liquid-like droplets in vitro, while the MD alone (FIB1ΔN) is unable to form droplets in vitro (mutations, particle size and count by microscopy). FIB1ΔC can phase separate into liquid-like droplets in vitro, even in the absence of RNA. By contrast, full-length FIB1 requires rRNA; however, this may be a non-specific consequence of the polyanionic nature of rRNA since heparin can also drive phase separation of full-length FIB1. In vitro FIB1 and NPM1 coexist as multiphase droplets, with the NPM1 rich phase tending to partially envelope the FIB1 rich phase (PMID:27212236). The N-terminal R/G domain of FIB1 is sufficient for droplet formation, but does not encode for a separate liquid-like DFC subcompartment; instead, the C-terminal MD of FIB1, which alone is not sufficient for droplet formation, confers immiscibility with proteins in the GC (PMID:27212236).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27212236); rheological traits (PMID:27212236); morphological traits (PMID:27212236)</experiment_state>
<rna_req type="str">
total RNA as well as specific RNA partner</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID:27212236); electrostatic (cation-anion) interaction (PMID:27212236)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q22053>
<P06748 type="dict">
<id type="str">
40</id>
<phase_id type="str">
40</phase_id>
<common_name type="str">
NPM1</common_name>
<name type="str">
Nucleophosmin</name>
<accession type="str">
P06748</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEDSMDMDMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESEDEEEEDVKLLSISGKRSAPGGGSKVPQKKVKLAADEDDDDDDEEDDDEDDDDDDFDDEEAEEKAPVKKSIRDTPAKNAQKSNQNGKDSKPSSTPRSKGQESFKKQEKTPKTPKGPSSVEDIKAKMQASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL</sequence>
<gene type="str">
NPM1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: oligomerization domain, linker with acidic tracts, RRM</segment>
<boundaries type="str">
1-294</boundaries>
<region_ref type="str">
26836305</region_ref>
<partners type="str">
1) (r)RNA (strictly required); 2) partner preotein(s) with multivalent (at least 2) R-motifs (strictly required)</partners>
<determinants type="str">
1) protein concentration; 2) valency of protein partners</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
nucleolus; granular component</organelles>
<pmids type="str">
26836305 (research article), 27212236 (research article), 25349213 (research article), 29483575 (research article), 30498217 (research article)</pmids>
<description type="str">
The nucleolus has a layered tripartite organization that consists of the fibrillar center (FC), where the RNA polymerase I (POL1) machinery is active; the dense fibrillar component (DFC) that is enriched in the protein fibrillarin (FIB1); and the granular component (GC) that is enriched in the protein nucleophosmin (NPM1/B23) (PMID:27212236). NPM1 participates in the organization of the liquid-like structure of the granular component of the nucleolus (PMID:25349213) and consequently may actively participate in stress signal integration and transmission, thereby explaining its known roles in ribosome biogenesis, tumor suppression and other processes. Of 132 NPM1-binding proteins, 97% exhibited at least one R-motif, multivalency of acidic tracts within NPM1 and R-motifs within nucleolar substrates mediates liquid-liquid phase separation. Nucleolar localization of NPM1 in vivo requires multi-modal interactions with both R-motif-containing nucleolar proteins and rRNA. Multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, are the structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli in vivo (PMID:26836305). Surfeit locus protein 6 (SURF6/S6N) tunes the composition and material properties of NPM1 droplet scaffolds. Electrostatically-driven interactions between disordered regions of NPM1 and SURF6 drive liquid-liquid phase separation. Co-existing heterotypic (NPM1-SURF6) and homotypic (NPM1-NPM1) scaffolding interactions within NPM1-SURF6 liquid-phase droplets dynamically and seamlessly interconvert in response to variations in molecular crowding and protein concentrations (PMID:30498217).</description>
<experiment_llps type="str">
In vivo NPM1 depletion is associated with disruption of nucleolar structure (morphology) (PMID:25349213). In vitro at 150 mM NaCl, NPM1 requires high concentrations of protein (2 μM) and rRNA (100 μg/ml). Phase separation of NPM1 required rRNA and cannot be induced by the addition of heparin or poly-U50. When deleting the N-terminal oligomerization domain to create NPM1ΔN, and deleting the C-terminal RNA binding domain to create NPM1ΔC neither mutant was able to form droplets (particle size and count by microscopy) in vitro. In vitro FIB1 and NPM1 coexist as multiphase droplets, with the NPM1 rich phase tending to partially envelope the FIB1 rich phase (PMID:27212236). In vitro, titration of four R-motif-containing peptides caused phase separation into liquid-like droplets (particle size and count by microscopy) at critical concentrations that varied with R-motif composition, valency and affinity for N130 segment of NPM1. Phase separation was not observed (particle size and count by microscopy) when a truncated NPM1 construct containing only the oligomerization domain OD (residues 1–122) was titrated with the rpL5 peptide, therefore the minimal multivalency requirements for phase separation are the acidic A1 and A2 tracts within NPM1 and at least two complementarily charged R-motifs within a polypeptide binding partner. The molecular basis of this type of NPM1 phase separation is the formation of non-covalent, inter-N130 pentamer interactions via the two R-motifs within the same rpL5 peptide molecule. These rpL5-mediated interactions establish the inter-pentamer spacing within the droplet phase. Full length NPM1 (N294) could phase separate with either rpL5 or wheat germ rRNA. Neither of the OD- or RRM-truncated constructs experienced phase separation in the presence of rRNA (particle size and count by microscopy), confirming that multivalent display of the NBD is required for the co-localization of rRNA with NPM1 within liquid-like droplets. Multi-modal binding to two classes of macromolecules, R-motif-containing nucleolar proteins (binding mode 1) and rRNA (binding mode 2), is likely critical for NPM1-dependent formation of multi-component liquid-like droplets (PMID:26836305).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:26836305, PMID:27212236); rheological traits (PMID:27212236); dynamic movement/reorganization of molecules within the droplet (PMID:27212236)</experiment_state>
<rna_req type="str">
wheat germ rRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:26836305); protein-RNA interaction (PMID:26836305); multivalent domain-motif interactions (PMID:26836305)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P06748>
<P91349 type="dict">
<id type="str">
42</id>
<phase_id type="str">
42</phase_id>
<common_name type="str">
SPD-5</common_name>
<name type="str">
Spindle-defective protein 5</name>
<accession type="str">
P91349</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MEDNSVLNEDSNLEHVEGQPRRSMSQPVLNVEGDKRTSSTSATQQQVLSGAFSSADVRSIPIIQTWEENKALKTKITILRGELQMYQRRYSEAKEASQKRVKEVMDDYVDLKLGQENVQEKMEQYKLMEEDLLAMQSRIETSEDNFARQMKEFEAQKHAMEERIKELELSATDANNTTVGSFRGTLDDILKKNDPDFTLTSGYEERKINDLEAKLLSEIDKVAELEDHIQQLRQELDDQSARLADSENVRAQLEAATGQGILGAAGNAMVPNSTFMIGNGRESQTRDQLNYIDDLETKLADAKKENDKARQALVEYMNKCSKLEHEIRTMVKNSTFDSSSMLLGGQTSDELKIQIGKVNGELNVLRAENRELRIRCDQLTGGDGNLSISLGQSRLMAGIATNDVDSIGQGNETGGTSMRILPRESQLDDLEESKLPLMDTSSAVRNQQQFASMWEDFESVKDSLQNNHNDTLEGSFNSSMPPPGRDATQSFLSQKSFKNSPIVMQKPKSLHLHLKSHQSEGAGEQIQNNSFSTKTASPHVSQSHIPILHDMQQILDSSAMFLEGQHDVAVNVEQMQEKMSQIREALARLFERLKSSAALFEEILERMGSSDPNADKIKKMKLAFETSINDKLNVSAILEAAEKDLHNMSLNFSILEKSIVSQAAEASRRFTIAPDAEDVASSSLLNASYSPLFKFTSNSDIVEKLQNEVSELKNELEMARTRDMRSPLNGSSGRLSDVQINTNRMFEDLEVSEATLQKAKEENSTLKSQFAELEANLHQVNSKLGEVRCELNEALARVDGEQETRVKAENALEEARQLISSLKHEENELKKTITDMGMRLNEAKKSDEFLKSELSTALEEEKKSQNLADELSEELNGWRMRTKEAENKVEHASSEKSEMLERIVHLETEMEKLSTSEIAADYCSTKMTERKKEIELAKYREDFENAAIVGLERISKEISELTKKTLKAKIIPSNISSIQLVCDELCRRLSREREQQHEYAKVMRDVNEKIEKLQLEKDALEHELKMMSSNNENVPPVGTSVSGMPTKTSNQKCAQPHYTSPTRQLLHESTMAVDAIVQKLKKTHNMSGMGPELKETIGNVINESRVLRDFLHQKLILFKGIDMSNWKNETVDQLITDLGQLHQDNLMLEEQIKKYKKELKLTKSAIPTLGVEFQDRIKTEIGKIATDMGGAVKEIRKK</sequence>
<gene type="str">
SPD-5</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied: coiled-coil domains</segment>
<boundaries type="str">
1-1198</boundaries>
<region_ref type="str">
25977552</region_ref>
<partners type="str">
1) SPD-2 (enhances SPD-5 polymerization, but not required)</partners>
<determinants type="str">
1) protein concentration of SPD-5; 2) crowding agent concentration; 3) phosphorylation state; 4) time; 5) crowding agent molecule size</determinants>
<forms type="str">
micrometer-sized porous networks</forms>
<organelles type="str">
pericentriolar material</organelles>
<pmids type="str">
24979791 (research article), 25977552 (research article), 28575670 (research article), 27591191 (research article), </pmids>
<description type="str">
The centrosome organizes microtubule arrays within animal cells and comprises two centrioles surrounded by an amorphous protein mass called pericentriolar material (PCM). In Caenorhabditis elegans, PCM assembly requires the coiled-coil protein SPD-5. Recombinant SPD-5 could polymerize to form micrometer-sized porous networks in vitro. Network assembly was accelerated by two conserved regulators that control PCM assembly in vivo, Polo-like kinase-1 and SPD-2/Cep192. Only the assembled SPD-5 networks, and not unassembled SPD-5 protein, functioned as a scaffold for other PCM proteins. Thus, PCM size and binding capacity emerge from the regulated polymerization of one coiled-coil protein to form a porous network (PMID:25977552). PCM client proteins, including microtubule-associated proteins, then partition into this network via interactions with SPD-5. While the SPD-5 scaffold becomes more stable over time, the clients remain loosely bound and are sufficient to recruit tubulin and form microtubule asters. Thus, the PCM scaffold acts as a selective compartment into which clients partition. Macromolecular crowding drives assembly of the key PCM scaffold protein SPD-5 into spherical condensates that morphologically and dynamically resemble in vivo PCM. These SPD-5 condensates recruited the microtubule polymerase ZYG-9 (XMAP215 homolog) and the microtubule-stabilizing protein TPXL-1 (TPX2 homolog). Together, these three proteins concentrated tubulin ∼4-fold over background, which was sufficient to reconstitute nucleation of microtubule asters in vitro.Results suggest that in vivo PCM is a selective phase that organizes microtubule arrays through localized concentration of tubulin by microtubule effector proteins (PMID:28575670). PLK-1 is required for rapid assembly of the PCM scaffold but not for scaffold maintenance or function. Probably PLK-1 phosphorylation-dependent conversion of SPD-5 into an assembly-competent form underlies PCM formation in vivo and that the rate of this conversion determines final PCM size and density (PMID:27591191).</description>
<experiment_llps type="str">
In vitro, purified full-length, GFP-fused SPD-5 (SPD-5::GFP) assembled into dense structures spanning several micrometers (morphology, particle size and count) at 23°C after 120 minutes in a concentration-dependent manner. Separate networks could be observed to coalesce and networks readily dissolved after dilution or mechanical disruption, indicating that network formation is reversible. Cryo-electron microscopy of in vitro formed SPD-5 networks revealed dense, amorphous assemblies interspersed with pores of various sizes that reach sizes comparable to fully expanded PCM (morphology). Using strains deleted for the endogenous plk1 gene (knockout) that also expressed either wild-type PLK-1 (PLK-1WT) or an analog-sensitive PLK-1 mutant (PLK-1AS) (genetic transformation) that can be inhibited by the drug 1NM-PP1 and monitoring the in vivo recruitment of the PCM marker GFP::γ-tubulin (microscopy) revealed that addition of 1NM-PP1 in S phase abolished mitotic GFP::γ-tubulin accumulation in embryos expressing PLK-1AS but not PLK-1WT (other change in phenotype/functional readout). Thus, PLK-1 activity is required for both assembly and maintenance of the mitotic PCM. Centrosomal SPD-5 accumulation (particle size and count by microscopy) was impaired in plk-1 depleted (RNAi) embryos in vivo. In vivo, in SPD-5 depleted (RNAi) embryos expressing RNAi-insensitive GFP::SPD-5_4A (mutant with 4 S→ A mutated phosphorylation sites), centrioles acquired a small shell of GFP::SPD-5_4A, but the PCM failed to expand, γ-tubulin recruitment was also impaired, and centrosomes failed to separate (other change in phenotype/functional readout). Using an initial concentration of 6.25 nM SPD-5::GFP in the absence of PLK-1, SPD-5WT::GFP networks appeared after 90 min. Addition of 6.25 nM PLK-1 (protein phosphorylation) and 0.2 mM ATP enhanced network formation, such that SPD-5 networks appeared after 30 min (particle size and count). Although SPD-54A::GFP formed networks at later time points in vitro, centrosomes did not expand in cells expressing the 4A mutant in vivo. A SPD-5 mutant harboring four phosphomimetic mutations (SPD-5_4E::GFP) already formed networks at t = 0 min, suggesting that phosphorylation at these four residues is sufficient to catalyze SPD-5 polymerization. Addition of 12.5 nM purified full-length SPD-2 (change in protein concentration) enhanced in vitro SPD-5::GFP network assembly, such that networks were seen after 60 min (particle size and count). SPD-2 and PLK-1 cooperatively enhance SPD-5 polymerization in vitro. PLK-1::GFP and GFP::SPD-2 were both recruited to SPD-5::TagRFP networks independently of each other while four noncentrosomal proteins were not, demonstrating that the association of PLK-1 and SPD-2 with SPD-5 networks is specific. SPD-5 networks, rather than unassembled SPD-5 molecules, serve as scaffolds for the recruitment of SPD-2 and PLK-1 in vitro (PMID:25977552).; In the presence of &gt; 4% PEG SPD-5::GFP formed micron-sized, round assemblies (particle size and count) similar to the size and shape of SPD-5-labeled PCM in vivo. Cryoelectron microscopy (cryo-EM) revealed that these SPD-5 assemblies were spherical and amorphous (morphology). High-throughput fluorescence imaging showed that the mass and number (particle size and count) of spherical SPD-5 assemblies increased with either PEG or SPD-5 concentration (change in protein concentration, change in the concentration of a crowding agent). When “young” (incubated for &lt; 2 min) SPD-5::TagRFP seeds (25 nM) were diluted into a solution containing unassembled SPD-5::GFP (500 nM), SPD-5::GFP incorporated into the seeds in vitro (co-localization). The seeds subsequently expanded, on average, ∼25% in diameter, and the RFP signal became concomitantly ∼20% dimmer, indicating that SPD-5 originally in the seeds redistributed within the growing assemblies. Once PCM expansion stops during mitosis in vivo, SPD-5::GFP signal does not recover after full bleach nor redistribute after half bleach of the PCM (morphology). Similarly, FRAP analysis showed that “aged” (incubated for &gt; 10 min) SPD-5::GFP spherical assemblies also did not recover after full or partial bleaching in vitro, indicating that neither monomer incorporation nor long-range internal rearrangement occurs in this state (morphology). 10-fold dilution of young SPD-5 assemblies (500 nM, 2 min old) into PEG-free buffer triggered their instantaneous dissolution. However, aged SPD-5 assemblies (18 min old) were 3.5-fold more resistant to dissolution after dilution. The PCM scaffold is an evolving material that becomes less dynamic as it matures with time. SPD-5 retains its helical secondary structure when assembled into spherical condensates. Under a condition in which SPD-5 condensates do not form spontaneously (3.25% PEG and 100 nM SPD-5; Figure 3A) addition of 100 nM PLK-1 or SPD-2 (change in protein concentration) promoted SPD-5 condensate formation (particle size and count) in vitro. When added to a solution of monomeric SPD-5::TagRFP (100 nM), SPD-2 seeds triggered the formation of (nucleated) SPD-5::TagRFP condensates. SPD-5 condensates recruited PCM client proteins with similar partition coefficients in vitro as PCM in vivo, suggesting that the SPD-5 scaffold per se determines the selectivity of the PCM for its clients. Condensates made with only SPD-5::TagRFP (500 nM) did not concentrate α/β tubulin in vitro. Addition of TPXL-1 or ZYG-9 made SPD-5 condensates competent to accumulate tubulin and enhanced microtubule nucleation, creating robust microtubule asters in vitro (other change in phenotype/functional readout) (PMID:28575670).; PLK-1 phosphorylation-dependent conversion of SPD-5 into an assembly-competent form underlies PCM formation in vivo by determining the rate of assembly, final size and density of PCM (PMID:27591191).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
reversibility of formation and dissolution (PMID:25977552); morphological traits (PMID:28575670); dynamic movement/reorganization of molecules within the droplet (PMID:28575670)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
658|S|phosphorylation|promotes|PMID:25977552|PLK-1|Notes: 4 PLK-1 phosphorylated sites have been confirmed, but only 658S and 653S seemed to promote LLPS.; 653|S|phosphorylation|promotes|PMID:25977552|PLK-1|Notes: 4 PLK-1 phosphorylated sites have been confirmed, but only 658S and 653S seemed to promote LLPS.; </ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
coiled-coil formation (PMID:25977552); linear oligomerization/self-association (PMID:25977552)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P91349>
<Q9UHD9 type="dict">
<id type="str">
43</id>
<phase_id type="str">
43</phase_id>
<common_name type="str">
UBQLN2</common_name>
<name type="str">
Ubiquilin-2</name>
<accession type="str">
Q9UHD9</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MAENGESSGPPRPSRGPAAAQGSAAAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLTVHLVIKSQNRPQGQSTQPSNAAGTNTTSASTPRSNSTPISTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQSQMQQQLMASPEMMIQIMENPFVQSMLSNPDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASVGSSSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTTSTGSGSGNSSSNATGNTVAAANYVASIFSTPGMQSLLQQITENPQLIQNMLSAPYMRSMMQSLSQNPDLAAQMMLNSPLFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFTPGVGVGVLGTAIGPVGPVTPIGPIGPIVPFTPIGPIGPIGPTGPAAPPGSTGSGGPTGPTVSSAAPSETTSPTSESGPNQQFIQQMVQALAGANAPQLPNPEVRFQQQLEQLNAMGFLNREANLQALIATGGDINAAIERLLGSQPS</sequence>
<gene type="str">
UBQLN2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
STI1-II domain; </segment>
<boundaries type="str">
450-624</boundaries>
<region_ref type="str">
29526694</region_ref>
<partners type="str">
1) ubiquitinated substrates (negative regulator)</partners>
<determinants type="str">
1) protein concentration of UBQLN2; 2) salt concentration; 3) temperature; 4) protein concentration of ubiquitin/ubiquitinated ligands</determinants>
<forms type="str">
stress granule, cytoplasmic puncta</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
29526694 (research article), 30333186 (research article), 30442662 (research article), 30982635 (research article); </pmids>
<description type="str">
Ubiquilins (UBQLNs) are shuttle proteins essential for cellular protein quality control machinery. UBQLN2 is a low complexity domain (LCD) containing protein structurally and functionally distinct from RNA-binding proteins. UBQLN2 colocalizes with stress granules in vivo and undergoes LLPS at physiological conditions in vitro. UBQLN2 oligomerization promotes weak multivalent interactions that can drive UBQLN2 self-assembly into dynamic phase-separated liquid droplets, particularly as the local concentration of UBQLN2 may be increased in cell in response to stress. Ubiquitin binding, which is obligatory for UBQLN2’s biological functions, induces a transition that reverses UBQLN2 phase separation. UBQLN2 LLPS enables the protein’s recruitment to stress granules, where its interactions with ubiquitinated substrates reverse LLPS to enable shuttling of clients out of stress granules (PMID:29526694).</description>
<experiment_llps type="str">
In vivo cell assays using immunostaining and microscopy in human cancer cells showed that endogenous UBQLN2 co-localized with stress granule marker eIF4G1. In in vitro studies using full length purified UBQLN2 expressed in bacterial cells via genetic transformation showed that the protein solution becomes turbid under native-like conditions. Using differential interference contrast (DIC) microscopy, it was determined that turbidity results from the presence of micron-sized droplets rich in UBQLN2, as demonstrated by fluorescent imaging using aDyLight-488 fluorophore conjugated to UBQLN2, evidenced by differential interference contrast (DIC) microscopy. After photobleaching a small portion of a droplet using FRAP, its fluorescence signal recoveredrelatively quickly, with a characteristic recovery time of 31.5s, within the range observed for many RNA-binding proteins connected to LLPS. These data are consistent with the observation that UBQLN2 droplets are dynamic. In vitro and in vivo study of various truncated versions of the protein showed that the region 450–624, which contains a portion of the STI1-II domain, did undergo LLPS, albeit to a reduced degree, suggesting that this constructrepresents the minimum length required for LLPS. However, deletion of various regions do modify characteristics of the granules formed. Most importantly the removal of the N-terminal UBL domain, that would normally interact with the C-terminal UBA region turning LLPS off, removes the negative control of the granule formation (PMID:29526694).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29526694); morphological traits (PMID:29526694); temperature-dependence (PMID:29526694); reversibility of formation and dissolution (PMID:29526694)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
T487I|None|Amyotrophic lateral sclerosis-15 (ALS15)|OMIM:300857|weakens|PMID:30982635|Notes: Mutants formed either amorphous droplets or aggregates.; P497H|dbSNP:rs387906709|Amyotrophic lateral sclerosis-15 (ALS15)|OMIM:300857|weakens|PMID:30982635|Notes: Significantly altered droplet morphology, even producing aggregates that did not change over time.; P497S|dbSNP:rs387906710|Amyotrophic lateral sclerosis-15 (ALS15)|OMIM:300857|weakens|PMID:30982635|Notes: Significantly altered droplet morphology, even producing aggregates that did not change over time.; P506T|dbSNP:rs387906711|Amyotrophic lateral sclerosis-15 (ALS15)|OMIM:300857|weakens|PMID:30982635|Notes: Mutants formed either amorphous droplets or aggregates. The mutation promoted higher-order oligomerization states not seen for wild type.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:29526694)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Bálint Mészáros; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir; sensor</functional_class>
<date type="str">
2019-09-11</date>
</Q9UHD9>
<D8V196 type="dict">
<id type="str">
44</id>
<phase_id type="str">
44</phase_id>
<common_name type="str">
cpeb4</common_name>
<name type="str">
Cytoplasmic polyadenylation element binding protein 4</name>
<accession type="str">
D8V196</accession>
<organism type="str">
Xenopus laevis</organism>
<sequence type="str">
MGDYGFGVLVQNNTGNKSAFPVRFHPHLQPPHHHQNTTPSPAAFINNTAANGSNAGSAWLFPAPAAHNIQDEILGSEKSKSQQQQQQEQQESLEKQQLSPSQSQEAGILPDPEKVKSEENQGDSSSENGKDKIRIESPVLTGFDYQEASGLGSSNQTLTSSASPLTGFSNWSAAIAPSSSTMINEDASFFHQGGVPAASANNGALLFQNFPHHVSPGFGGSFSPQIGPLSQHHPHHPHFQHHHNQHQQQRRSPASPHPPPFTHRNAAFNQLPHLANNLNKPPSPWSSYQSPSPTPSSSWSPGGSGYGGWGGSQGRDHRRGLNGGITPLNSISPLKKNFGNNHIQLQKYGRPNSAFAPKSWMDDSLNRADNIFPFADRTRAFDMHSLESSLIDIMRAENDSLKGQSSLFPMEDGFLDDGRSDQPLHSGLGSPHCFPHQNGERVERYSRKVFVGGLPPDIDEDEITASFRRFGPLIVDWPHKAESKSYFPPKGYAFLLFQDESSVQALIDACIEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDGSQPLDPRKTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAISARFVQLQHGEIDKRVEVKPYVLDDQLCDECQGARCSGKFAPFFCANVTCLQYYCEYCWAAIHSRAGREFHKPLVKEGGDRPRHISFRWN</sequence>
<gene type="str">
CPEB4</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal repetitive LC IDR</segment>
<boundaries type="str">
1-409</boundaries>
<region_ref type="str">
27802129</region_ref>
<partners type="str">
1) CPE-containing mRNAs (not required but influences dynamics)</partners>
<determinants type="str">
1) phosphorylation state</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
cytoplasmic protein granule</organelles>
<pmids type="str">
27802129 (research article)</pmids>
<description type="str">
CPEB4 activity is regulated by ERK2- and Cdk1-mediated hyperphosphorylation. CPEB4 is phosphorylated in 12 residues by ERK2 and Cdk1. These phosphorylation events additively activate CPEB4 in M-phase by maintaining it in its monomeric state. In contrast, unphosphorylated CPEB4 phase separates into inactive, liquid-like droplets through its intrinsically disordered regions in the N-terminal domain. CPEB4 phosphorylation is required for cytoplasmic polyadenylation and meiotic progression. This dynamic and reversible regulation of CPEB4 is coordinated with that of CPEB1 through Cdk1, which inactivates CPEB1 while activating CPEB4, thereby integrating phase-specific signal transduction pathways to regulate cell cycle progression (PMID:27802129).</description>
<experiment_llps type="str">
In vitro phosphorylation and mutation studies showed that the N-terminal domain (NTD) of the protein contains 12 phosphosites. Mass spectrometry of in vivo produced protein fragments show that these phosphorylation events occur in the cell. In vivo studies in oocytes showed that the mutation of the phospho-residues abolishes protein function, and that the phospho-mimetic mutant was constitutively active. An overexpressed HA-tagged construct was studied in vivo using immunodetection assay and mass spectrometry to show that both the mutants and the wild type proteins share the same physical interactions. GFP-tagged wild type and mutant proteins were knocked-in into and were overexpressed in human U2OS cells, showing that only the wild-type and the non-phosphorylable mutants were capable of LLPS. FRAP measurements with the NTD and the full length protein (containing the RNA-binding region) were used to confirm the liquid state of the condensate, also indicating that most probably the bound mRNA is not required for the self-assembly but influences the dynamics of these droplets. The in vivo morphology of liquid droplets were observed and fusion events were followed using microscopy. The primary experimental results were generated for the Xanopus laevis protein; however the high sequence identity (93%), and auxiliary results indicate that the phase separation occurs in human cells too (PMID:27802129).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27802129); morphological traits (PMID:27802129)</experiment_state>
<rna_req type="str">
other type of RNA: CPE-containing mRNAs</rna_req>
<ptm_affect type="str">
18-362|ST|hyperphosphorylation|abolishes|PMID:27802129|Cdk1,ERK2|Notes: Hyperphosphorylation at at least 12 sites</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Bálint Mészáros; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</D8V196>
<Q16082 type="dict">
<id type="str">
45</id>
<phase_id type="str">
45</phase_id>
<common_name type="str">
HSPB2</common_name>
<name type="str">
Heat shock protein beta-2</name>
<accession type="str">
Q16082</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSGRSVPHAHPATAEYEFANPSRLGEQRFGEGLLPEEILTPTLYHGYYVRPRAAPAGEGSRAGASELRLSEGKFQAFLDVSHFTPDEVTVRTVDNLLEVSARHPQRLDRHGFVSREFCRTYVLPADVDPWRVRAALSHDGILNLEAPRGGRHLDTEVNEVYISLLPAPPDPEEEEEAAIVEP</sequence>
<gene type="str">
HSPB2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal negatively charged P-rich IDR with RGG motif</segment>
<boundaries type="str">
147-182</boundaries>
<region_ref type="str">
28854361</region_ref>
<partners type="str">
1) HSPB3 (negatively affects HSPB2 LLPS); 2) LMNA (colocalizes with HSPB2 in nuclear foci)</partners>
<determinants type="str">
1) protein concentration of HSPB2</determinants>
<forms type="str">
cytoplasmic and nuclear foci with liquid- like properties</forms>
<organelles type="str">
cytoplasmic protein granule; nuclear protein granule</organelles>
<pmids type="str">
28854361 (research article)</pmids>
<description type="str">
Small heat shock proteins (HSPBs), which belong to the family of molecular chaperones, contain intrinsically disordered regions (IDRs). A member of this family, HSPB2 is expressed in mammalian differentiated skeletal and cardiac muscle cells, where, in the cytoplasm, it can form a complex with HSPB3 through phase separation. HSPB2 also phase separates to form intranuclear compartments with liquid-like properties, which partly colocalize with the nuclear intermediate filament protein lamin-A/C (LMNA) in differentiating myoblasts. HSPB2 phase separation therefore affects LMNA and chromatin distribution and impairs gene transcription and nuclear integrity. The phase separation requires the disordered C-terminal domain of HSPB2. HSPB2 phase separation is involved in reorganizing the nucleoplasm during myoblast differentation and in the cytoplasm it’s negatively regulated by its binding partner HSPB3. Aberrant HSPB2 phase separation, due to HSPB3 loss-of-function mutations, contributes to myopathy. Compartment formation is a specific property of HSPB2, which is independent of the cell type, but dependent on HSPB2 concentration (PMID:28854361).</description>
<experiment_llps type="str">
HSPB2 and HSPB3 mRNA and protein were undetectable in cycling LHCNM2 cells in vivo but upregulated during differentiation (protein localization). During the early steps of myoblast differentiation, HSPB2 forms two types of structures: nuclear foci that do not colocalize with HSPB3, in mono- and multinucleated cells, and cytoplasmic spherical foci (protein localization, morphology, particle size and count by microscopy) that partly colocalize with HSPB3. Overexpressed HSPB2 forms nuclear compartments in vivo in a HSPB3-independent manner (protein localization). Compartment formation is a specific property of HSPB2 among HSPBs, which is independent of the cell type but dependent on HSPB2 concentration (change in protein concentration). Nuclear (protein localization) HSPB2 compartments co-localized with LMNA in vivo independent of their size; moreover, HSPB2 also changed LMNA distribution which subsequently affected chromatin distribution and, occasionally, nuclear shape (morphology). While HSPB2 and mutant ΔN-HSPB2 still formed intranuclear compartments that sequestered LMNA (protein co-localization), mutant ΔC-HSPB2 showed a diffuse staining in vivo in the cytoplasm and nucleus and did not affect the distribution of LMNA (protein localization). GFP-fused HSPB2 was overexpressed in vivo at a very low concentration, together with higher concentrations of untagged HSPB2, dN-HSPB2, or dC-HSPB2 mutants. Upon co-transfection with full-length HSPB2 or dN-HSPB2, GFP-HSPB2 formed cytoplasmic and nuclear foci as well as large intranuclear assemblies (morphology, particle size and count by microscopy). However, GFP-HSPB2 displayed a diffuse distribution when co-expressed with dC-HSPB2 (protein localization). HSPB2 forms a stoichiometric complex with HSPB3 (3:1) (physical interaction), and their interaction co-stabilizes both proteins. Co-transfection of HSPB3 prevented the formation of nuclear HSPB2 droplets and abolished the association between HSPB2 and LMNA. R116P-HSPB3 and A33AfsX50-HSPB3 mutations disrupt HSPB2-HSPB3 complex formation and thus HSPB3 cannot regulate HSPB2 aberrant phase separation, leading to myopathies. HSPB3 depletion (RNAi) in LHCNM2 cells in vivo significantly decreased the expression of myogenin, increased the number of HSPB2-positive foci in the nucleus and cytoplasm (particle size and count) and induced nuclear morphology abnormalities, with a significant increase of micronuclei. No in vitro studies have been carried out on HSPB2 LLPS (PMID:28854361).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID:28854361); dynamic movement/reorganization of molecules within the droplet (PMID:28854361)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q16082>
<P10636-8 type="dict">
<id type="str">
89</id>
<phase_id type="str">
46</phase_id>
<common_name type="str">
Tau-F, Tau</common_name>
<name type="str">
Isoform Tau-F of Microtubule-associated protein tau</name>
<accession type="str">
P10636-8</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQARMVSKSKDGTGSDDKKAKGADGKTKIATPRGAAPPGQKGQANATRIPAKTPPAPKTPPSSGEPPKSGDRSGYSSPGSPGTPGSRSRTPSLPTPPTREPKKVAVVRTPPKSPSSAKSRLQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKCGSKDNIKHVPGGGSVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKKIETHKLTFRENAKAKTDHGAEIVYKSPVVSGDTSPRHLSNVSSTGSIDMVDSPQLATLADEVSASLAKQGL</sequence>
<gene type="str">
MAPT</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Tau/MAP repeats</segment>
<boundaries type="str">
244-368</boundaries>
<region_ref type="str">
28819146</region_ref>
<partners type="str">
1) tRNA; 2) heparin; 3) tubulin</partners>
<determinants type="str">
1) protein concentration of Tau; 2) phosphorylation state; 3) alternative splicing; 4) salt concentration; 5) temperature; 6) crowding agent concentration; 7) modification state</determinants>
<forms type="str">
liquid droplets, complex coacervates</forms>
<organelles type="str">
cytoplasmic microtubule; condensed compartments of microtubule bundling</organelles>
<pmids type="str">
29472250 (research article), 28683104 (research article), 28819146 (research article), 28877466 (research article), 29734651 (research article), 30950394 (research article), 30068389 (research article), 31097543 (research article), 31260737 (review), 31036717 (research article), 31456657 (research article)</pmids>
<description type="str">
Non-centrosomal microtubule bundles play important roles in cellular organization and function. The concentration of tubulin into a condensed, liquid-like compartment composed of the unstructured neuronal protein tau is sufficient to nucleate microtubule bundles.Under conditions of molecular crowding, tau forms liquid-like drops. Tubulin partitions into these drops, where it nucleates and drives the formation of microtubule bundles. These bundles deform the drops and remain enclosed by diffusible tau molecules, exhibiting a liquid-like behavior. (PMID:28877466) Alternative splicing of Tau can regulate the formation of Tau-containing membrane-less compartments. Phosphorylation of Tau repeats promotes liquid–liquid phase separation at cellular protein conditions. Liquid droplets formed by the positively charged microtubule-binding domain of Tau undergo coacervation with negatively charged molecules to promote amyloid formation. LLPS promotes Tau fibrillization in the presence of heparin (polyanion) (PMID:28819146). Tau complexes with RNA to form droplets. Uniquely, the pool of RNAs to which tau binds in living cells are tRNAs. The LLPS process is directly and sensitively tuned by salt concentration and temperature, implying it is modulated by both electrostatic interactions between the involved protein and nucleic acid constituents, as well as net changes in entropy. Despite the high protein concentration within the complex coacervate phase, tau is locally freely tumbling and capable of diffusing through the droplet interior. However, prolonged residency within the droplet state can result in the emergence of detectable β-sheet structures. Thus the droplet state can incubate tau and predispose the protein toward the formation of insoluble fibrils (PMID:28683104). Liquid demixing of tau does not require phosphorylation. Tau LLPS is driven by attractive electrostatic intermolecular interactions between the negatively charged N-terminal and positively charged middle/C-terminal domains of the protein, with hydrophobic interactions playing a surprisingly small role. (PMID: 31097543) In Alzheimer&apos;s disease, tau is predominantly acetylated at K174, K274, K280, and K281 residues. The acetylation of K274-tau is linked with memory loss and dementia. Acetylation mimicking mutation at K274 (K→Q) residue of tau strongly reduces the ability of tau to bind to tubulin and also to polymerize tubulin and  strongly decreases the critical concentration for the liquid-liquid phase separation of tau. (PMID: 31036717)</description>
<experiment_llps type="str">
To exclude the influence of intramolecular and intermolecular cross-linking through Tau’s two native cysteine residues, C291 and C322, in vitro turbidity measurements were performed in the presence of tris(2-carboxyethyl)phosphine (TCEP), mimicking the reducing environment inside neurons. Changes in solution turbidity can arise from liquid–liquid demixing/LLPS, but also from formation of other types of aggregates. To support the presence of a liquid phase separated state of the repeat domain of Tau, differential interference contrast (DIC) microscopy were performed. To demonstrate the presence of tau proteins in the liquid droplets, confocal microscopy of fluorescently labeled protein was used and at 37 °C, but not at 5 °C, fluorescent droplets were observed. To dissect the consequences of LLPS on the molecular properties of the repeat domain of Tau, NMR spectroscopy was used. The NMR data suggest that the protein stays largely disordered within liquid droplets, in agreement with the overall low content of regular secondary structure observed by CD spectroscopy. NMR measurements using attached paramagnetic nitroxide tag to the two native cysteines demonstrate that LLPS of Tau repeats results in a tight molecular mesh of amyloid-promoting elements. (PMID:28819146) Bright-field and fluorescence microscopy show that tau/tau-EGFP form drops in vitro in the presence of crowding agents. Fusion of tau droplets was visualized using dual-trap optical tweezers and Internal rearrangement of tau drops was monitored using fluorescence recovery after photo-bleaching (FRAP). (PMID:28877466) In vitro tau-RNA binding were detected using gel shift mobility assay and tau LLPS in the presence of RNA was investigated with light and confocal microscopy images of fluorescence-labeled proteins. Light microscopy images show that tau-RNA droplets form a complex coacervate phase. In vivo experiments show that tRNA transfection accumulates sarkosyl insoluble tau in human-induced pluripotent stem cell (hiPSC) derived neurons. (PMID:28683104) In vitro, upon addition to non-phosphorylated tau441 of polyethylene glycol (PEG), the volume-excluding polymer frequently used to mimic ntracellular crowding, a rapid increase in sample turbidity was observed, strongly suggesting LLPS. The decreased tendency of tau441 to form liquid droplets at increasing salt concentrations - confirmed by fluorescence microscopy using Alexa488-labeled tau441 - strongly suggests that LLPS is at least partly driven by attractive electrostatic interactions. (PMID: 31097543).; EFhd2 alters tau liquid phase behavior in a calcium and coiled-coil domain dependent manner. Co-incubation of EFhd2 and tau in the absence of calcium leads to the formation of solid-like structures containing both proteins, while in the presence of calcium these two proteins phase separate together into liquid droplets. EFhd2&apos;s coiled-coil domain is necessary to alter tau&apos;s liquid phase separation, indicating that protein-protein interaction is required (PMID:31456657).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
rheological traits (PMID:28819146, PMID:28877466); morphological traits (PMID:28819146, PMID:28877466, PMID:28683104); dynamic movement/reorganization of molecules within the droplet (PMID:28819146, PMID:28877466); temperature-dependence (PMID:28819146, PMID:28683104); reversibility of formation and dissolution (PMID:28683104)</experiment_state>
<rna_req type="str">
other type of RNA: tRNA</rna_req>
<ptm_affect type="str">
262|S|phosphorylation|promotes|PMID:28819146|MARK2|Notes:none; 324|S|phosphorylation|promotes|PMID:28819146|MARK2|Notes:none; 356|S|phosphorylation|promotes|PMID:28819146|MARK2|Notes:none; 148-395|K|hyperacetylation|weakens|PMID:29734651|p300|Notes:15 sites; 274|K|acetylation|promotes|PMID:31036717|Notes: It increases tau aggregation and enhances the cytotoxicity of tau oligomers</ptm_affect>
<disease type="str">
K280del|dbSNP:rs1168968768|Frontotemporal dementias (FTD)|OMIM: 600274|affects|PMID:29472250|Notes: It causes tau oligomerization and aggregation.; P301L|dbSNP:rs63751273|Frontotemporal dementias (FTD)|OMIM: 600274|affects|PMID:29472250|Notes: It causes tau oligomerization and aggregation.; P301S|dbSNP:rs63751438|Frontotemporal dementias (FTD)|OMIM: 600274|affects|PMID:29472250|Notes: It causes tau oligomerization and aggregation.; A152T|dbSNP:rs143624519|Frontotemporal dementias (FTD)|OMIM: 600274|affects|PMID:29472250|Notes: It causes tau oligomerization and aggregation.; K274Q|None|Alzheimer disease (AD)|OMIM:104300|affects|PMID:31036717|Notes: It increases tau aggregation and enhances the cytotoxicity of tau oligomers.</disease>
<splice type="str">
Isoform P10636-5|weakened|PMID:28819146</splice>
<interaction type="str">
linear oligomerization/self-association (PMID:28683104); formation of amyloid-like/cross-beta/kinked/stacked beta-sheet structures (PMID:28819146); protein-RNA interaction (PMID:28683104); electrostatic (cation-anion) interaction (PMID:31097543)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Éva Schád</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P10636-8>
<Q9UPQ9 type="dict">
<id type="str">
46</id>
<phase_id type="str">
47</phase_id>
<common_name type="str">
TNRC6B, GW182</common_name>
<name type="str">
Trinucleotide repeat-containing gene 6B protein</name>
<accession type="str">
Q9UPQ9</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MREKEQEREEQLMEDKKRKKEDKKKKEATQKVTEQKTKVPEVTKPSLSQPTAASPIGSSPSPPVNGGNNAKRVAVPNGQPPSAARYMPREVPPRFRCQQDHKVLLKRGQPPPPSCMLLGGGAGPPPCTAPGANPNNAQVTGALLQSESGTAPDSTLGGAAASNYANSTWGSGASSNNGTSPNPIHIWDKVIVDGSDMEEWPCIASKDTESSSENTTDNNSASNPGSEKSTLPGSTTSNKGKGSQCQSASSGNECNLGVWKSDPKAKSVQSSNSTTENNNGLGNWRNVSGQDRIGPGSGFSNFNPNSNPSAWPALVQEGTSRKGALETDNSNSSAQVSTVGQTSREQQSKMENAGVNFVVSGREQAQIHNTDGPKNGNTNSLNLSSPNPMENKGMPFGMGLGNTSRSTDAPSQSTGDRKTGSVGSWGAARGPSGTDTVSGQSNSGNNGNNGKEREDSWKGASVQKSTGSKNDSWDNNNRSTGGSWNFGPQDSNDNKWGEGNKMTSGVSQGEWKQPTGSDELKIGEWSGPNQPNSSTGAWDNQKGHPLPENQGNAQAPCWGRSSSSTGSEVGGQSTGSNHKAGSSDSHNSGRRSYRPTHPDCQAVLQTLLSRTDLDPRVLSNTGWGQTQIKQDTVWDIEEVPRPEGKSDKGTEGWESAATQTKNSGGWGDAPSQSNQMKSGWGELSASTEWKDPKNTGGWNDYKNNNSSNWGGGRPDEKTPSSWNENPSKDQGWGGGRQPNQGWSSGKNGWGEEVDQTKNSNWESSASKPVSGWGEGGQNEIGTWGNGGNASLASKGGWEDCKRSPAWNETGRQPNSWNKQHQQQQPPQQPPPPQPEASGSWGGPPPPPPGNVRPSNSSWSSGPQPATPKDEEPSGWEEPSPQSISRKMDIDDGTSAWGDPNSYNYKNVNLWDKNSQGGPAPREPNLPTPMTSKSASVWSKSTPPAPDNGTSAWGEPNESSPGWGEMDDTGASTTGWGNTPANAPNAMKPNSKSMQDGWGESDGPVTGARHPSWEEEEDGGVWNTTGSQGSASSHNSASWGQGGKKQMKCSLKGGNNDSWMNPLAKQFSNMGLLSQTEDNPSSKMDLSVGSLSDKKFDVDKRAMNLGDFNDIMRKDRSGFRPPNSKDMGTTDSGPYFEKLTLPFSNQDGCLGDEAPCSPFSPSPSYKLSPSGSTLPNVSLGAIGTGLNPQNFAARQGGSHGLFGNSTAQSRGLHTPVQPLNSSPSLRAQVPPQFISPQVSASMLKQFPNSGLSPGLFNVGPQLSPQQIAMLSQLPQIPQFQLACQLLLQQQQQQQLLQNQRKISQAVRQQQEQQLARMVSALQQQQQQQQRQPGMKHSPSHPVGPKPHLDNMVPNALNVGLPDLQTKGPIPGYGSGFSSGGMDYGMVGGKEAGTESRFKQWTSMMEGLPSVATQEANMHKNGAIVAPGKTRGGSPYNQFDIIPGDTLGGHTGPAGDSWLPAKSPPTNKIGSKSSNASWPPEFQPGVPWKGIQNIDPESDPYVTPGSVLGGTATSPIVDTDHQLLRDNTTGSNSSLNTSLPSPGAWPYSASDNSFTNVHSTSAKFPDYKSTWSPDPIGHNPTHLSNKMWKNHISSRNTTPLPRPPPGLTNPKPSSPWSSTAPRSVRGWGTQDSRLASASTWSDGGSVRPSYWLVLHNLTPQIDGSTLRTICMQHGPLLTFHLNLTQGTALIRYSTKQEAAKAQTALHMCVLGNTTILAEFATDDEVSRFLAQAQPPTPAATPSAPAAGWQSLETGQNQSDPVGPALNLFGGSTGLGQWSSSAGGSSGADLAGASLWGPPNYSSSLWGVPTVEDPHRMGSPAPLLPGDLLGGGSDSI</sequence>
<gene type="str">
TNRC6B</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Disordered N/G/W-rich N-terminal Argonaute binding domain (ABD) with Trp residues in motifs I and II</segment>
<boundaries type="str">
437-1056</boundaries>
<region_ref type="str">
29576456</region_ref>
<partners type="str">
1) Ago2 (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration of Ago2; 2) salt concentration; 3) crowding agent concentration; 4) valency of Ago2</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
RISC complex; P-body; micro-ribonucleoprotein complex; miRISC; GW-body</organelles>
<pmids type="str">
29576456 (research article)</pmids>
<description type="str">
miRISC is a multi-protein assembly that uses microRNAs (miRNAs) to identify mRNAs targeted for repression. Two core protein components of human miRISC, Argonaute2 (Ago2) and TNRC6B, condense into phase-separated droplets in vitro and in live cells. Phase separation is promoted by multivalent interactions between the glycine/tryptophan (GW)-rich domain of TNRC6B and three evenly spaced tryptophan-binding pockets in the Ago2 PIWI domain. When exposed to mammalian cell lysate, miRISC droplets also recruit components of the CCR4-NOT complex as well as deadenylase activity, which can be accelerated by more than two orders of magnitude upon phase separation. These observations suggest a model in which miRISC uses molecular condensation to sequester miRNA targets and concentrate them with factors that mediate mRNA decay. The use of phase separating systems to control RNA localization and stability may be a feature common to many aspects of RNA metabolism (PMID:29576456).</description>
<experiment_llps type="str">
The combined results of in vitro protein-protein interaction detection assays and X-ray crystallography with multiple Ago2 and TNRC6B mutants indicate that all three pockets in the trp-binding region of Ago2 contribute to physical interaction with TNRC6B. Specific Trp residues in TNRC6B Ago-binding domain (ABD) have pocket preferences, suggesting that the three trp-binding pockets are not perfectly redundant with each other, however, each pocket is able to interact with multiple different trp residues in TNRC6B, thus the interaction is multivalent and the structures formed may be heterogeneous and complex. Under physiological salt concentrations, in vitro, solutions containing both Ago2 and the TNRC6B-ABD quickly became opaque (change in optical properties), indicative of the formation of massive particles. Concentrated solutions of the ABD alone (but not that of Ago2) also became turbid at temperatures below 15°C. The fluorescently labeled TNRC6B ABD and Ago2 formed liquid droplets (morphology) in a protein concentration-dependent and salt concentration-dependent manner (particle size and count) as assessed by confocal microscopy. Ago valency (finetuned with mutations of the Trp-binding pockets) had a strong effect on droplet formation (particle size and count by microscopy). In a 293 HEK cell line stably overexpressing GFP-fused TNRC6B (genetic transformation) GFP-labeled, dynamic foci formed in vivo with 0.2 to 1mm in size (particle size and count by microscopy). Transfecting cells with a plasmid encoding mCherry-fused Ago2 revealed that Ago2 co-localized with TNRC6B foci in vivo. Ago2-TNRC6B droplets selectively sequester miRNA targets from the bulk solution: when mixed with droplets containing Ago2-let7 (Ago2 loaded with the miRNA let-7) in vitro, a target RNA with eight seed-matched let-7 binding sites (8xlet7) appeared almost exclusively in the pellet fraction (co-localization). In contrast, the 8xlet7 target RNA remained in the supernatant when added to droplets formed with Ago2-miR122. Ago2 kept its endonucleolytic cleavage (termed‘‘slicing’’) activity towards target RNAs within the condensates in the presence of a small RNA guide and the required ions in vitro (enzymatic activity assay). Ago2 and TNRC6B were mixed in the presence of soluble lysate from HEK293 cells, and the resulting droplets were isolated by centrifugation. Analysis by proteomics techniques (western blot) revealed that subunits of the CCR4-NOT deadenylase complex (a known miRISC component) co-pelleted with TNRC6B, while actin, which is not a component of miRISC, did not. (PMID:29576456).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29576456); dynamic exchange of molecules with surrounding solvent (PMID:29576456); morphological traits (PMID:29576456)</experiment_state>
<rna_req type="str">
other type of RNA: miRNAs</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:29576456)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9UPQ9>
<J3QQ18 type="dict">
<id type="str">
121</id>
<phase_id type="str">
48</phase_id>
<common_name type="str">
SynGAP</common_name>
<name type="str">
Ras/Rap GTPase-activating protein SynGAP</name>
<accession type="str">
J3QQ18</accession>
<organism type="str">
Mus musculus</organism>
<sequence type="str">
MSRSRASIHRGSIPAMSYAPFRDVRGPPMHRTQYVHSPYDRPGWNPRFCIISGNQLLMLDEDEIHPLLIRDRRSESSRNKLLRRTVSVPVEGRPHGEHEYHLGRSRRKSVPGGKQYSMEAAPAAPFRPSQGFLSRRLKSSIKRTKSQPKLDRTSSFRQILPRFRSADHDRARLMQSFKESHSHESLLSPSSAAEALELNLDEDSIIKPVHSSILGQEFCFEVTTSSGTKCFACRSAAERDKWIENLQRAVKPNKDNSRRVDNVLKLWIIEARELPPKKRYYCELCLDDMLYARTTSKPRSASGDTVFWGEHFEFNNLPAVRALRLHLYRDSDKKRKKDKAGYVGLVTVPVATLAGRHFTEQWYPVTLPTGSGGSGGMGSGGGGGSGGGSGGKGKGGCPAVRLKARYQTMSILPMELYKEFAEYVTNHYRMLCAVLEPALNVKGKEEVASALVHILQSTGKAKDFLSDMAMSEVDRFMEREHLIFRENTLATKAIEEYMRLIGQKYLKDAIGEFIRALYESEENCEVDPIKCTASSLAEHQANLRMCCELALCKVVNSHCVFPRELKEVFASWRLRCAERGREDIADRLISASLFLRFLCPAIMSPSLFGLMQEYPDEQTSRTLTLIAKVIQNLANFSKFTSKEDFLGFMNEFLELEWGSMQQFLYEISNLDTLTNSSSFEGYIDLGRELSTLHALLWEVLPQLSKEALLKLGPLPRLLNDISTALRNPNIQRQPSRQSERTRSQPMVLRGPSAEMQGYMMRDLNSSIDLQSFMARGLNSSMDMARLPSPTKEKPPPPPPGGGKDLFYVSRPPLARSSPAYCTSSSDITEPEQKMLSVNKSVSMLDLQGDGPGGRLNSSSVSNLAAVGDLLHSSQASLTAALGLRPAPAGRLSQGSGSSITAAGMRLSQMGVTTDGVPAQQLRIPLSFQNPLFHMAADGPGPPAGHGGSSGHGPPSSHHHHHHHHHHRGGEPPGDTFAPFHGYSKSEDLSSGVPKPPAASILHSHSYSDEFGPSGTDFTRRQLSLQDSLQHMLSPPQITIGPQRPAPSGPGGGSGGGSGGGQPPPLQRGKSQQLTVSAAQKPRPSSGNLLQSPEPSYGPARPRQQSLSKEGSIGGSGGSGGGGGGGLKPSITKQHSQTPSTLNPTMPASERTVAWVSNMPHLSADIESAHIEREEYKLKEYSKSMDESRLDRVKEYEEEIHSLKERLHMSNRKLEEYERRLLSQEEQTSKILMQYQARLEQSEKRLRQQQVEKDSQIKSIIGRLMLVEEELRRDHPAMAEPLPEPKKRLLDAQELGRGSFPPWVQQTRV</sequence>
<gene type="str">
SYNGAP1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal domain (coiled coil region dominated by hydrophobic residues, followed by a PDZ binding motif/PBM)</segment>
<boundaries type="str">
1147-1308</boundaries>
<region_ref type="str">
27565345</region_ref>
<partners type="str">
1) PSD-95 PDZ3 domain/SH3 domain/guanylate kinase fragment (strictly required)</partners>
<determinants type="str">
1) protein concentration; 2) temperature</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
postsynaptic density</organelles>
<pmids type="str">
28524815 (research article), 27565345 (research article)</pmids>
<description type="str">
SynGAP forms a stable trimer in solution. Trimeric SynGAP CC-PBM (coiled-coil domain and the following PDZ binding motif) recruits two PSD-95 PSG (3 PDZ+SH3+GK domains) to form a 3:2 complex. The SynGAP/PSD-95 3:2 complex undergoes LLPS and evolves into a postsynaptic density (PSD). PSDs are assemblies responsible for receiving, interpreting and storage of signals transmitted by presynaptic axonal termini. They are disc-shaped, electron-dense thickenings that contact with postsynaptic membranes on its one face and with cytoplasm on the other face, forming semi-open mesoscale cellular compartments. Mutations altering the SynGAP/PSD-95 interaction can contribute to various brain disorders, including autism and IDs (intellectual disordes) (PMID:27565345).</description>
<experiment_llps type="str">
Physical interaction between SynGAP and PSD-95 was verified in vitro using purified proteins. Isothermal titration calorimetry (ITC)-based titration assay showed that N-terminal thioredoxin-tagged last 30 residues of SynGAP binds to each of the three PDZ domains of PSD-95 with comparable and weak affinities, and this interaction is enhanced by the alpha helix following the third PDZ domain. Similar in vitro analysis using fast protein liquid chromatog-raphy (FPLC) coupled with a static light-scattering assay and circular dichroism revealed that SynGAP forms a paraller coiled-coil trimer. In vitro structural studies also showed that trimeric SynGAP CC-PBM (residues 1147-1308) recruits two PSD-95 PSG (306-721) to form a 3:2 stochiometric complex (physical interaction). In vitro mixing of purified SynGAP CC-PBM andPSD-95 PSG above certain concentrations caused the sample solutions to become opalescent immediately owing to the formation of small spherical (morphology) droplets spanning various diameters (particle size and count), as followed using light microscopy. Neither SynGAP CC-PBM nor PSD-95PSG alone could form condensed liquid phase. Liquid-to-liquid phase separation and condensed liquid phase droplets fusion of the SynGAP/PSD-95 complex (particle size and count) was followed using Alexa488-labeled SynGAP CC-PBM and Cy3-labeled PSD-95 PSG (fluorescent tagging) by fluorescence microscopy. Fluorescence recovery after photobleaching (FRAP) analysis of Cy3-labled PSD-95 droplets demonstrated that PSD-95 molecules constantly exchange between droplets and the surrounding aqueous solution (PMID:27565345). When GFP-SynGAP CC-PBM and RFP-PSD-95 PSG were co-expressed in HeLa cells in vivo, many bright puncta were observed containing both GFP and RFP signals. Both GFP and RFP signal intensities were much brighter within the puncta than the surrounding cytoplasm, indicating enrichment with SynGAP and PSD-95. No puncta were observed in cells when only PSD-95 PSG or SynGAP CC-PBM was expressed (PMID:27565345).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27565345); dynamic exchange of molecules with surrounding solvent (PMID:27565345); morphological traits (PMID:27565345); temperature-dependence (PMID:27565345)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif (PMID:27565345); coiled-coil formation (PMID:27565345); ; </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Bálint Mészáros; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; sensor</functional_class>
<date type="str">
2019-09-11</date>
</J3QQ18>
<P17931 type="dict">
<id type="str">
47</id>
<phase_id type="str">
49</phase_id>
<common_name type="str">
Galectin-3</common_name>
<name type="str">
Galectin-3</name>
<accession type="str">
P17931</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MADNFSLHDALSGSGNPNPQGWPGAWGNQPAGAGGYPGASYPGAYPGQAPPGAYPGQAPPGAYPGAPGAYPGAPAPGVYPGPPSGPGAYPSSGQPSATGAYPATGPYGAPAGPLIVPYNLPLPGGVVPRMLITILGTVKPNANRIALDFQRGNDVAFHFNPRFNENNRRVIVCNTKLDNNWGREERQSVFPFESGKPFKIQVLVEPDHFKVAVNDAHLLQYNHRVKKLNEISKLGISGDIDLTSASYTMI</sequence>
<gene type="str">
LGALS3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Repeats of Y-P-G-X(3)-P-G-A</segment>
<boundaries type="str">
20-100</boundaries>
<region_ref type="str">
28893908</region_ref>
<partners type="str">
1) glycoconjugated extracellular domains of transmembrane receptors</partners>
<determinants type="str">
1) protein concentration of galectin-3; 2) temperature; 3) salt concentration</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
galectin complex; galectin lattice</organelles>
<pmids type="str">
28893908 (research article), 30951647 (review), 26092931 (review)</pmids>
<description type="str">
Galectins are a family of widely expressed β-galactoside-binding lectins in metazoans. The 15 mammalian galectins have either one or two conserved carbohydrate recognition domains (CRDs), with galectin-3 being able to pentamerize; they form complexes that crosslink glycosylated ligands to form a dynamic lattice. The galectin lattice regulates the diffusion, compartmentalization and endocytosis of plasma membrane glycoproteins and glycolipids. The galectin lattice also regulates the selection, activation and arrest of T cells, receptor kinase signaling and the functionality of membrane receptors, including the glucagon receptor, glucose and amino acid transporters, cadherins and integrins (PMID:26092931). Galectin-3 self-associates via inter- and intramolecular NTD–CRD interactions and intermolecular NTD–NTD contacts driven by hydrophobic interactions. Galectin-3 also self-associates when it binds to glycoconjugates, such as those present on the cell surface, resulting in aggregation of these glycoconjugates or the formation of galectin lattices (PMID:28893908). The extracellular domains of transmembrane receptors can be modified with monosaccharides and polysaccharides to create binding sites for the carbohydrate recognition domain of galectin-3. The IDR of galectin-3 self-associates with other IDRs of neighboring galectin-3 molecules to form a multivalent network with modified transmembrane receptors (PMID:30951647).</description>
<experiment_llps type="str">
Galectin-3 self-associates via inter- and intramolecular NTD–CRD interactions and intermolecular NTD–NTD contacts (physical interaction) driven by hydrophobic interactions as demonstrated by NMR in vitro. These interactions are sensitive to change in salt concentration. In high concentration, the N-terminal domain of galectin-3 undergoes LLPS in a temperature-dependent, reversible manner as assessed by observing the change in optical properties (tubidity) of the sample. Liquid droplets were obderved by microscopy, and their observed fusion events further support their liquid-like property (morphology). PMID:28893908.</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28893908); reversibility of formation and dissolution (PMID:28893908); morphological traits (PMID:28893908)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:26092931); simple coacervation of hydrophobic residues (PMID:28893908) </interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</P17931>
<Q7YU08 type="dict">
<id type="str">
49</id>
<phase_id type="str">
51</phase_id>
<common_name type="str">
Rbfox1</common_name>
<name type="str">
LD15974p</name>
<accession type="str">
Q7YU08</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MYYPHMVQAGVAPFPGAPAGYAAAPNPGAAVVAAAAAAQQQQQQQQQQQQQQQQAQQQQQQQVAGGPPSAADSLSMAVAAAAAKQSADPVTQMKSGSEAAGSGNSNNNNTAGAGTGAPGAAGGLTTEYSSGGCGGGGASTANSVVVATSVSDVVNASLYMQQKSTVLIANEAAESQQSSAMQNAGGGGNTGGGGGGGGGGTPSSPLSNSPSSATASQAGGCGLTLNGSATEGSMSGDTSPVASGEPLLQTPPAHQQQQQQQQPLLCSSPTSMQSSGTSVTGSSIASGTLAATSSSGVGLLPTTGLDSIANGGAPTGCAVVPASTSQVIAHLNAAAAAASGIVSPSANVATSLSSALVPAQSVAAVAAASLDAKSQPKRLHVSNIPFRFRDPDLRAMFGQFGTILDVEIIFNERGSKGFGFVTFANSNDAERARERLHGTVVEGRKIEVNNATARVQTKKVTAVPNVCVQWPEAAVAAAMRGVAIQRGHVGVVGATPYHHPHHPHHHPALLAASAAAAQQQQQRQLAAAAVATAAVAQQQQQQQQAVVQQQQQQVAAAAQQQHQQQQQQQQQAVQQQQAVQQQQQHQQQQQQQQQQQHAAVAAAAAAASHPHMHAAHAHAHAHALGPQLAQLQAVAVPTAASNAAALQQSLAAAIQNPSGNPNAAAAAAAYAARLSAATGATQSPQTAAAAAAAASMAASANAANNAAALHGFAPVYYDPFLAAAASADPNLRFQAAKPVTEVPAAQPAAILNRRTVTTLNSNPHTINRIPVPQNVLATAPLLKTPLSQAQQQAYATAATTYTAVAARAAYGAAAAAAAQPALAGYATVAGYAREYADPYLGHGIGPVPGYGATMYRGGFNRFTPY</sequence>
<gene type="str">
RBFOX1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-865</boundaries>
<region_ref type="str">
29358748</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of Rbfox1; 2) b-isox concentration; 3) temperature</determinants>
<forms type="str">
cytoplasmic and nuclear granules</forms>
<organelles type="str">
cytoplasmic ribonucleoprotein granule; nuclear body</organelles>
<pmids type="str">
29358748 (research article)</pmids>
<description type="str">
D. melanogaster Rbfox1 is an LCD-containing protein that aggregates into liquid droplets and amyloid-like fibers and promiscuously joins different nuclear and cytoplasmic RNP granules. Rbfox1 precipitated with b-isox in a b-isox concentration and protein concentration-dependent manner. Rbfox1 formed SDS-resistant aggregates, most of which were disintegrated by boiling. In non-transfected cells low endogenous Rbfox1 protein levels were detected with anti-Rbfox1 antibodies in the cytoplasm and nucleus. Stress treatment with sodium arsenite stimulated Rbfox1 aggregation into cytoplasmic and nuclear granular structures that have liquid droplet properties. Rbfox1 colocalized with polyadenylated mRNAs, confirming that Rbfox1-positive granules contain RNA and are thus bonafide RNP granules. Rbfox1 can be localized in the nucleolus and Rbfox1 levels affect nucleolar ultrastructure. Rbfox1 levels also have an effect on Cajal body size and number. Depending on developmental stage and environmental conditions, Rbfox1 can associate with membraneless organelles that have previously been described to have a liquid droplet character and to contain proteins regulating cytoplasmic RNA metabolism. It might require partners for LLPS, as it has not been seen to undergo LLPS alone in vitro, just in cells (PMID:29358748).</description>
<experiment_llps type="str">
Rbfox1 precipitated in a b-isox concentration and protein concentration-dependent manner in vitro. Rbfox1 formed SDS-resistant aggregates. Some of the in vivo Rbfox-positive aggregates remained stable even after high temperature treatment, suggesting insolubility. Addition of 1,6-hexanediol led to the partial disintegration of sodium arsenit stress-induced Rbfox1 granules in vivo. These results were also confirmed using S2R+ cells expressing FLAG-tagged Rbfox1-PE isoform, which, when expressed under normal conditions predominantly localizes in the nucleus in vivo. Upon stress (perturbation of the cell environment to induce phenotypic changes), Rbfox1-PE assembled into nuclear and cytoplasmic granules (protein localization), appearance of which could be reduced upon 1,6-hexanediol treatment (morphology). Sometimes, even long, filamentous Rbfox1-positive aggregates (morphology) were observed in the starved, Rbfox1-expressing S2R+ cells. Rbfox1 co-localized with polyadenylated mRNAs. Immunohistochemical analysis (immunodetection assay) revealed that upon prolonged starvation stress, Rbfox1 assembled into round, granular (morphology) structures in Drosophila ovaries (protein localization). A portion of ThioflavinT-positive cytoplasmic and nuclear assemblies also co-stained with anti-Rbfox1 antibodies, confirming that Rbfox1 protein forms amyloid-like fibers and aggregates in vivo. No in vitro evidence available, thus requirement for partners and PTMs is difficult to judge (PMID:29358748).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
sensitivity to 1,6-hexanediol (PMID:29358748); </experiment_state>
<rna_req type="str">
cellular polyA RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
formation of amyloid-like/cross-beta/kinked/stacked beta-sheet structures (PMID:29358748); protein-RNA interaction (PMID:29358748), </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
Not known.</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q7YU08>
<Q13501 type="dict">
<id type="str">
50</id>
<phase_id type="str">
52</phase_id>
<common_name type="str">
p62</common_name>
<name type="str">
Sequestosome-1</name>
<accession type="str">
Q13501</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEKKECRRDHRPPCAQEAPRNMVHPNVICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLHRGHTKLAFPSPFGHLSEGFSHSRWLRKVKHGHFGWPGWEMGPPGNWSPRPPRAGEARPGPTAESASGPSEDPSVNFLKNVGESVAAALSPLGIEVDIDVEHGGKRSRLTPVSPESSSTEEKSSSQPSSCCSDPSKPGGNVEGATQSLAEQMRKIALESEGRPEEQMESDNCSGGDDDWTHLSSKEVDPSTGELQSLQMPESEGPSSLDPSQEGPTGLKEAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL</sequence>
<gene type="str">
SQSTM1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
PB1 domain (oligomerization); UBA (polyUbi chain binding)</segment>
<boundaries type="str">
3-102; 389-440</boundaries>
<region_ref type="str">
29507397</region_ref>
<partners type="str">
1) K63 polyubiquitin chains (strictly required for LLPS)</partners>
<determinants type="str">
1) valence of the polyubiquitin chains</determinants>
<forms type="str">
viscous liquid-like droplets</forms>
<organelles type="str">
inclusion body; p62 body</organelles>
<pmids type="str">
29507397 (research article), 29929426 (research article), 30287680 (review), 29572488 (review)</pmids>
<description type="str">
During the autophagy of misfolded, ubiquitinated proteins, referred to as aggrephagy, substrate proteins are clustered into larger structures in a SQSTM1/p62-dependent manner before they are sequestered by phagophores, the precursors to autophagosomes (PMID:29929426). SQSTM1/p62 and ubiquitinated proteins spontaneously phase separate into micrometer-sized clusters in vitro. p62 has an N-terminal PB1 domain (aa 3 – 102) and a C-terminal ubiquitin associated (UBA; aa 389 – 440) domain; the PB1 domain, which is required for p62 polymerization, and M404 in the UBA domain, which is essential for ubiquitin binding, are required for p62 body formation and autophagic degradation of p62 in vivo. Polyubiquitin chain-induced p62 phase separation was markedly impaired by p62-M404V and p62-ΔPB1. Also, recombinant p62 does not undergo phase separation in vitro, however, adding a K63 polyubiquitin chain to p62 induces p62 phase separation. These data suggest that p62 polymerization, as well as the interaction between polyubiquitin chains and p62, play critical roles in p62 phase separation (PMID:29507397). Aggrephagy is triggered by the accumulation of substrates with multiple ubiquitin chains and the process can be inhibited by active proteasomes (PMID:29929426).</description>
<experiment_llps type="str">
In cultured cells, endogenous or ectopically expressed p62 forms cytoplasmic inclusion bodies (p62 bodies) (protein localization, particle size and count by microscopy). p62 bodies contain polyubiquitin chains and K63 polyubiquitin chains are preferentially recruited into p62 bodies (protein co-localization). In p62-GFP-expressing autophagy-defective Atg12−/− cells (genetic transformation, knock-out, overexpression, fusion protein), p62 bodies were spherical and could undergo fusion (morphology). Furthermore, FRAP experiments revealed that the fluorescent signal recovered after bleaching of p62 bodies. No phase separation occurs in a solution containing even as much as 120 µM recombinant mCherry-fused p62 in vitro (particle size and count by microscopy), only when adding a solution of K63 polyubiquitin chains. In the control reaction, which did not contain adenosine triphosphate (ATP) and therefore did not form K63 polyubiquitin chains, p62 phase separation was not induced. Thus, K63 polyubiquitin chains, but not monoubiquitin can induce p62 phase separation. When adding cytosol from p62−/− cells to recombinant mCherry-fused p62 in vitro LLPS occured (particle size and count by microscopy). However treatment of the p62−/− cytosol with UPS5, a deubiquitinating enzyme that removes polyubiquitin chains abolished in vitro LLPS. Polyubiquitinated proteins are segregated into p62 droplets (co-localization). Although both Ubx8 and Ubx6 could cause p62 phase separation, Ubx8 could induce p62 phase separation at a much lower concentration; moreover, when the concentrations of both p62 and Ub were fixed, Ubx8 induced much stronger p62 phase separation than Ubx6, thus the valence of the polyubiquitin chain is important for p62 LLPS. LC3 co-localized with p62 bodies in Atg12−/− cells (it could be recruited to the p62 bodies) in vivo and also showed similar behaviour in vitro. In vivo polyubiquitin chain-induced p62 phase separation (particle size and count by microscopy) was markedly impaired by mCherry-p62-M404V and mCherry-p62-ΔPB1 mutations. Phosphorylation of S403 promotes polyubiquitin chain-induced phase separation, p62 body formation, and autophagic degradation (particle size and count by microscopy). The M404T and G411S Paget’s disease of bone mutations both markedly impaired polyubiquitin chain-induced p62 phase separation (particle size and count by microscopy). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29507397); morphological traits (PMID:29507397)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
403|S|phosphorylation|promotes|PMID:29507397|CK2|Notes: Phosphorylation of S403 by casein kinase 2 (CK2) increases the interaction between UBA and polyubiquitin chains, thereby promoting polyubiquitin chain-induced phase separation, p62 body formation, and autophagic degradation.</ptm_affect>
<disease type="str">
M404T|dbSNP:rs1247551175|Paget’s disease of bone (PDB)|OMIM:167250|weakens|PMID:29507397|Notes:none; G411S|dbSNP:rs143511494|Paget’s disease of bone (PDB)|OMIM:167250|weakens|PMID:29507397|Notes:none; </disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
linear oligomerization/self-association (PMID:29507397); multivalent domain-PTM interactions (PMID:29507397)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q13501>
<O43561 type="dict">
<id type="str">
51</id>
<phase_id type="str">
53</phase_id>
<common_name type="str">
LAT</common_name>
<name type="str">
Linker for activation of T-cells family member 1</name>
<accession type="str">
O43561</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEEAILVPCVLGLLLLPILAMLMALCVHCHRLPGSYDSTSSDSLYPRGIQFKRPHTVAPWPPAYPPVTSYPPLSQPDLLPIPRSPQPLGGSHRTPSSRRDSDGANSVASYENEGASGIRGAQAGWGVWGPSWTRLTPVSLPPEPACEDADEDEDDYHNPGYLVVLPDSTPATSTAAPSAPALSTPGIRDSAFSMESIDDYVNVPESGESAEASLDGSREYVNVSQELHPGAAKTEPAALSSQEAEEVEEEGAPDYENLQELN</sequence>
<gene type="str">
LAT</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Disordered cytoplasmic tail with four (phospho)tyrosine residues</segment>
<boundaries type="str">
28-262</boundaries>
<region_ref type="str">
27056844</region_ref>
<partners type="str">
1) GRB2 (strictly required for LLPS); 2) SOS1 (strictly required for LLPS)</partners>
<determinants type="str">
1) protein density in membrane of LAT; 2) valency of LAT; 3) valency of GRB2</determinants>
<forms type="str">
liquid-like, micrometer-sized clusters</forms>
<organelles type="str">
TCR signalosome; LAT signalosome; </organelles>
<pmids type="str">
27056844 (research article), 30951647 (review)</pmids>
<description type="str">
Many cell surface receptors and downstream signaling molecules coalesce into micrometer- or submicrometer-sized clusters upon initiation of signaling. However, the effect of this clustering on signal transduction is poorly understood. T cell receptor (TCR) signaling is a well-studied example of this general phenomenon. In the upstream module, the TCR is phosphorylated by Lck, a membrane-bound protein kinase of the Src family. TCR phosphorylation is opposed by a transmembrane phosphatase, CD45. The phosphorylated cytoplasmic domains of the TCR complex recruit and activate the cytosolic tyrosine kinase ZAP70, which then phosphorylates the transmembrane protein LAT on multiple tyrosine residues. These phosphotyrosines are binding sites for the SH2 domains of adapter protein Grb2 (or Gads), which further interacts with Pro-rich motifs within Sos1 (or SLP-76) through its SH3 domains. LAT and its binding partners coalesce into micrometer- or submicrometer-sized clusters at the plasma membrane upon TCR activation. Dephosphorylation of pLAT by high concentrations of the soluble protein tyrosine phosphatase 1B (PTP1B, 2 µM) caused the clusters to disassemble. Components of the LAT complex activate several downstream modules that mediate calcium mobilization, mitogen-activated protein kinase (MAPK) activation, and actin polymerization. Actin polymerization is initiated from and can reorganize LAT clusters. The experiments suggest that both the phosphorylation state and pY valency of LAT as well as the presence of both SH3 domains in GRB2 are important for cluster formation (PMID:27056844). ; </description>
<experiment_llps type="str">
Phosphorylated and fluorescently tagged LAT was shown to form liquid-like clusters interacting with GRB2 and SOS1 using microscopy imaging (TIRF) in vitro; and protein dephosphorylation led to the decrease of the particle size and count, marking the disassembly of the condensate. The liquid-like property was evidenced by FRAP. Induced mutation removing the second SH3 domain of GRB2 led to the disassembly of the condensate, demonstrating the importance of valency of the interacting partners. Similarly, stepwise induced mutations of the phosphorylated tyrosines to phenylalanines of LAT correlated with the degree of disruption of the condensate. Functional readout in in vivo studies showed that the clustering of mCitrine-fused LAT is localized to the plasma membrane, and promotes MAPK(ERK) signaling in T cells, thus the in vitro determined effects are biologically relevant in the cellular context. In vitro LAT clusters co-localized with CD45 (a physiological phosphatase of LAT) in artificial membranes, serving as a dephosphorylation assay. The in vivo morphology of liquid droplets were observed and fusion events were followed using microscopy. In vitro LAT clusters enhanced the polymerization of actin, given that the required components are available. PMID:27056844.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27056844); morphological traits (PMID:27056844)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
200|Y|phosphorylation|promotes|PMID:27056844|ZAP70|Notes:none; 220|Y|phosphorylation|promotes|PMID:27056844|ZAP70|Notes:none </ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:27056844); multivalent domain-PTM interactions (PMID:27056844)</interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</O43561>
<P62993 type="dict">
<id type="str">
92</id>
<phase_id type="str">
53</phase_id>
<common_name type="str">
GRB2</common_name>
<name type="str">
Growth factor receptor-bound protein 2</name>
<accession type="str">
P62993</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPTYVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPVNRNV</sequence>
<gene type="str">
GRB2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: SH3-SH2-SH3 domain structure</segment>
<boundaries type="str">
1-217</boundaries>
<region_ref type="str">
27056844</region_ref>
<partners type="str">
1) LAT (strictly required for LLPS); 2) SOS1 (strictly required for LLPS)</partners>
<determinants type="str">
1) protein density in membrane of LAT; 2) valency of LAT; 3) valency of GRB2</determinants>
<forms type="str">
liquid-like, micrometer-sized clusters</forms>
<organelles type="str">
TCR signalosome; LAT signalosome; </organelles>
<pmids type="str">
27056844 (research article), 30951647 (review)</pmids>
<description type="str">
Many cell surface receptors and downstream signaling molecules coalesce into micrometer- or submicrometer-sized clusters upon initiation of signaling. However, the effect of this clustering on signal transduction is poorly understood. T cell receptor (TCR) signaling is a well-studied example of this general phenomenon. In the upstream module, the TCR is phosphorylated by Lck, a membrane-bound protein kinase of the Src family. TCR phosphorylation is opposed by a transmembrane phosphatase, CD45. The phosphorylated cytoplasmic domains of the TCR complex recruit and activate the cytosolic tyrosine kinase ZAP70, which then phosphorylates the transmembrane protein LAT on multiple tyrosine residues. These phosphotyrosines are binding sites for the SH2 domains of adapter protein Grb2 (or Gads), which further interacts with Pro-rich motifs within Sos1 (or SLP-76) through its SH3 domains. LAT and its binding partners coalesce into micrometer- or submicrometer-sized clusters at the plasma membrane upon TCR activation. Dephosphorylation of pLAT by high concentrations of the soluble protein tyrosine phosphatase 1B (PTP1B, 2 µM) caused the clusters to disassemble. Components of the LAT complex activate several downstream modules that mediate calcium mobilization, mitogen-activated protein kinase (MAPK) activation, and actin polymerization. Actin polymerization is initiated from and can reorganize LAT clusters. The experiments suggest that both the phosphorylation state and pY valency of LAT as well as the presence of both SH3 domains in GRB2 are important for cluster formation (PMID:27056844). ; </description>
<experiment_llps type="str">
Phosphorylated and fluorescently tagged LAT was shown to form liquid-like clusters interacting with GRB2 and SOS1 using microscopy imaging (TIRF) in vitro; and protein dephosphorylation led to the decrease of the particle size and count, marking the disassembly of the condensate. The liquid-like property was evidenced by FRAP. Induced mutation removing the second SH3 domain of GRB2 led to the disassembly of the condensate, demonstrating the importance of valency of the interacting partners. Similarly, stepwise induced mutations of the phosphorylated tyrosines to phenylalanines of LAT correlated with the degree of disruption of the condensate. Functional readout in in vivo studies showed that the clustering of mCitrine-fused LAT is localized to the plasma membrane, and promotes MAPK(ERK) signaling in T cells, thus the in vitro determined effects are biologically relevant in the cellular context. In vitro LAT clusters co-localized with CD45 (a physiological phosphatase of LAT) in artificial membranes, serving as a dephosphorylation assay. The in vivo morphology of liquid droplets were observed and fusion events were followed using microscopy. In vitro LAT clusters enhanced the polymerization of actin, given that the required components are available. PMID:27056844.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27056844); morphological traits (PMID:27056844)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:27056844); multivalent domain-PTM interactions (PMID:27056844)</interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</P62993>
<Q07889 type="dict">
<id type="str">
93</id>
<phase_id type="str">
53</phase_id>
<common_name type="str">
SOS1</common_name>
<name type="str">
Son of sevenless homolog 1</name>
<accession type="str">
Q07889</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MQAQQLPYEFFSEENAPKWRGLLVPALKKVQGQVHPTLESNDDALQYVEELILQLLNMLCQAQPRSASDVEERVQKSFPHPIDKWAIADAQSAIEKRKRRNPLSLPVEKIHPLLKEVLGYKIDHQVSVYIVAVLEYISADILKLVGNYVRNIRHYEITKQDIKVAMCADKVLMDMFHQDVEDINILSLTDEEPSTSGEQTYYDLVKAFMAEIRQYIRELNLIIKVFREPFVSNSKLFSANDVENIFSRIVDIHELSVKLLGHIEDTVEMTDEGSPHPLVGSCFEDLAEELAFDPYESYARDILRPGFHDRFLSQLSKPGAALYLQSIGEGFKEAVQYVLPRLLLAPVYHCLHYFELLKQLEEKSEDQEDKECLKQAITALLNVQSGMEKICSKSLAKRRLSESACRFYSQQMKGKQLAIKKMNEIQKNIDGWEGKDIGQCCNEFIMEGTLTRVGAKHERHIFLFDGLMICCKSNHGQPRLPGASNAEYRLKEKFFMRKVQINDKDDTNEYKHAFEIILKDENSVIFSAKSAEEKNNWMAALISLQYRSTLERMLDVTMLQEEKEEQMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIARDNGPGHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNPRPGTMRHPTPLQQEPRKISYSRIPESETESTASAPNSPRTPLTPPPASGASSTTDVCSVFDSDHSSPFHSSNDTVFIQVTLPHGPRSASVSSISLTKGTDEVPVPPPVPPRRRPESAPAESSPSKIMSKHLDSPPAIPPRQPTSKAYSPRYSISDRTSISDPPESPPLLPPREPVRTPDVFSSSPLHLQPPPLGKKSDHGNAFFPNSPSPFTPPPPQTPSPHGTRRHLPSPPLTQEVDLHSIAGPPVPPRQSTSQHIPKLPPKTYKREHTHPSMHRDGPPLLENAHSS</sequence>
<gene type="str">
SOS1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Region containing multiple P-rich motifs</segment>
<boundaries type="str">
1117-1319</boundaries>
<region_ref type="str">
27056844</region_ref>
<partners type="str">
1) LAT (strictly required for LLPS); 2) GRB2 (strictly required for LLPS)</partners>
<determinants type="str">
1) protein density in membrane of LAT; 2) valency of LAT; 3) valency of GRB2</determinants>
<forms type="str">
liquid-like, micrometer-sized clusters</forms>
<organelles type="str">
TCR signalosome; LAT signalosome; </organelles>
<pmids type="str">
27056844 (research article), 30951647 (review)</pmids>
<description type="str">
Many cell surface receptors and downstream signaling molecules coalesce into micrometer- or submicrometer-sized clusters upon initiation of signaling. However, the effect of this clustering on signal transduction is poorly understood. T cell receptor (TCR) signaling is a well-studied example of this general phenomenon. In the upstream module, the TCR is phosphorylated by Lck, a membrane-bound protein kinase of the Src family. TCR phosphorylation is opposed by a transmembrane phosphatase, CD45. The phosphorylated cytoplasmic domains of the TCR complex recruit and activate the cytosolic tyrosine kinase ZAP70, which then phosphorylates the transmembrane protein LAT on multiple tyrosine residues. These phosphotyrosines are binding sites for the SH2 domains of adapter protein Grb2 (or Gads), which further interacts with Pro-rich motifs within Sos1 (or SLP-76) through its SH3 domains. LAT and its binding partners coalesce into micrometer- or submicrometer-sized clusters at the plasma membrane upon TCR activation. Dephosphorylation of pLAT by high concentrations of the soluble protein tyrosine phosphatase 1B (PTP1B, 2 µM) caused the clusters to disassemble. Components of the LAT complex activate several downstream modules that mediate calcium mobilization, mitogen-activated protein kinase (MAPK) activation, and actin polymerization. Actin polymerization is initiated from and can reorganize LAT clusters. The experiments suggest that both the phosphorylation state and pY valency of LAT as well as the presence of both SH3 domains in GRB2 are important for cluster formation (PMID:27056844). ; </description>
<experiment_llps type="str">
Phosphorylated and fluorescently tagged LAT was shown to form liquid-like clusters interacting with GRB2 and SOS1 using microscopy imaging (TIRF) in vitro; and protein dephosphorylation led to the decrease of the particle size and count, marking the disassembly of the condensate. The liquid-like property was evidenced by FRAP. Induced mutation removing the second SH3 domain of GRB2 led to the disassembly of the condensate, demonstrating the importance of valency of the interacting partners. Similarly, stepwise induced mutations of the phosphorylated tyrosines to phenylalanines of LAT correlated with the degree of disruption of the condensate. Functional readout in in vivo studies showed that the clustering of mCitrine-fused LAT is localized to the plasma membrane, and promotes MAPK(ERK) signaling in T cells, thus the in vitro determined effects are biologically relevant in the cellular context. In vitro LAT clusters co-localized with CD45 (a physiological phosphatase of LAT) in artificial membranes, serving as a dephosphorylation assay. The in vivo morphology of liquid droplets were observed and fusion events were followed using microscopy. In vitro LAT clusters enhanced the polymerization of actin, given that the required components are available. PMID:27056844.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27056844); morphological traits (PMID:27056844)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:27056844); multivalent domain-PTM interactions (PMID:27056844)</interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</Q07889>
<Q15233 type="dict">
<id type="str">
52</id>
<phase_id type="str">
54</phase_id>
<common_name type="str">
NONO</common_name>
<name type="str">
Non-POU domain-containing octamer-binding protein</name>
<accession type="str">
Q15233</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MQSNKTFNLEKQNHTPRKHHQHHHQQQHHQQQQQQPPPPPIPANGQQASSQNEGLTIDLKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKEREQPPRFAQPGSFEYEYAMRWKALIEMEKQQQDQVDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRRQEELRRMEELHNQEVQKRKQLELRQEEERRRREEEMRRQQEEMMRRQQEGFKGTFPDAREQEIRMGQMAMGGAMGINNRGAMPPAPVPAGTPAPPGPATMMPDGTLGLTPPTTERFGQAATMEGIGAIGGTPPAFNRAAPGAEFAPNKRRRY</sequence>
<gene type="str">
NONO</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
NOPS domain for homodimerization or heterodimerization with SFPQ/PSF or PSPC1</segment>
<boundaries type="str">
218-272</boundaries>
<region_ref type="str">
29932899</region_ref>
<partners type="str">
1) NEAT1 lncRNA middle domain (strictly required); 2) SFPQ; 3) PSPC1</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
foci</forms>
<organelles type="str">
paraspeckle</organelles>
<pmids type="str">
29932899 (research article), 30355755 (review), 31044562 (review)</pmids>
<description type="str">
Paraspeckles were initially defined as the foci found in close proximity to nuclear speckles and are enriched with characteristic DBHS (Drosophila Behavior Human Splicing) RBPs including NONO, SFPQ, and PSPC1. The function of paraspeckles is not completely understood. NEAT1 serves as an essential architectural component of paraspeckle NBs. The functional subdomains in the major paraspeckle scaffold NEAT1_2 architectural lncRNA middle domain are required for the assembly step in which some of the essential paraspeckle proteins likely interact to dictate the function. Indeed, tethering of NONO, SFPQ, or FUS but not RBM14 to the NEAT1 middle domain C2 subdomain rescued paraspeckle assembly, strongly suggesting that the C2 subdomain, which binds essential PSPs including NONO and SFPQ in vitro and in vivo, shows an ability to facilitate higher-order assembly in vitro and functionally recruits these PSPs to initiate paraspeckle assembly. The experimental results suggest that the actual function of the subdomains is to recruit NONO or SFPQ to form the primary dimers on NEAT1_2 that become the scaffold to initiate oligomerization with other PSPs to form the structure of massive paraspeckles. NONO plays an essential role in paraspeckle formation by maintaining NEAT1_2 levels and is also involved in the assembly of paraspeckles (PMID:29932899). </description>
<experiment_llps type="str">
It has been examined if tethering of paraspeckle proteins, PSPs, (NONO, SFPQ, FUS, and RBM14) to a functionally defective NEAT1 second domain (NEAT1_2) can rescue paraspeckle assembly in vivo. MS2-binding sites have been introduced into NEAT1_2 (genetic transformation) and PSPs have been expressed as a fusion with the MS2 coat protein (MCP; e.g., MCP-NONO) in the same cell line. By expressing MCP-NONO, MCP-SFPQ, or MCP-FUS, paraspeckle formation was rescued in the m13–16.6k/6 3 MS2BS cells, while neither negative control MCP-GFP-NLS nor MCP-RBM14 could rescue paraspeckle formation. Superresolution microscopy revealed that the paraspeckles rescued by the tethering possessed the properly ordered core-shell structure (particle size and count, morphology). Tethering of mutant NONO variants lacking one of its functional domains showed that the rescue activity requires the NOPS domain, which is required for dimerization with itself or the DBHS proteins (physical interaction). Interestingly, tethering of mutant NONO variants lacking the coiled coil domain (CC) or the prion-like domain maintain the rescue activity even though the CC is required for the polymerization of NONO that likely underlies paraspeckle assembly. Coimmunoprecipitation revealed that MCP-NONO WT interacted (physical interaction) with NONO, SFPQ, and PSPC1, whereas MCP-NONO ΔNOPS did not and MCP-NONO ΔCC interacted only weakly. Substantial amounts of NEAT1_2 were detectable in vivo in MG132-treated NONO KO cells, although they were much smaller than in WT cells (particle size and count) and structurally disordered (morphology) as revealed by microscopy (PMID:29932899).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:21170033); sensitivity to 1,6-hexanediol (PMID:29932899)</experiment_state>
<rna_req type="str">
other specific RNA: NEAT1 architectural lncRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:29932899); protein-RNA interaction (PMID:29932899)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q15233>
<P23246 type="dict">
<id type="str">
94</id>
<phase_id type="str">
54</phase_id>
<common_name type="str">
SFPQ</common_name>
<name type="str">
Splicing factor, proline- and glutamine-rich</name>
<accession type="str">
P23246</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSRDRFRSRGGGGGGFHRRGGGGGRGGLHDFRSPPPGMGLNQNRGPMGPGPGQSGPKPPIPPPPPHQQQQQPPPQQPPPQQPPPHQPPPHPQPHQQQQPPPPPQDSSKPVVAQGPGPAPGVGSAPPASSSAPPATPPTSGAPPGSGPGPTPTPPPAVTSAPPGAPPPTPPSSGVPTTPPQAGGPPPPPAAVPGPGPGPKQGPGPGGPKGGKMPGGPKPGGGPGLSTPGGHPKPPHRGGGEPRGGRQHHPPYHQQHHQGPPPGGPGGRSEEKISDSEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAKDKLESEMEDAYHEHQANLLRQDLMRRQEELRRMEELHNQEMQKRKEMQLRQEEERRRREEEMMIRQREMEEQMRRQREESYSRMGYMDPRERDMRMGGGGAMNMGDPYGSGGQKFPPLGGGGGIGYEANPGVPPATMSGSMMGSDMRTERFGQGGAGPVGGQGPRGMGPGTPAGYGRGREEYEGPNKKPRF</sequence>
<gene type="str">
SFPQ</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-707</boundaries>
<region_ref type="str">
29932899</region_ref>
<partners type="str">
1) NEAT1 lncRNA middle domain (strictly required); 2) NONO; 3) PSPC1</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
foci</forms>
<organelles type="str">
paraspeckle</organelles>
<pmids type="str">
29932899 (research article), 30355755 (review), 31044562 (review)</pmids>
<description type="str">
Paraspeckles were initially defined as the foci found in close proximity to nuclear speckles and are enriched with characteristic DBHS (Drosophila Behavior Human Splicing) RBPs including NONO, SFPQ, and PSPC1. The function of paraspeckles is not completely understood. NEAT1 serves as an essential architectural component of paraspeckle NBs. The functional subdomains in the major paraspeckle scaffold NEAT1_2 architectural lncRNA middle domain are required for the assembly step in which some of the essential paraspeckle proteins likely interact to dictate the function. Indeed, tethering of NONO, SFPQ, or FUS but not RBM14 to the NEAT1 middle domain C2 subdomain rescued paraspeckle assembly, strongly suggesting that the C2 subdomain, which binds essential PSPs including NONO and SFPQ in vitro and in vivo, shows an ability to facilitate higher-order assembly in vitro and functionally recruits these PSPs to initiate paraspeckle assembly. The experimental results suggest that the actual function of the subdomains is to recruit NONO or SFPQ to form the primary dimers on NEAT1_2 that become the scaffold to initiate oligomerization with other PSPs to form the structure of massive paraspeckles. NONO plays an essential role in paraspeckle formation by maintaining NEAT1_2 levels and is also involved in the assembly of paraspeckles (PMID:29932899). </description>
<experiment_llps type="str">
It has been examined if tethering of paraspeckle proteins, PSPs, (NONO, SFPQ, FUS, and RBM14) to a functionally defective NEAT1 second domain (NEAT1_2) can rescue paraspeckle assembly in vivo. MS2-binding sites have been introduced into NEAT1_2 (genetic transformation) and PSPs have been expressed as a fusion with the MS2 coat protein (MCP; e.g., MCP-NONO) in the same cell line. By expressing MCP-NONO, MCP-SFPQ, or MCP-FUS, paraspeckle formation was rescued in the m13–16.6k/6 3 MS2BS cells, while neither negative control MCP-GFP-NLS nor MCP-RBM14 could rescue paraspeckle formation. Superresolution microscopy revealed that the paraspeckles rescued by the tethering possessed the properly ordered core-shell structure (particle size and count, morphology). Tethering of mutant NONO variants lacking one of its functional domains showed that the rescue activity requires the NOPS domain, which is required for dimerization with itself or the DBHS proteins (physical interaction). Interestingly, tethering of mutant NONO variants lacking the coiled coil domain (CC) or the prion-like domain maintain the rescue activity even though the CC is required for the polymerization of NONO that likely underlies paraspeckle assembly. Coimmunoprecipitation revealed that MCP-NONO WT interacted (physical interaction) with NONO, SFPQ, and PSPC1, whereas MCP-NONO ΔNOPS did not and MCP-NONO ΔCC interacted only weakly. Substantial amounts of NEAT1_2 were detectable in vivo in MG132-treated NONO KO cells, although they were much smaller than in WT cells (particle size and count) and structurally disordered (morphology) as revealed by microscopy. PMID:29932899.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:21170033); sensitivity to 1,6-hexanediol (PMID:29932899)</experiment_state>
<rna_req type="str">
other specific RNA: NEAT1 architectural lncRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:29932899); protein-RNA interaction (PMID:29932899)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P23246>
<Q9W1V3 type="dict">
<id type="str">
53</id>
<phase_id type="str">
55</phase_id>
<common_name type="str">
Fib</common_name>
<name type="str">
rRNA 2-O-methyltransferase fibrillarin</name>
<accession type="str">
Q9W1V3</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MGKPGFSPRGGGGGGGGGGGGFRGRGGGGGGGGGGFGGGRGRGGGGDRGGRGGFGGGRGGGGRGGGGGGGRGAFGGRGGGGGRGGGGRGGGGRGGGGRGGGAGGFKGGKTVTIEPHRHEGVFIARGKEDALVTRNFVPGSEVYGEKRISVETNGEKIEYRVWNPFRSKLAAAVLGGVEQIHMPPGSKVLYLGAASGTTVSHVSDVVGPEGLVYAVEFSHRSGRDLINVAKKRTNIIPIIEDARHPHKYRMLVGMVDTIFADVAQPDQGRIVALNAQHFLKNGGHFVISIKASCIDSTAQPEAVFAAEVKKMQADKLKPQEQLTLEPYERDHAVVVGVYRPPPKQ</sequence>
<gene type="str">
FIB</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-344</boundaries>
<region_ref type="str">
28115706</region_ref>
<partners type="str">
1) rDNA (modulates the kinetics, variability of the process but not required)</partners>
<determinants type="str">
1) temperature</determinants>
<forms type="str">
nucleolus</forms>
<organelles type="str">
nucleolus; dense fibrillar component; nuclear body</organelles>
<pmids type="str">
28115706 (research article)</pmids>
<description type="str">
Nucleoli represent the site of ribosome biogenesis. The temperature-dependence and reversibility of the association of 6 nucleolar proteins have been studied to address if they assemble into nucleoli according to an LLPS-based mechanism or through active recruitement. Fib, Nopp140 and Pit assembled into the nucleoli of D. melanogaster embryos in a temparature-dependant and reversible manner, which suggest an LLPS-based mechanism. Other investigated components showed hallmarks of active recruitement (PMID:28115706).</description>
<experiment_llps type="str">
In vivo overexpression of Fib, Nopp140 and Pit proteins fused with fluorescent fusion proteins coupled with microscopy detection showed that they assemble into the nucleoli of D. melanogaster embryos (protein localization, protein co-localization). Applying a microfluidic device to achieve precisely controllable changes in temperature, the three proteins were observed to associate with nucleoli in a temparature-dependant and reversible manner, which suggest an LLPS-based mechanism PMID:28115706. No in vitro LLPS studies have been carried out with these proteins and the regions responsible for LLPS were not investigated.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28115706); reversibility of formation and dissolution (PMID:28115706)</experiment_state>
<rna_req type="str">
other type of RNA: rRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9W1V3>
<Q7KTV5 type="dict">
<id type="str">
54</id>
<phase_id type="str">
56</phase_id>
<common_name type="str">
Nopp140</common_name>
<name type="str">
Nopp140, isoform B</name>
<accession type="str">
Q7KTV5</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MTDLLKIADAIVLEYLQSKDKNLAKVFQQKTKAASVAKSSPKLSEILQFYQTKSPKKIPAIKATAGDSSEDSDSDSESDAAPKKPATAPALTNGKAVKKAASSTSEDSDSEEEKKPAAKATPAKAVGKKAKSSSEDSSSEEEAPKKAAPVKAPPAKAAPAKKVESSSEDSSSEEEPAKPAVKATTTKVAPAKKADSSSEESSSDEETKPAAKPVAKAAPAKKAASSSEESDSDDEPAAKKPAVQPAAKPAPKAAASSSEDSSSEEEVKPAAKSAAKLAPAKKGASSSDDSSSEDEAPKKAATLAKPISKAAPTKKADSSTEDSSSEDDAPKKVAPAKATPAKAIPAKKAASSDDSSSEEEAPKKAAPANATPARAPPAKKAASSDDSSSEEEAPKKAAPAKATPAKATPAKKAASSDDSSSEEEAPKKAAAPAKATPAKKAKSSSEDSDSDEEEAPKKPAAKAVAKAASSEDSDSSEDEKPAKAAPKALAKSAKAASSDSDDSSDEETPAVKPAVKKTAAPAKKADSSSDESDSGEESGEVKPNSATNGNEKTAQKRKFSGGDQDEATPNKKYNNFVKSGEQQKNDFTSTPNNTFSRNHNMNNSGGGSGRRSPFRRVRTEDVVVDSRVQDMSFEAKKNAAGSWGERANKDLKHTRGKSFKHEKTKKKRGSYRGGQIDVGVNSIKFD</sequence>
<gene type="str">
NOPP140</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-686</boundaries>
<region_ref type="str">
28115706</region_ref>
<partners type="str">
1) rDNA (modulates the kinetics, variability of the process but not required)</partners>
<determinants type="str">
1) temperature</determinants>
<forms type="str">
nucleolus</forms>
<organelles type="str">
nucleolus</organelles>
<pmids type="str">
28115706 (research article)</pmids>
<description type="str">
Nucleoli represent the site of ribosome biogenesis. The temperature-dependence and reversibility of the association of 6 nucleolar proteins have been studied to address if they assemble into nucleoli according to an LLPS-based mechanism or through active recruitement. Fib, Nopp140 and Pit assembled into the nucleoli of D. melanogaster embryos in a temparature-dependant and reversible manner, which suggest an LLPS-based mechanism. Other investigated components showed hallmarks of active recruitement (PMID:28115706).</description>
<experiment_llps type="str">
In vivo overexpression of Fib, Nopp140 and Pit proteins fused with fluorescent fusion proteins coupled with microscopy detection showed that they assemble into the nucleoli of D. melanogaster embryos (protein localization, protein co-localization). Applying a microfluidic device to achieve precisely controllable changes in temperature, the three proteins were observed to associate with nucleoli in a temparature-dependant and reversible manner, which suggest an LLPS-based mechanism PMID:28115706. No in vitro LLPS studies have been carried out with these proteins and the regions responsible for LLPS were not investigated.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28115706); reversibility of formation and dissolution (PMID:28115706)</experiment_state>
<rna_req type="str">
other type of RNA: rRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q7KTV5>
<Q9VD51 type="dict">
<id type="str">
55</id>
<phase_id type="str">
57</phase_id>
<common_name type="str">
Pit</common_name>
<name type="str">
Probable ATP-dependent RNA helicase pitchoune</name>
<accession type="str">
Q9VD51</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MSIREKLLMKKIVKREKMKKELSQKKGNKNAQKQEPPKQNGNKPSKKPEKLSKKHVAKDEDDDLEEDFQEAPLPKKKQQKQPPKKQQIQVANSDSESDDDEQEDEADEDSDLDEVAEVDEEDVDSGSEDDDQQEDEDEEEPVPAKKTKLLPNKSKAQNGKPAKDDEPFTVESSLAALDYRDSDDRSFASLKGAVSEATLRAIKEMGFTEMTEIQSKSLTPLLKGRDLVGAAQTGSGKTLAFLIPAVELINKLRFMPRNGTGVIIISPTRELSMQTFGVLKELMAHHHHTYGLVMGGSNRQVESEKLGKGINILVATPGRLLDHLQNSPDFLYKNLQCLIIDEVDRILEIGFEEELKQIINLLPKRRQTMLFSATQTARIEALSKLALKSEPIYVGVHDNQDTATVDGLEQGYIVCPSEKRLLVLFTFLKKNRKKKVMVFFSSCMSVKYHHELFNYIDLPVTSIHGKQKQTKRTTTFFQFCNAESGILLCTDVAARGLDIPQVDWIVQYDPPDDPREYIHRVGRTARGSGTSGHALLLMRPEELGFLRYLKAAKVPLNEFEFSWQKIADIQLQLEKLIAKNYFLNQSAKEAFKSYVRAYDSHQLKQIFNVNTLDLQAVAKSFGFLVPPVVDLKVGAAKRERPEKRVGGGGFGFYKKMNEGSASKQRHFKQVNRDQAKKFMR</sequence>
<gene type="str">
PIT</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-680</boundaries>
<region_ref type="str">
28115706</region_ref>
<partners type="str">
1) rDNA (modulates the kinetics, variability of the process but not required)</partners>
<determinants type="str">
1) temperature</determinants>
<forms type="str">
nucleolus</forms>
<organelles type="str">
nucleolus</organelles>
<pmids type="str">
28115706 (research article)</pmids>
<description type="str">
Nucleoli represent the site of ribosome biogenesis. The temperature-dependence and reversibility of the association of 6 nucleolar proteins have been studied to address if they assemble into nucleoli according to an LLPS-based mechanism or through active recruitement. Fib, Nopp140 and Pit assembled into the nucleoli of D. melanogaster embryos in a temparature-dependant and reversible manner, which suggest an LLPS-based mechanism. Other investigated components showed hallmarks of active recruitement (PMID:28115706).</description>
<experiment_llps type="str">
In vivo overexpression of Fib, Nopp140 and Pit proteins fused with fluorescent fusion proteins coupled with microscopy detection showed that they assemble into the nucleoli of D. melanogaster embryos (protein localization, protein co-localization). Applying a microfluidic device to achieve precisely controllable changes in temperature, the three proteins were observed to associate with nucleoli in a temparature-dependant and reversible manner, which suggest an LLPS-based mechanism PMID:28115706. No in vitro LLPS studies have been carried out with these proteins and the regions responsible for LLPS were not investigated.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:28115706); reversibility of formation and dissolution (PMID:28115706)</experiment_state>
<rna_req type="str">
other type of RNA: rRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9VD51>
<P53297 type="dict">
<id type="str">
95</id>
<phase_id type="str">
58</phase_id>
<common_name type="str">
Pbp1</common_name>
<name type="str">
PAB1-binding protein 1</name>
<accession type="str">
P53297</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MKGNFRKRDSSTNSRKGGNSDSNYTNGGVPNQNNSSMFYENPEITRNFDDRQDYLLANSIGSDVTVTVTSGVKYTGLLVSCNLESTNGIDVVLRFPRVADSGVSDSVDDLAKTLGETLLIHGEDVAELELKNIDLSLDEKWENSKAQETTPARTNIEKERVNGESNEVTKFRTDVDISGSGREIKERKLEKWTPEEGAEHFDINKGKALEDDSASWDQFAVNEKKFGVKSTFDEHLYTTKINKDDPNYSKRLQEAERIAKEIESQGTSGNIHIAEDRGIIIDDSGLDEEDLYSGVDRRGDELLAALKSNSKPNSNKGNRYVPPTLRQQPHHMDPAIISSSNSNKNENAVSTDTSTPAAAGAPEGKPPQKTSKNKKSLSSKEAQIEELKKFSEKFKVPYDIPKDMLEVLKRSSSTLKSNSSLPPKPISKTPSAKTVSPTTQISAGKSESRRSGSNISQGQSSTGHTTRSSTSLRRRNHGSFFGAKNPHTNDAKRVLFGKSFNMFIKSKEAHDEKKKGDDASENMEPFFIEKPYFTAPTWLNTIEESYKTFFPDEDTAIQEAQTRFQQRQLNSMGNAVPGMNPAMGMNMGGMMGFPMGGPSASPNPMMNGFAAGSMGMYMPFQPQPMFYHPSMPQMMPVMGSNGAEEGGGNISPHVPAGFMAAGPGAPMGAFGYPGGIPFQGMMGSGPSGMPANGSAMHSHGHSRNYHQTSHHGHHNSSTSGHK</sequence>
<gene type="str">
PBP1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Low complexity region</segment>
<boundaries type="str">
571-722</boundaries>
<region_ref type="str">
30982603</region_ref>
<partners type="str">
1) Pbp4; 2) Lsm12; 3) TORC1; 4) Kog1</partners>
<determinants type="str">
1) redox state of methinonin; 2) temperature</determinants>
<forms type="str">
liquid-like droplets, condensates, perimithocondrial condensate</forms>
<organelles type="str">
cytoplasmic stress granule</organelles>
<pmids type="str">
30982603 (research article), 30982600 (research article)</pmids>
<description type="str">
Intrinsically disordered protein and a negative regulator of TORC1 by binding it during respiratory growth. At normal expression levels and physiological temperatures, Pbp1 does not form foci-like granules and is instead present in the form of pelletable assemblies during respiratory growth. The low-complexity (LC) domain of Pbp1 forms labile, cross-b polymers that facilitate phase transition of the protein into liquid-like or gel-like states. In place of tyrosine or phenylalanine residues prototypically used for phase separation, Pbp1 contains 24 similarly disposed methionine residues. The Pbp1 methionine residues are sensitive to hydrogen peroxide (H₂O₂)-mediated oxidation in vitro and in living cells. Methionine oxidation melts Pbp1 liquid-like droplets, which in turn activates TORC1 signaling, in a manner reversed by methionine sulfoxide reductase enzymes. These observations explain how reversible formation of labile polymers by the Pbp1 LC domain enables the protein to function as a sensor of cellular redox state. Pbp1 may therefore sense respiratory status and mitochondrial dysfunction to properly modulate TORC1 signaling, thus it appears that mitochondrial dysfunction and cell death may emerge due to loss of Pbp1 following prolonged metabolic or nutritional stress, or as a function of age (PMID:30982603, PMID:30982600).</description>
<experiment_llps type="str">
In vitro droplet formation and dissolution (particle size and count) was followed by light microscopy using 2 mg/ml His-tagged LC region of the protein, evidencing H2O2-mediated melting of Pbp1 droplets at intermediate concentrations. Concomitant mutation of eight methionine residues to serine, including residues M591, M595, M605, M606, M614, M616, M618, and M625 (M7–14 within the LC domain), yielded a protein variant designated ‘‘MS8a’’. This mutated variant of Pbp1 was observed to be incapable of polymerizing into labile cross-b polymers and was functionally inactive in its ability to couple mitochondrial activity state to autophagy in living yeast cells. The MS8a variant did become phase separated into liquid-like droplets, but these droplets differed from those formed from the native LC domain of Pbp1 in showing aberrantly rapid protein exchange (morphology). A second variant of Pbp1 also bearing eight methionine-to-serine mutations, including residues M635, M638, M659, M667, M681, M682, M689, and M696 (M17–24 within the LC domain), yielded a protein variant designated ‘‘MS8b,’’ which was fully capable of polymerizing into labile cross-b polymers. As deduced from fluorescence recovery after photo-bleaching (FRAP) experiments, droplets formed from the MS8b variant are endowed with a slow exchange rate indistinguishable from droplets derived from the native LC domain. Finally, the MS8b variant effectively recapitulated the function of Pbp1 in living yeast cells. In vivo, in yeast cells, under culture conditions demanding intense mitochondrial respiration, the majority of Pbp1 partitions to the pellet fraction following centrifugation, which reflects propensity of the protein to self-associate into a condensate. Administration of H2O2 to cells caused a significant portion of Pbp1 to shift to the soluble fraction, and the protein became more uniformly distributed throughout the cell (protein localization), suggesting that oxidation of the LC domain may promote dissolution of Pbp1 condensates. Moreover, modest concentrations of H2O2 also resulted in significant inhibition of autophagy, consistent with the melting of Pbp1 condensates and corresponding activation of TORC1 signaling (PMID:30982603).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
reversibility of formation and dissolution (PMID:30982603, PMID:30982600); morphological traits (PMID:30982603, PMID:30982600)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
formation of amyloid-like/cross-beta/kinked/stacked beta-sheet structures (PMID:30982603, PMID:30982603)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Márton Kovács; Ágnes Tantos</annotator>
<functional_class type="str">
sensor</functional_class>
<date type="str">
2019-09-11</date>
</P53297>
<O13828 type="dict">
<id type="str">
96</id>
<phase_id type="str">
59</phase_id>
<common_name type="str">
Dcp2</common_name>
<name type="str">
mRNA decapping complex subunit 2</name>
<accession type="str">
O13828</accession>
<organism type="str">
Schizosaccharomyces pombe</organism>
<sequence type="str">
MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNTTKEKNISVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSSFDIKQKILHLLNEGNEPKSPIQLPPVSNLPLNPPIQSSNSRLSHDNNSFDPFAYLGLDPKNPSASFPRVVSQNNMLTNKPVLNNHFQQSMYSNLLKDQNSVQHLFAASDMPSPMELPSPSTVYHQVFYPPTSTSVSSYGLGKTPQPAYGSSSPYVNGHQTQQISSLPPFQSQTQFLARNSDNSGQSYNSEGDSNSKRLLSMLSQQDTTPSSSTLSKEANVQLANLFLTPNSLETKKFSDNSQGEEISDNLHGESCNNPNANSVHSAQLLQALLHPSATETKEETPKKTSDSLSLLTLLKSGLPTPANDLQNKSQNNERKASSQVKELEVKNYSKSTDLLKKTLRIPRNDEPLEAANQFDLLKVSPQQKSEVPPKRNELSQSKLKNRKKKENSETNKNHVDMSPGFVKILKRSPLADQKKEDTQESDFKGSDDHFLSYLQSVVSSNSNGLH</sequence>
<gene type="str">
DCP2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal; and C-terminal regions</segment>
<boundaries type="str">
1-289; 553-771</boundaries>
<region_ref type="str">
24862735</region_ref>
<partners type="str">
1) Edc3</partners>
<determinants type="str">
1) protein concentration; 2) molar ratio of the partners</determinants>
<forms type="str">
droplet-like structures, P-bodies</forms>
<organelles type="str">
P-body</organelles>
<pmids type="str">
24862735 (research article)</pmids>
<description type="str">
During the formation of yeast P-bodies LLPS in vitro is mediated by the interaction of Edc3 with either Dcp2 or Pcd1 (PMID:24862735). Phase separation is mediated by the helical Leu-rich motifs (HLMs) found in both Dcp2 and Pcd1 (PMID:24862735), while interaction between Dcp2 and Edc3 is mediated by the catalytic domain of Dcp2 (PMID:17984320). According to the model presented in PMID:24862735, one Edc3 dimer can interact with two Dcp enzymes, with two Pdc1 proteins or with one decapping complex (Dcp1/Dcp2) and one Pdc1 dimer. In addition, one Pdc1 dimer can interact with two decapping complexes.</description>
<experiment_llps type="str">
Binding (physical interaction) of Dcp2 and Pdc1 to Edc3 was characterized in vitro using NMR measurements, while droplet formation was followed by bright field and fluorescent microscopy (particle size and count). Edc3-Oregon green (fluorescent tagging) and unlabeled Dcp2 or Pdc1 were mixed at different molar ratios and concentrations and colocalization was measured (PMID:24862735). In vivo P-body formation and protein localization was detected using mCherry-fused Edc3 and GFP-fused Dcp2 (PMID:24862735). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:24862735); reversibility of formation and dissolution (PMID:24862735)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Ágnes Tantos</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</O13828>
<O94752 type="dict">
<id type="str">
97</id>
<phase_id type="str">
59</phase_id>
<common_name type="str">
Edc3</common_name>
<name type="str">
Enhancer of mRNA-decapping protein 3</name>
<accession type="str">
O94752</accession>
<organism type="str">
Schizosaccharomyces pombe</organism>
<sequence type="str">
MSVADFYGSNVEVLLNNDSKARGVITNFDSSNSILQLRLANDSTKSIVTKDIKDLRILPKNEIMPKNGTKSPSTNSTKLKSAETYSSKNKWSMDCDEEFDFAANLEKFDKKQVFAEFREKDKKDPAKLLVSHNKSPNRNYHHKQNVLGPSVKDEFVDLPSAGSQINGIDAVLSSSSNGHVTPGSKKGSRETLKKKPFVDENIPAELHTTTGDILKPITPEQLSQGIALAIAKTSTDIVVENAAQLLSQFVFSVLGGHKRLSSRNHNSQPLVCILVGSHDHASAAVAAGRRLCAIGIKVVLRLLTPFNVDNRQLLMFQAAGGYIPTENFDQFLNKLTSPIELVVDVLTGFHPSIDKNSHALIQWANDLNVLILSVDIPSGYTVQKKNTAILPKWTLALGAVTTTLAQAALVKQAAGVSVFVGNLGTGSQTWAELGILESQVTGQYLAQISCTSTN</sequence>
<gene type="str">
EDC3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal region; YjeF domain</segment>
<boundaries type="str">
1-86; 231-551</boundaries>
<region_ref type="str">
17984320</region_ref>
<partners type="str">
1) Dcp2; 2) Pdc1</partners>
<determinants type="str">
1) concentration; 2) molar ratio of the partners</determinants>
<forms type="str">
droplet-like structures, P-bodies</forms>
<organelles type="str">
P-body</organelles>
<pmids type="str">
24862735 (research article)</pmids>
<description type="str">
During the formation of yeast P-bodies LLPS in vitro is mediated by the interaction of Edc3 with either Dcp2 or Pcd1 (PMID:24862735). Phase separation is mediated by the helical Leu-rich motifs (HLMs) found in both Dcp2 and Pcd1 (PMID:24862735), while interaction between Dcp2 and Edc3 is mediated by the catalytic domain of Dcp2 (PMID:17984320). According to the model presented in PMID:24862735, one Edc3 dimer can interact with two Dcp enzymes, with two Pdc1 proteins or with one decapping complex (Dcp1/Dcp2) and one Pdc1 dimer. In addition, one Pdc1 dimer can interact with two decapping complexes.</description>
<experiment_llps type="str">
Binding (physical interaction) of Dcp2 and Pdc1 to Edc3 was characterized in vitro using NMR measurements, while droplet formation was followed by bright field and fluorescent microscopy (particle size and count). Edc3-Oregon green (fluorescent tagging) and unlabeled Dcp2 or Pdc1 were mixed at different molar ratios and concentrations and colocalization was measured (PMID:24862735). In vivo P-body formation and protein localization was detected using mCherry-fused Edc3 and GFP-fused Dcp2 (PMID:24862735). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:24862735); reversibility of formation and dissolution (PMID:24862735)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Ágnes Tantos</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</O94752>
<Q09737 type="dict">
<id type="str">
124</id>
<phase_id type="str">
59</phase_id>
<common_name type="str">
Pdc1</common_name>
<name type="str">
Putative pyruvate decarboxylase C13A11.06</name>
<accession type="str">
Q09737</accession>
<organism type="str">
Schizosaccharomyces pombe</organism>
<sequence type="str">
MSGDILVGEYLFKRLEQLGVKSILGVPGDFNLALLDLIEKVGDEKFRWVGNTNELNGAYAADGYARVNGLSAIVTTFGVGELSAINGVAGSYAEHVPVVHIVGMPSTKVQDTGALLHHTLGDGDFRTFMDMFKKVSAYSIMIDNGNDAAEKIDEALSICYKKARPVYIGIPSDAGYFKASSSNLGKRLKLEEDTNDPAVEQEVINHISEMVVNAKKPVILIDACAVRHRVVPEVHELIKLTHFPTYVTPMGKSAIDETSQFFDGVYVGSISDPEVKDRIESTDLLLSIGALKSDFNTGSFSYHLSQKNAVEFHSDHMRIRYALYPNVAMKYILRKLLKVLDASMCHSKAAPTIGYNIKPKHAEGYSSNEITHCWFWPKFSEFLKPRDVLITETGTANFGVLDCRFPKDVTAISQVLWGSIGYSVGAMFGAVLAVHDSKEPDRRTILVVGDGSLQLTITEISTCIRHNLKPIIFIINNDGYTIERLIHGLHASYNEINTKWGYQQIPKFFGAAENHFRTYCVKTPTDVEKLFSDKEFANADVIQVVELVMPMLDAPRVLVEQAKLTSKINKQ</sequence>
<gene type="str">
SPAC13A11.06</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal; and C-terminal regions</segment>
<boundaries type="str">
1-750; 880-1076</boundaries>
<region_ref type="str">
24862735</region_ref>
<partners type="str">
1) Edc3</partners>
<determinants type="str">
1) concentration; 2) molar ratio of the partners</determinants>
<forms type="str">
droplet-like structures, P-bodies</forms>
<organelles type="str">
P-body</organelles>
<pmids type="str">
24862735 (research article)</pmids>
<description type="str">
During the formation of yeast P-bodies LLPS in vitro is mediated by the interaction of Edc3 with either Dcp2 or Pcd1 (PMID:24862735). Phase separation is mediated by the helical Leu-rich motifs (HLMs) found in both Dcp2 and Pcd1 (PMID:24862735), while interaction between Dcp2 and Edc3 is mediated by the catalytic domain of Dcp2 (PMID:17984320). According to the model presented in PMID:24862735, one Edc3 dimer can interact with two Dcp enzymes, with two Pdc1 proteins or with one decapping complex (Dcp1/Dcp2) and one Pdc1 dimer. In addition, one Pdc1 dimer can interact with two decapping complexes.</description>
<experiment_llps type="str">
Binding (physical interaction) of Dcp2 and Pdc1 to Edc3 was characterized in vitro using NMR measurements, while droplet formation was followed by bright field and fluorescent microscopy (particle size and count). Edc3-Oregon green (fluorescent tagging) and unlabeled Dcp2 or Pdc1 were mixed at different molar ratios and concentrations and colocalization was measured (PMID:24862735). In vivo P-body formation and protein localization was detected using mCherry-fused Edc3 and GFP-fused Dcp2 (PMID:24862735). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:24862735); reversibility of formation and dissolution (PMID:24862735)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Ágnes Tantos</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q09737>
<Q9W4I7 type="dict">
<id type="str">
57</id>
<phase_id type="str">
61</phase_id>
<common_name type="str">
Pon</common_name>
<name type="str">
Partner of numb</name>
<accession type="str">
Q9W4I7</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MLETKSIAALAFTETPRKRKRETLYKNAAPPPNPQQQPPEKDAQDAAVASTESCFTNAAFSSTPKKLMVARRRLAKENSQPNPFPGLEVKSIADLAQKQQHQQHHQQQQQQQQKLPTNPFEVLRQPPKKKKREHACFENPGLNLELPEKQFNPYEVVRSATTPAKGFVNPALNLRGSDAPASLNPFEIHRPSEASEAACNPSGVANPALADRDSEEQLPTSLKIGLPFTPTLGCRIDFHGMSLTQLTPSKLLAEKLVFSPVPAPKRSLGAISEESSMDIGKELDRYQLELENSINEAKLRKNGVLVDRELPRNSLEVELPKNTKVSLVMETNTQELMMQEVVTVDTQVERRLVCTRRRTLTEISEASEVEEDTEKLLEQDREAEVILEQEKILEQEMVSERERHLTREKQLKQEKLLEREKHLEREKLQEKLHEQLREKLQERAKHLEKEKLEEEELLERQLEEEREKEPTDGDVAYASESESDDEPDDLDFKAPARFVRAYRPAALPSKAASKESLQSIGSSKSAKSAEVKPSIGMKGMIRKSIRRLMHPTSHTTPSEVKSEDKDEHGHGQGHGQHNILNSIRHSLRRRPQKAAELEEQMEPVLADVSIIDTSERTMKLRSSVAQTEYMTIEQLTNEKKHSLRNSIRRSTRDVLRHVFHKSHDAYATAK</sequence>
<gene type="str">
PON</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal fragment with two NUMB-interacting motifs</segment>
<boundaries type="str">
1-228</boundaries>
<region_ref type="str">
29467404</region_ref>
<partners type="str">
1) Numb PTB (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration; 2) valency of Pon; 3) stoichiometry of the components</determinants>
<forms type="str">
highly concentrated assemblies,; liquid droplets; </forms>
<organelles type="str">
cytoplasmic protein granule; basal Numb-Pon crescent in dividing neuroblasts</organelles>
<pmids type="str">
29467404 (research article)</pmids>
<description type="str">
Uneven distribution and local concentration of protein complexes on distinct membrane cortices is a fundamental property in numerous biological processes, including Drosophila neuroblast (NB) asymmetric cell divisions (ACD) and cell polarity in general. In NBs, the cell fate determinant Numb forms a basal crescent together with Pon and is segregated into the basal daughter cell to initiate its differentation. Numb PTB domain, using two distinct binding surfaces, recognizes repeating motifs within Pon in a previously unrecognized mode. Several repeating motifs have been found in Pon: type A „FxNxx[F/L]” motif and type B „NP[F/Y]E[V/I]xR” motif; the isolated motifs barely interact with Numb, however, the proper combination of both motifs dramatically increases the interaction with Numb PTB. The multivalent Numb-Pon interaction leads to high binding specificity and LLPS of the complex both in vitro and in living cells. The direct interaction between Pon and Numb PTB is responsible for the correct localization of Numb during ACD. The proper targeting and local concentration of Numb by Pon on the basal cortex is essential for its subsequent inhibition of Notch signaling. Such phase-transition-mediated protein condensations on distinct membrane cortices may be a general mechanism for various cell polarity regulatory complexes (PMID:29467404).</description>
<experiment_llps type="str">
Specific physical interaction was confirmed between Numb PTB and an N-terminal fragment (amino acids (aa) 1–228) of Pon (truncated) in vitro by pull-down assays. Proper combination and valency of type A “FxNxx[F/L]” and type B “NP[F/Y]E[V/I]xR” motifs (mutation) dramatically increased the interaction with Numb PTB in vitro (physical interaction confirmed by ITC and pull-down). The complex structures of Numb PTB with either Pon A2B2 or Pon B1A2 was solved by X-ray crystallography. Numb PTB and Pon A1B3 formed liquid droplets (morphology, particle size and count by microscopy) in vitro and droplet formation was protein concentration-dependent. High-affinity monovalent Pon peptide (change in the concentration of a small molecule) dispersed the droplets in vitro (microscopy). Fluorescently tagged Pon and Numb showed co-localization in vitro by epifluorescence microscopy. In vivo overexpression of GFP-fused Pon and mCherry-fused Numb PTB in HeLa cells led to bright puncta in the nucleus (protein localization) showing the co-localization of the two proteins with time-lapse microscopy. Overexpression of only one of the fusion proteins, or both fusion proteins but with mutations perturbing the interaction in at least one of them did not result in in vivo puncta formation. In vivo, in transgenic flies, overexpression of the Flag-tagged wild type or mutant forms showed that during neuroblast division Pon together with Numb is basally localized and is segregated into the basal daughter cell after assymmetric cell division. The interaction between Pon and Numb PTB is responsible for the correct, basal localization of Numb (by microscopy) as it is disturbed for Pon-binding deficient Numb mutants. PMID:29467404.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:29467404); sensitivity to 1,6-hexanediol (PMID:29467404); dynamic exchange of molecules with surrounding solvent (PMID:29467404)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:29467404)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</Q9W4I7>
<P16554 type="dict">
<id type="str">
98</id>
<phase_id type="str">
61</phase_id>
<common_name type="str">
NUMB</common_name>
<name type="str">
Protein numb</name>
<accession type="str">
P16554</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MGNSSSHTHEPLERGFTRGKFGDVKNGKSASFRFSKKSPKKMDRLRRSFRDSFRRRKDRVPESSKPHQWQADEEAVRSATCSFSVKYLGCVEVFESRGMQVCEEALKVLRQSRRRPVRGLLHVSGDGLRVVDDETKGLIVDQTIEKVSFCAPDRNHERGFSYICRDGTTRRWMCHGFLACKDSGERLSHAVGCAFAVCLERKQRRDKECGVTMTFDTKNSTFTRTGSFRQQTLTERLAMATVGTNERSVDGPGSAMPGPPAATVKPFNPFAIERPHATPNMLERQSSFRLSTIGSQSPFKRQMSLRINDLPSNADRQRAFLTAAAGNPMQTPLRSVSPIAEVSPAKSAGADPLSAAAVAADSVSQLCQELSQGLSLLTQTDALLAAGEDLNFNNNRSINQNIIAAEKQVQHVHSYAPPTAQVTPRVASTTPTYQTLHSQSPSRSEQSIETSTELPNAEQWLGHVVRSTSPAAPKRPTYLANVGRAQTLASGTGAAVGGGGPDDPFDAEWVANVAAAKQLSPDLPIPSTARSPLARHSTNPFISPPKAPAQSFQVQL</sequence>
<gene type="str">
NUMB</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
PTB domain</segment>
<boundaries type="str">
65-203</boundaries>
<region_ref type="str">
29467404</region_ref>
<partners type="str">
1) Pon N-terminal fragment (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration; 2) valency of Pon; 3) stoichiometry of the components</determinants>
<forms type="str">
highly concentrated assemblies; liquid droplets; </forms>
<organelles type="str">
cytoplasmic protein granule; basal Numb-Pon crescent in dividing neuroblasts</organelles>
<pmids type="str">
29467404 (research article)</pmids>
<description type="str">
Uneven distribution and local concentration of protein complexes on distinct membrane cortices is a fundamental property in numerous biological processes, including Drosophila neuroblast (NB) asymmetric cell divisions (ACD) and cell polarity in general. In NBs, the cell fate determinant Numb forms a basal crescent together with Pon and is segregated into the basal daughter cell to initiate its differentation. Numb PTB domain, using two distinct binding surfaces, recognizes repeating motifs within Pon in a previously unrecognized mode. Several repeating motifs have been found in Pon: type A „FxNxx[F/L]” motif and type B „NP[F/Y]E[V/I]xR” motif; the isolated motifs barely interact with Numb, however, the proper combination of both motifs dramatically increases the interaction with Numb PTB. The multivalent Numb-Pon interaction leads to high binding specificity and LLPS of the complex both in vitro and in living cells. The direct interaction between Pon and Numb PTB is responsible for the correct localization of Numb during ACD. The proper targeting and local concentration of Numb by Pon on the basal cortex is essential for its subsequent inhibition of Notch signaling. Such phase-transition-mediated protein condensations on distinct membrane cortices may be a general mechanism for various cell polarity regulatory complexes (PMID:29467404).</description>
<experiment_llps type="str">
Specific physical interaction was confirmed between Numb PTB and an N-terminal fragment (amino acids (aa) 1–228) of Pon (mutation, truncation) in vitro by pull-down assays (protein-protein interaction detection assay). Proper combination and valency of type A “FxNxx[F/L]” and type B “NP[F/Y]E[V/I]xR” motifs (mutation) dramatically increased the interaction with Numb PTB in vitro (physical interaction confirmed by ITC and pull-down protein-protein interaction detection assays). The complex structures of Numb PTB with either Pon A2B2 or Pon B1A2 was solved by X-ray crystallography. Numb PTB and Pon A1B3 formed liquid droplets (morphology, particle size and count by microscopy) in vitro and droplet formation was protein concentration-dependent. High-affinity monovalent Pon peptide (change in the concentration of a small molecule) dispersed the droplets in vitro (microscopy). Fluorescently tagged Pon and Numb showed co-localization in vitro by epifluorescence microscopy. In vivo overexpression of GFP-fused Pon and Cherry-fused Numb PTB in HeLa cells led to bright puncta in the nucleus (protein localization) showing the co-localization of the two proteins with time-lapse microscopy. Overexpression of only one of the fusion proteins, or both fusion proteins but with mutations perturbing the interaction in at least one of them did not result in in vivo puncta formation. In vivo, in transgenic flies, overexpression of the Flag-tagged wild type (creation of a fusion protein) or mutant forms showed that during neuroblast division Pon together with Numb is basally localized (protein localization) and is segregated into the basal daughter cell after assymmetric cell division. The interaction between Pon and Numb PTB is responsible for the correct, basal localization of Numb (protein localization, microscopy) as it is disturbed for Pon-binding deficient Numb mutants. PMID:29467404.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:29467404); sensitivity to 1,6-hexanediol (PMID:29467404); dynamic exchange of molecules with surrounding solvent (PMID:29467404)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:29467404)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</P16554>
<P05453 type="dict">
<id type="str">
58</id>
<phase_id type="str">
62</phase_id>
<common_name type="str">
Sup35</common_name>
<name type="str">
Eukaryotic peptide chain release factor GTP-binding subunit</name>
<accession type="str">
P05453</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MSDSNQGNNQQNYQQYSQNGNQQQGNNRYQGYQAYNAQAQPAGGYYQNYQGYSGYQQGGYQQYNPDAGYQQQYNPQGGYQQYNPQGGYQQQFNPQGGRGNYKNFNYNNNLQGYQAGFQPQSQGMSLNDFQKQQKQAAPKPKKTLKLVSSSGIKLANATKKVGTKPAESDKKEEEKSAETKEPTKEPTKVEEPVKKEEKPVQTEEKTEEKSELPKVEDLKISESTHNTNNANVTSADALIKEQEEEVDDEVVNDMFGGKDHVSLIFMGHVDAGKSTMGGNLLYLTGSVDKRTIEKYEREAKDAGRQGWYLSWVMDTNKEERNDGKTIEVGKAYFETEKRRYTILDAPGHKMYVSEMIGGASQADVGVLVISARKGEYETGFERGGQTREHALLAKTQGVNKMVVVVNKMDDPTVNWSKERYDQCVSNVSNFLRAIGYNIKTDVVFMPVSGYSGANLKDHVDPKECPWYTGPTLLEYLDTMNHVDRHINAPFMLPIAAKMKDLGTIVEGKIESGHIKKGQSTLLMPNKTAVEIQNIYNETENEVDMAMCGEQVKLRIKGVEEEDISPGFVLTSPKNPIKSVTKFVAQIAIVELKSIIAAGFSCVMHVHTAIEEVHIVKLLHKLEKGTNRKSKKPPAFAKKGMKVIAVLETEAPVCVETYQDYPQLGRFTLRDQGTTIAIGKIVKIAE</sequence>
<gene type="str">
SUP35</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal prion domain (N) and a charged middle domain (M); </segment>
<boundaries type="str">
5-250</boundaries>
<region_ref type="str">
29301985</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) pH; 2) salt concentration; 3) protein concentration of Sup35</determinants>
<forms type="str">
gel-like condensates, a porous polymer meshwork</forms>
<organelles type="str">
cytoplasmic protein granule; Sup35 condensate</organelles>
<pmids type="str">
29301985 (research article), 30963611 (review)</pmids>
<description type="str">
Sup35 forms irreversible heritable aggregates, and these aggregates have been proposed to be either a disease or an adaptation that generates heritable phenotypic variation in populations of budding yeast. The PrD of Sup35 can also mediate reversible phase separation of Sup35 into non-fibrillar structures in energy-depleted yeast cells by sensing the intracellular pH, which, drops during starvation and other stresses (PMID:30877200). These condensates are distinct and different from fibrillar amyloid-like prion particles. The protective condensate rescues the essential GTPase domain of Sup35 from irreversible aggregation so that it remains functional during harsh environmental conditions. The condensates are liquid-like initially but subsequently solidify to form protective protein gels. Cryo–electron tomography demonstrates that these gel-like condensates consist of crosslinked Sup35 molecules forming a porosus meshwork. A cluster of negatively charged amino acids functions as a pH sensor and regulates condensate formation. The prion domain rescues the essential GTPase domain of Sup35 from irreversible aggregation, thus ensuring that the translation termination factor remains functional during harsh environmental conditions. Phase separation is regulated by the adjacent stress sensor. The synergy of these two modules enables the essential translation termination factor to rapidly form protective condensates during stress. This suggests that prion domains are protein-specific stress sensors and modifiers of protein phase transitions that allow cells to respond to specific environmental conditions (PMID:29301985).; </description>
<experiment_llps type="str">
Energy depletion causes reversible condensation of Sup35 into intracellular puncta in S. cerevisiae cells expressing GFP-fused Sup35 (in vivo). Sup35 particles dissolved within a few minutes of removing energy stress when cells started growing independent of the presence of chaperones (e.g. Hsp104). Stress-induced Sup35 particles also did not have any of the biochemical features of amyloid-like aggregates (morphology). Starved and energy-depleted yeast experience a reduction in cytosolic pH. By manipulating the cytosolic pH it turned out that acidification was sufficient to induce Sup35 condensates. When 2 μM of purified Sup35 was incubated in physiological buffer in vitro, the protein remained diffuse (protein localization), however, when the pH was reduced from 7.5 to 6.0, condensates of Sup35 formed (protein localization, particle size and count). Sup35 condensates adopted spherical shapes in solution, fused when brought together, deformed when contacting the microscope slide and their photobleached regions quickly recovered fluorescence (morphology), suggesting that they are liquid-like. Sup35 was mobile in growing cells in vivo, but it became immobile (protein localization) when sequestered into condensates, upon stress. This behavior was confirmed in vitro, where Sup35 initially phase-separated to form liquid droplets but then solidified into a gel-like state (morphology) as suggested by fusion and photobleaching experiments. Cryo–electron tomography (imaging assay evidence) of Sup35 droplets revealed that gel-like droplets consisted of an amorphous, yet well-defined, meshwork with an average mesh size of ~10 nm (morphology). Gel-like condensates dissolved (particle size and count) when the salt concentration or pH was raised or in the presence of small amounts of detergents, demonstrating reversibility in vitro. A minimal module consisting only of the prion (N) and the M domain (NM) (mutation, truncation) formed droplets in a reversible and pH-dependent manner in vitro. Removing a linear cluster of ionizable glutamic acid residues within the M domain (mutation, Sup35M3 variant) yields a fully functional Sup35 variant but with altered phase behavior, such that protein-rich droplets formed at pH 7.5 and the pH dependence of droplet formation was discernibly reduced in vitro and in vivo (particle size and count, other change in phenotype/functional readout). Deletion studies suggest that the disordered NM domain alters the phase behavior of the C domain by promoting the formation of reversible gels instead of irreversible aggregates (morphology). The fitness of cells expressing similar levels of full-length Sup35 and the C domain alone (in vivo deletion mutants) have been compared: in the absence of stress the C domain was diffuse and soluble (protein localization) and cells grew normally, showing that the C domain is not aggregation-prone in the cellular environment, presumably because of the presence of ligands such as guanosine 5′-triphosphate. After stress (perturbation of the cell environment to induce phenotypic changes), however, the C domain aggregated in a manner that was similar to that of the full-length protein but after removal of stress, dissolution of C domain aggregates could take several hours, while full length Sup35 condensates dissolved within minutes in wild-type cells (other change in phenotype/functional readout, protein localization). Concomitantly, Sup35C cells took longer to restart growth and exhibited reduced fitness when recovering from stationary phase. This suggests that the NM domain determines the material properties (reversible gel versus irreversible aggregate) of Sup35 in vivo (PMID:29301985)</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
reversibility of formation and dissolution (PMID:29301985); morphological traits (PMID:29301985); dynamic movement/reorganization of molecules within the droplet (PMID:29301985)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID:29301985); electrostatic (cation-anion) interaction (PMID:29301985)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P05453>
<O62011 type="dict">
<id type="str">
59</id>
<phase_id type="str">
63</phase_id>
<common_name type="str">
MUT-16</common_name>
<name type="str">
MUTator</name>
<accession type="str">
O62011</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MSESDDDYPELDISDQYIDPLGIVVGPPPASYTETDREETPMQNRTEDDTNSYGNSSGEHDYDSYLDSGDDDFDVDAYYANDNMDEPPPETIPDNLIQNVIGRNDNADYDFSDASNPEIMKRDLQLFLSSSLLSNPLKFRSGYSSDELDDCLKSCMGYSLQVTAVLLLPPEIISQLPNDSKTEHAHALVRGGWLQSKEGAFFPVISDSERETVVSLMNGSEEQHKRQERKKKEADTFESEEKEIRTLLTFNMIAELLMAVRNEYSIRSVKYQILSTAYTNMVTGAAHANIFRKYKDILQLDPEKLWNNDWFKEYTNRGTLKKFLTTARFSEIVVSQANGKTVELYFRADDEGNRPVVLFTDEHIADVRNKWKTGNQRNQNYGSQGNYRAGGQRSDDRRGPQQRRNVIVPDPNYQPSTFAGGISNNADDDGSLQPTTSSHFNRNTDRSTSRPPRAPTSPVNRVMETDPLMGQGTSSGAPQRSAIPNPFGGAPALSRSTITNGNRGPSYGDRGERVQDVGDTTSDSEITSEGSYSDEDPEQKEIKRQRRKDKLKKKQERELRSREKHTKSKQQPPSKIETRFNTYKKKSESSATDTSNTPPVDTVNVALPTPVVESSSTTAAPSIPVSTRPEVVVPPENPAPLREVGNFYSKSNHDEDRRNVQLPFTPADTHKPIKVAPKEPVRNPLLKERPSANGFINRRLPSHPAPPPVNQSQPANQPMQTAVYQNSHPGAPYIPQQPTYQPQLPVQQPQPHQYAPQPIHHQQPIHQPMHGQQYPPVNQQQPIYQQPAPQYPPYNSIQNNPQHGPSPFNYSQVPQPAYNHVGQQPSHMSNQPHINQNGYQNSYNPNQGPTSSDPNYGCNPQFNHYGSRSVYHEDHSSQRRRSPDQFPPNPPEYDPHGNFKLADYERDRMTVGYSQNPHQFDHHGSHMPHQSQPQGYDNFNGNSAPYFNKNGGQSNHQPEAQRSFSVLSSNRQPSNRELIFQDGIEKELRDIILRYRSMNLTVLTVQELRTEVSRRPAIPRYIDIVQYIRDSSSVAIVERGDIEPYVVLKDDIRN</sequence>
<gene type="str">
MUT-16</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal Q/N/P-rich disordered domain</segment>
<boundaries type="str">
773-1033</boundaries>
<region_ref type="str">
30036386</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of MUT-16; 2) temperature</determinants>
<forms type="str">
liquid-like mutator foci</forms>
<organelles type="str">
mutator focus; small RNA amplification complex</organelles>
<pmids type="str">
30036386 (research article)</pmids>
<description type="str">
In C. elegans, efficient RNA silencing requires small RNA amplification mediated by RNA-dependent RNA polymerases. The Mutator foci are perinuclear germline foci that associate with nuclear pores and P granules to facilitate small RNA amplification. Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci. The C-terminal region of the Mutator complex protein MUT-16, a portion of which contains predicted intrinsic disorder, is necessary and sufficient to promote Mutator foci assembly through LLPS. The Mutator complex is critical to the amplification of high levels of small RNAs. MUT-16 functions as a scaffold, bringing together many other proteins required for small RNA biogenesis and amplification, each being recruited by different regions of MUT-16 (PMID:30036386).</description>
<experiment_llps type="str">
In vivo overexpression of different MUT-16 segment deletion mutants in a strain containing a null mutation in the mut-16 gene (knock-out) indicated that not many of the segments have an impact on somatic RNAi (other change in phenotype/functional readout) but most of them affect germline RNAi (other change in phenotype/functional readout). The C-terminal region of MUT-16 (mutation) proved to be critical and sufficient for Mutator foci formation as assessed by microscopy. Other regions of the protein are responsible for recruiting different Mutator proteins as assessed by in vitro protein-protein interaction detection assays and in vivo characterization of foci formation (particle size and count by microscopy). In vivo GFP-fused MUT-16 at the endogenous mut-16 locus showed higher levels of expression in the germline compared to somatic tissues and protein concentration dependent formation of foci. Mutator foci showed diverse traits of liquid condensates (e.g. by FRAP). (PMID:30036386). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30036386); sensitivity to 1,6-hexanediol (PMID:30036386); temperature-dependence (PMID:30036386); reversibility of formation and dissolution (PMID:30036386); dynamic exchange of molecules with surrounding solvent (PMID:30036386)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known (PMID:30036386)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</O62011>
<P17600 type="dict">
<id type="str">
60</id>
<phase_id type="str">
64</phase_id>
<common_name type="str">
SYN1</common_name>
<name type="str">
Synapsin-1</name>
<accession type="str">
P17600</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPGAHSPGATPGPGTATAERSSGVAPAASPAAPSPGSSGGGGFFSSLSNAVKQTTAAAAATFSEQVGGGSGGAGRGGAASRVLLVIDEPHTDWAKYFKGKKIHGEIDIKVEQAEFSDLNLVAHANGGFSVDMEVLRNGVKVVRSLKPDFVLIRQHAFSMARNGDYRSLVIGLQYAGIPSVNSLHSVYNFCDKPWVFAQMVRLHKKLGTEEFPLIDQTFYPNHKEMLSSTTYPVVVKMGHAHSGMGKVKVDNQHDFQDIASVVALTKTYATAEPFIDAKYDVRVQKIGQNYKAYMRTSVSGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEIFGGLDICAVEALHGKDGRDHIIEVVGSSMPLIGDHQDEDKQLIVELVVNKMAQALPRQRQRDASPGRGSHGQTPSPGALPLGRQTSQQPAGPPAQQRPPPQGGPPQPGPGPQRQGPPLQQRPPPQGQQHLSGLGPPAGSPLPQRLPSPTSAPQQPASQAAPPTQGQGRQSRPVAGGPGAPPAARPPASPSPQRQAGPPQATRQTSVSGPAPPKASGAPPGGQQRQGPPQKPPGPAGPTRQASQAGPVPRTGPPTTQQPRPSGPGPAGRPKPQLAQKPSQDVPPPATAAAGGPPHPQLNKSQSLTNAFNLPEPAPPRPSLSQDEVKAETIRSLRKSFASLFSD</sequence>
<gene type="str">
SYN1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
P/Q-rich C-terminal IDR with P-rich motifs</segment>
<boundaries type="str">
421-705</boundaries>
<region_ref type="str">
29976799</region_ref>
<partners type="str">
1) intersectin (not required, but promotes LLPS); 2) GRB2 (not required, but promotes LLPS)</partners>
<determinants type="str">
1) protein concentration of SYN1; 2) salt concentration; 3) crowding agent concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
presynaptic cytosol; a matrix holding together clusters of synaptic vesicles (SVs)</organelles>
<pmids type="str">
29976799 (research article), 28279363 (review), 30093586 (review)</pmids>
<description type="str">
Neurotransmitter-containing synaptic vesicles (SVs) form tight clusters at synapses. These clusters act as a reservoir from which SVs are drawn for exocytosis during sustained activity. Several components associated with SVs that are likely to help form such clusters have been reported, including synapsin. Synapsin can form a distinct liquid phase in an aqueous environment. Other scaffolding proteins, for example SH3 domain-containing proteins, could coassemble into this condensate but were not necessary for its formation. Importantly, the synapsin phase could capture small lipid vesicles in vitro. The synapsin phase rapidly disassembled upon phosphorylation by calcium/calmodulin-dependent protein kinase II (CaMKII), this calcium-dependent phosphorylation probably serves the release of vesicles from clusters during sustained activity of the nerve terminal. In synapsin KO mice the number and packing of SVs were significantly lower and this decrease is selective for SVs away from active zones. Thus synapsin can form a separate liquid biomolecular condensate either alone or together with binding partners for its IDR, with lipid vesicles, or with both (PMID:29976799).</description>
<experiment_llps type="str">
The enhanced green fluorescent protein, eGFP-fused synapsin 1 IDR formed micrometer-sized droplets (particle size and count) when incubated in a physiological buffer in vitro as assessed by microscopy. The amount and size of droplets correlated with protein concentraion and salt concentration in vitro, while addition of a crowding agent resulted in instant droplet formation. Turbidity (change in optical properties) of the samples was also observed. Synapsin 1 co-localized with SH3 domain-containing partners GRB2 and intersectin within the droplets. Also, synapsin 1 condensates sequenstered lipid vesicles (liposomes) in vitro by electron microscopy. Phosphorylation of SYN1 by CaMKII (but not by PKC) dispersed the droplets of either SYN1 alone or SYN1 and liposomes. In vivo, knock-out mice wherein all three synapsin genes were knocked out showed a decrease in the number and packing of synaptic vesicles away from active zones (morphology) by electron microscopy. PMID:29976799.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29976799); morphological traits (PMID:29976799)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
421-705|S|phosphorylation|abolishes|PMID:29976799|CaMKII|Notes: Phosphorylation is calcium-dependent and happens in response to sustained nerve-terminal stimulation. CaMKII can disperse Syn1 droplets and also Syn1-liposome droplets in the presence of Ca, calmoulin and ATP.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:29976799); discrete oligomerization (PMID:29976799)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P17600>
<Q8N884 type="dict">
<id type="str">
61</id>
<phase_id type="str">
65</phase_id>
<common_name type="str">
cGAS</common_name>
<name type="str">
Cyclic GMP-AMP synthase</name>
<accession type="str">
Q8N884</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MQPWHGKAMQRASEAGATAPKASARNARGAPMDPTESPAAPEAALPKAGKFGPARKSGSRQKKSAPDTQERPPVRATGARAKKAPQRAQDTQPSDATSAPGAEGLEPPAAREPALSRAGSCRQRGARCSTKPRPPPGPWDVPSPGLPVSAPILVRRDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF</sequence>
<gene type="str">
CGAS</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Disordered and positively charged N-terminal region for DNA binding; positively charged region for self association</segment>
<boundaries type="str">
1-146; 161-522</boundaries>
<region_ref type="str">
29976794</region_ref>
<partners type="str">
1) DNA (strictly required); 2) Zn²⁺ ions (enhance LLPS)</partners>
<determinants type="str">
1) protein concentration of CGAS; 2) DNA concentration; 3) presence of Zn²⁺ ions; 4) salt concentration; 5) valency of DNA; 6) valency of cGAS </determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
intracellular DNA/protein granule; cGAS foci</organelles>
<pmids type="str">
29976794 (research article), 31142647 (research article)</pmids>
<description type="str">
Cyclic GMP-AMP synthase (cGAS) is a DNA-sensing enzyme that catalyzes the conversion of GTP and ATP to cyclic GMP-AMP (cGAMP), which activates the adaptor protein STING. This, in turn, induces type I interferons and other cytokines. DNA arising in the cytoplasm activates cGAS and drives the formation of cytoplasmic foci containing cGAS and DNA. Liquid phase separation with DNA is insufficient for cGAS activation in the absence of the correct conformational change induced by DNA. DNA binding to cGAS induces a robust phase transition to liquidlike droplets, which function as microreactors in which the enzyme and reactants are concentrated to greatly enhance the production of cGAMP. The binding between cGAS and DNA involves extensive ionic interactions between the positively charged surfaces of cGAS and negatively charged DNA. The cGAS-DNA droplets gradually undergo a liquid-to-solid transition and mature into a gel-like state. Zinc facilitated cGAS activation in cells by promoting cGAS phase transition in the presence of cytosolic DNA. The DNA induced formation of cGAS condensates is a mechanism by which cGAS activity is tightly regulated to trigger an appropriate immune response to pathogens while simultaneously avoiding autoimmune reactions to self-tissues PMID:29976794. Identification of a second cGAS CD-DNA interface (labeled site-C; CD, catalytic domain) in the crystal structure of a human SRY.cGASCD-DNA complex, and showing that mutations along this basic site-C cGAS interface disrupts liquid-phase condensation demonstrates the importance of multivalency in the cGAS-DNA interaction for LLPS (PMID:31142647).</description>
<experiment_llps type="str">
Fluorescently tagged cGAS protein formed micrometer-sized liquid droplets (particle size and count, morphology) with double-stranded DNA oligonucleotides (100 bp) within 2 minutes in vitro as followed by time-lapse microscopy. cGAS and DNA formed liquid droplets in vitro when the concentration of each exceeded 30 nM in a physiological buffer (change in protein concentration, change in DNA concentration, particle size and count). Formation of the droplets were sensitive to changes in salt concentration. Although cGAS could phase separate with RNA in vitro, RNA did not activate cGAS to produce cGAMP. Phase separation was unaffected by the addition of ATP, GTP, or a combination thereof. In the human fibroblast cell line BJ-5ta stably expressing a Halo-tagged cGAS (fusion protein), cGAS formed puncta with fluorescein-labeled ISD in the cytoplasm (protein localization, protein co-localization) in vivo. cGAS appeared to form heavy particles with transfected DNA that were distinct from cellular organelles and vesicles (morphology), and which contained active cGAS. When purified full-length (FL-cGAS) and N-terminally truncated (ΔN146) cGAS were incubated with DNA of different lengths in the physiological buffer (15 mM NaCl and 135 mM KCl) or a buffer containing 300 mM NaCl in vitro, FL-cGAS formed more numerous and larger liquid droplets with longer DNA (particle size and count). Both human and mouse FL-cGAS exhibited stronger phase separation and stronger enzymatic activity (enzymatic activity assay) than N-terminally truncated cGAS (mutation) with DNA of the same length. In cGAS-deficient MEF cells (knock-out) reconstituted with human FL-cGAS or ΔN160-cGAS (genetic transformation, overexpression) FL-cGAS formed puncta with Cy5-DNA, whereas ΔN160-cGAS formed fewer puncta (co-localization, particle size and count). cGAMP production was also higher in cells stably expressing FL-cGAS. Zinc ions significantly promoted the activity and phase separation capability of recombinant cGAS in the physiological buffer in vitro. PMID:29976794. </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29976794); morphological traits (PMID:29976794)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-DNA interaction (PMID:29976794); electrostatic (cation-anion) interaction (PMID:29976794); discrete oligomerization (PMID:30295605)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
sensor</functional_class>
<date type="str">
2019-09-11</date>
</Q8N884>
<Q15648 type="dict">
<id type="str">
62</id>
<phase_id type="str">
66</phase_id>
<common_name type="str">
MED1</common_name>
<name type="str">
Mediator of RNA polymerase II transcription subunit 1</name>
<accession type="str">
Q15648</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MKAQGETEESEKLSKMSSLLERLHAKFNQNRPWSETIKLVRQVMEKRVVMSSGGHQHLVSCLETLQKALKVTSLPAMTDRLESIARQNGLGSHLSASGTECYITSDMFYVEVQLDPAGQLCDVKVAHHGENPVSCPELVQQLREKNFDEFSKHLKGLVNLYNLPGDNKLKTKMYLALQSLEQDLSKMAIMYWKATNAGPLDKILHGSVGYLTPRSGGHLMNLKYYVSPSDLLDDKTASPIILHENNVSRSLGMNASVTIEGTSAVYKLPIAPLIMGSHPVDNKWTPSFSSITSANSVDLPACFFLKFPQPIPVSRAFVQKLQNCTGIPLFETQPTYAPLYELITQFELSKDPDPIPLNHNMRFYAALPGQQHCYFLNKDAPLPDGRSLQGTLVSKITFQHPGRVPLILNLIRHQVAYNTLIGSCVKRTILKEDSPGLLQFEVCPLSESRFSVSFQHPVNDSLVCVVMDVQDSTHVSCKLYKGLSDALICTDDFIAKVVQRCMSIPVTMRAIRRKAETIQADTPALSLIAETVEDMVKKNLPPASSPGYGMTTGNNPMSGTTTPTNTFPGGPITTLFNMSMSIKDRHESVGHGEDFSKVSQNPILTSLLQITGNGGSTIGSSPTPPHHTPPPVSSMAGNTKNHPMLMNLLKDNPAQDFSTLYGSSPLERQNSSSGSPRMEICSGSNKTKKKKSSRLPPEKPKHQTEDDFQRELFSMDVDSQNPIFDVNMTADTLDTPHITPAPSQCSTPPTTYPQPVPHPQPSIQRMVRLSSSDSIGPDVTDILSDIAEEASKLPSTSDDCPAIGTPLRDSSSSGHSQSTLFDSDVFQTNNNENPYTDPADLIADAAGSPSSDSPTNHFFHDGVDFNPDLLNSQSQSGFGEEYFDESSQSGDNDDFKGFASQALNTLGVPMLGGDNGETKFKGNNQADTVDFSIISVAGKALAPADLMEHHSGSQGPLLTTGDLGKEKTQKRVKEGNGTSNSTLSGPGLDSKPGKRSRTPSNDGKSKDKPPKRKKADTEGKSPSHSSSNRPFTPPTSTGGSKSPGSAGRSQTPPGVATPPIPKITIQIPKGTVMVGKPSSHSQYTSSGSVSSSGSKSHHSHSSSSSSSASTSGKMKSSKSEGSSSSKLSSSMYSSQGSSGSSQSKNSSQSGGKPGSSPITKHGLSSGSSSTKMKPQGKPSSLMNPSLSKPNISPSHSRPPGGSDKLASPMKPVPGTPPSSKAKSPISSGSGGSHMSGTSSSSGMKSSSGLGSSGSLSQKTPPSSNSCTASSSSFSSSGSSMSSSQNQHGSSKGKSPSRNKKPSLTAVIDKLKHGVVTSGPGGEDPLDGQMGVSTNSSSHPMSSKHNMSGGEFQGKREKSDKDKSKVSTSGSSVDSSKKTSESKNVGSTGVAKIIISKHDGGSPSIKAKVTLQKPGESSGEGLRPQMASSKNYGSPLISGSTPKHERGSPSHSKSPAYTPQNLDSESESGSSIAEKSYQNSPSSDDGIRPLPEYSTEKHKKHKKEKKKVKDKDRDRDRDKDRDKKKSHSIKPESWSKSPISSDQSLSMTSNTILSADRPSRLSPDFMIGEEDDDLMDVALIGN</sequence>
<gene type="str">
MED1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
S-rich IDR, acidic and basic regions</segment>
<boundaries type="str">
948-1574</boundaries>
<region_ref type="str">
29930091</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of MED1; 2) salt concentration</determinants>
<forms type="str">
nuclear puncta, coactivator puncta,; phase-separated biomolecular condensates; </forms>
<organelles type="str">
enhanceosome; nuclear body; nuclear bodies that occur at super enhancers in mESCs</organelles>
<pmids type="str">
29930091 (research article), 29930094 (research article), 30449618 (research article)</pmids>
<description type="str">
Enhancers are gene regulatory elements bound by transcription factors (TFs) and other components of the transcription apparatus that function to regulate expression of cell type-specific genes. Super enhancers (SEs) – clusters of enhancers that are occupied by exceptionally high densities of transcriptional machinery – regulate genes with especially important roles in cell identity. Two key components of SEs, BRD4 and MED1, form nuclear condensates at sites of SE-driven transcription. The IDRs of BRD4 and MED1 are sufficient to form phase-separated droplets in vitro. Droplets formed by MED1-IDR are capable of concentrating transcriptional machinery, including BRD4, in a transcriptionally competent nuclear extract. This offers insights into mechanisms involved in the control of key cell-identity genes since a study of RNA Pol II clusters which may be phase-separated condensates, suggests a correlation between condensate lifetime and transcriptional output (PMID:29930091). Purified recombinant MED1-IDR-GFP fusion protein exhibited concentration-dependent liquid-liquid phase separation. Droplets of MED1-IDR could incorporate and concentrate purified OCT4-GFP to form heterotypic droplets (PMID:30449618).</description>
<experiment_llps type="str">
In vitro immunofluorescent tagging of the proteins BRD4 and MED1 with anti-bodies in fixed murine embryonic stem cells (mESCs) revealed nuclear puncta for both factors (protein localization). The mEGFP-fused proteins showed similar localization in vivo by epifluorescence microscopy (particle size and count). ChIP-seq (chromatinimmunoprecipitation followed by sequencing) data for BRD4 and MED1 show that superenhancers are especially enriched in these coactivators (protein co-localization). BRD4 and MED1 puncta consistently overlapped the DNA-FISH foci or RNA-FISH foci for the genomic region containing the Nanog gene. Based o FRAP measurements and 1,6-hexanediol treatment BRD4 and MED1 nuclear puncta exhibited liquid properties. The mEGFP-fused MED1 and BRD4 IDRs samples showed a change in optical properties (turbidity) with the addition of a crowding agent. The number and size of droplets (particle size and count) formed by the mEGFP-fused MED1 and BRD4 IDRs in vitro were depending on changes in protein concentration, salt concentration and crowding agent. The overexpressed mCh-fused MED1 IDR formed phase separated droplets in cells in vivo. The serines to alannes mutant MED1 IDR was incapable to form droplets in vitro. The MED1 IDR droplets could incorporate and concentrate BRD4-IDR in vitro under conditions where the BRD4 IDR could not form droplets on its own (protein co-localization) as assessed by epifluorescence microscopy. PMID:29930091.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29930091); sensitivity to 1,6-hexanediol (PMID:29930091); morphological traits (PMID:29930091)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
simple coacervation of hydrophobic residues (PMID:29930091); electrostatic (cation-anion) interaction (PMID:29930091)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q15648>
<O60885 type="dict">
<id type="str">
63</id>
<phase_id type="str">
67</phase_id>
<common_name type="str">
BRD4</common_name>
<name type="str">
Bromodomain-containing protein 4</name>
<accession type="str">
O60885</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSAESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAASTNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRGRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMTVVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTIDPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVAVSSPAVPPPTKVVAPPSSSDSSSDSSSDSDSSTDDSEEERAQRLAELQEQLKAVHEQLAALSQPQQNKPKKKEKDKKEKKKEKHKRKEEVEENKKSKAKEPPPKKTKKNNSSNSNVSKKEPAPMKSKPPPTYESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETLKPSTLRELERYVTSCLRKKRKPQAEKVDVIAGSSKMKGFSSSESESSSESSSSDSEDSETEMAPKSKKKGHPGREQKKHHHHHHQQMQQAPAPVPQQPPPPPQQPPPPPPPQQQQQPPPPPPPPSMPQQAAPAMKSSPPPFIATQVPVLEPQLPGSVFDPIGHFTQPILHLPQPELPPHLPQPPEHSTPPHLNQHAVVSPPALHNALPQQPSRPSNRAAALPPKPARPPAVSPALTQTPLLPQPPMAQPPQVLLEDEEPPAPPLTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPLPPPPHPSVQQQLQQQPPPPPPPQPQPPPQQQHQPPPRPVHLQPMQFSTHIQQPPPPQGQQPPHPPPGQQPPPPQPAKPQQVIQHHHSPRHHKSDPYSTGHLREAPSPLMIHSPQMSQFQSLTHQSPPQQNVQPKKQELRAASVVQPQPLVVVKEEKIHSPIIRSEPFSPSLRPEPPKHPESIKAPVHLPQRPEMKPVDVGRPVIRPPEQNAPPPGAPDKDKQKQEPKTPVAPKKDLKIKNMGSWASLVQKHPTTPSSTAKSSSDSFEQFRRAAREKEEREKALKAQAEHAEKEKERLRQERMRSREDEDALEQARRAHEEARRRQEQQQQQRQEQQQQQQQQAAAVAAAATPQAQSSQPQSMLDQQRELARKREQERRRREAMAATIDMNFQSDLLSIFEENLF</sequence>
<gene type="str">
BRD4</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
P/Q-rich IDR, acidic and basic regions</segment>
<boundaries type="str">
674-1351</boundaries>
<region_ref type="str">
29930091</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of BRD4; 2) salt concentration</determinants>
<forms type="str">
nuclear puncta, coactivator puncta,; phase-separated biomolecular condensates; </forms>
<organelles type="str">
enhanceosome; nuclear body; nuclear bodies that occur at super enhancers in mESCs</organelles>
<pmids type="str">
29930091 (research article), 31065677 (research article)</pmids>
<description type="str">
Enhancers are gene regulatory elements bound by transcription factors (TFs) and other components of the transcription apparatus that function to regulate expression of cell type-specific genes. Super enhancers (SEs) – clusters of enhancers that are occupied by exceptionally high densities of transcriptional machinery – regulate genes with especially important roles in cell identity. Two key components of SEs, BRD4 and MED1, form nuclear condensates at sites of SE-driven transcription. The IDRs of BRD4 and MED1 are sufficient to form phase-separated droplets in vitro. BRD4 is compartmentalized and therefore concentrated in MED1-IDR droplets, which compartmentalize and concentrate other transcriptional components in a transcriptionally competent nuclear extract as well. This offers insights into mechanisms involved in the control of key cell-identity genes since a study of RNA Pol II clusters which may be phase-separated condensates, suggests a correlation between condensate lifetime and transcriptional output (PMID:29930091). A  mouse  model  expressing the BRD4 protein without the LCD domain helped establish an essential role of the BRD4 C-terminal LCD in vivo (PMID:31065677).</description>
<experiment_llps type="str">
In vitro immunofluorescent tagging of the proteins BRD4 and MED1 with anti-bodies in fixed murine embryonic stem cells (mESCs) revealed nuclear puncta for both factors (protein localization). The mEGFP-fused proteins showed similar localization in vivo by epifluorescence microscopy (particle size and count). ChIP-seq (chromatinimmunoprecipitation followed by sequencing) data for BRD4 and MED1 show that superenhancers are especially enriched in these coactivators (protein co-localization). BRD4 and MED1 puncta was found consistently overlapped with the DNA-FISH foci or RNA-FISH foci for the genomic region containing the Nanog gene. Based o FRAP measurements and 1,6-hexanediol treatment BRD4 and MED1 nuclear puncta exhibited liquid properties. The mEGFP-fused MED1 and BRD4 IDRs samples showed a change in optical properties (turbidity) with the addition of a crowding agent. The number and size of droplets (particle size and count) formed by the mEGFP-fused MED1 and BRD4 IDRs in vitro were depending on changes in protein concentration, salt concentration and crowding agent. The MED1 IDR droplets could incorporate and concentrate BRD4-IDR in vitro under conditions where the BRD4 IDR could not form droplets on its own (protein co-localization) as assessed by epifluorescence microscopy. PMID:29930091.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29930091); sensitivity to 1,6-hexanediol (PMID:29930091); morphological traits (PMID:29930091)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
simple coacervation of hydrophobic residues (PMID:29930091); electrostatic (cation-anion) interaction (PMID:29930091)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</O60885>
<H0WFA5 type="dict">
<id type="str">
64</id>
<phase_id type="str">
68</phase_id>
<common_name type="str">
Buc</common_name>
<name type="str">
Bucky ball</name>
<accession type="str">
H0WFA5</accession>
<organism type="str">
Danio rerio</organism>
<sequence type="str">
MEGINNNSQPMGVGQPHHPVNHTRPFFYVQPPSQPYFMYQWPMNPYGHYGFPGPALHFGRPYMAPYQFMQYPGYVIPHAPMQPIDYRRINPHYPSVASYDLRVRHHFQNAGMHRETACSEVQTDPSDSVNKLIDKIESLKACELGSDKGPNNVVSSTPDVVQGEKLTRLNEDSNLEVATKECKEDPVTRPTTYSDSAYDAESSQGRLDECVFSDVLPLDSSSVHEEEEEEEKDVNEEDEPQTVADEICSQNEMSASTTSNVFCSGVQSIADPTECHDLEKLGDEQKQDIPSADAAAVIEPLISLSEDFDLPYQILRLPCNKTTTGLSLEREIDPLVYFDSPSTLLPPQNYLSSIGSAYSYSYYPQVTQERQSVLSPSIDELSSRDEMFSTDVEDLEVVPGHVYVGGGRLAEASDMPVRSRKELPSVDKTCSVCQKTCACCGSTLQDEVGMCKMAEHSHPERDEMSDQDCDYDLEAEVRSNCESPRVSKRKCCSRHALPSCGHHCAKHRHRKLLCEGQESCDLREQARVHPKGECCEEYGALAKADKRIQKGALCRPCIEQQWREGVVSDQENWASCGAKPRSWRQVTGPQDQGRTPLRRSTCKSIHQQRPRSEYNDYDETEFTYCQRGRGSMKKRGSRY</sequence>
<gene type="str">
BUC</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal tri-RG motif region</segment>
<boundaries type="str">
621-639</boundaries>
<region_ref type="str">
30086300</region_ref>
<partners type="str">
1) Tdrd6a (strictly required)</partners>
<determinants type="str">
1) protein concentration of Buc; 2) protein concentration of Tdrd6</determinants>
<forms type="str">
membrane-less organelles that display amyloid-like features</forms>
<organelles type="str">
mitochondrial cloud; germ plasm; Balbiani body</organelles>
<pmids type="str">
30086300 (research article)</pmids>
<description type="str">
In zebrafish, the Balbiani body (Bb) and the germ plasm (Gp) are intimately linked phase-separated structures essential for germ cell specification and home to many germ-cell specific mRNAs and proteins. Throughout development, these structures occur as a single large aggregate (Bb), which disperses throughout oogenesis and upon fertilization accumulates again into relatively large assemblies (Gp). Formation of the Bb requires Bucky ball (Buc), a protein with prion-like properties. It is found that the multi-tudor domain-containing protein Tdrd6a interacts with Buc via symmetrically dimethylated arginines within its tri-RG motif, affecting its mobility and aggregation properties. Importantly, lack of this regulatory interaction leads to significant defects in germ cell development. Tdrd6a is required for the higher level organization and integrity of Balbiani bodies and of germ plasm mRNPs (PMID:30086300).</description>
<experiment_llps type="str">
In vivo immunodetection assay (immunohistochemistry) and the localization of transgenic Tdrd6a-mCherry fusion protein confirmed that Tdrd6a is expressed in the ovary, where it localizes to nuage and to the Balbiani body (Bb, protein localization). To map physical interactions of Tdrd6a, immunoprecipitation (IP, protein-protein interaction detection assay) was performed with ovary lysates, followed by label-free quantitative mass spectrometry (proteomics), which identified Buc as a strong interactor of Tdrd6a. Loss of Tdrd6a has an effect on the formation of primordial germ cells (PGCs): maternal-zygotic tdrd6a -/- embryos showed a significant reduction in PGC number, irrespective of the genotype of the father. Tdrd6a physically interacts with Gp-residing mRNAs based on RNA-IP followed by sequencing (RIPseq). In tdrd6a mutant oocytes, the Bb often appears to be smaller relative to the entire oocyte, lacking a well-defined edge or even being further distorted (morphology). In the Bb, Buc-eGFP and Tdrd6a form a continuous structure in which Gp mRNAs are embedded (morphology by microscopy). In tdrd6a mutant oocytes, the Buc-eGFP signal is more irregular, however, Gp-transcripts still localize to the Bb (co-localization), indicating that Tdrd6a is not essential for these transcripts to accumulate in the Bb. Electron microscopy (EM) revealed that the electron-dense structures in the Bb display a heterogeneous, fibrillary appearance (morphology). Tdrd6a and Buc interact via symmetrically dimethylated arginines (sDMAs) in the C-terminus of Buc as confirmed by pull-down experiments with modified and unmodified Buc peptides. Expression of Buc in BmN4 transgenic cells results in abundant, cytoplasmic, small granules (particle size and count). In contrast, Tdrd6a displays a ubiquitous cytoplasmic signal (protein localization). Co-transfection results in two possible outcomes: the presence of both Tdrd6a and Buc either results in co-localization in enlarged, cytoplasmic aggregates (morphology) with a broad variety in size or in diffuse cytoplasmic localization of both proteins. Tdrd6a recovers rapidly upon bleaching of Buc-Tdrd6a double-positive granules (FRAP). Interestingly, Buc recovery increases from 35% to 55% in the presence of Tdrd6a. Without Tdrd6a Buc-eGFP cannot be detected in the soluble fraction of BmN4 lysates and is predominantly found in the pellet. In contrast, in the presence of Tdrd6a, significant amounts of Buc-eGFP were soluble. Tdrd6a positively stimulates Buc mobility and solubility and that this can contribute to growth of Buc granules. Tdrd6a and its interaction with arginine-methylated Buc affect the aggregation behavior of Buc-containing structures by stimulating their growth, heterogeneity, and mobility, both in cell culture as well as in vivo (PMID:30086300).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30086300) </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
627|R|methylation|enables|PMID:30086300||Notes: Tudor domain-containing protein Tdrd6a can only interact with Buc via symmetrically dimethylated arginines (sDMAs) in the C-terminus of Buc.; 629|R|methylation|enables|PMID:30086300||Notes: Tudor domain-containing protein Tdrd6a can only interact with Buc via symmetrically dimethylated arginines (sDMAs) in the C-terminus of Buc.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-PTM interactions (PMID:30086300)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
regulator of spatial patterns; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</H0WFA5>
<F1R237 type="dict">
<id type="str">
99</id>
<phase_id type="str">
68</phase_id>
<common_name type="str">
Tdrd6</common_name>
<name type="str">
Tudor domain-containing 6</name>
<accession type="str">
F1R237</accession>
<organism type="str">
Danio rerio</organism>
<sequence type="str">
MCSIPGLPSKGSNVPVLITRVNLNPSCVLVEFWGNFDEDRKFAYQQLKKEIQYPRECFSESDGNPGDLCLVQVYETWYRARIVSRDSDEYSVFLIDEGRTLRAAVNTLAWGKSDFFYLPPEVEFCILANALPLSPENNWSSMALEFMKTFCGRRVNATVQDVLVAHRTFLLDIPCLSRQMFEMGFAKKLYSDQFMEFVVRSLQASTGTSDLKRISSIRTKPVEIIEQKEKQQAYMFPELQTDTVETVVITEVTSPFRIFCQLKVFSQELKKLTEQITQYYEGRVGSYFARAENLGSPCASRGSDGKWYRSVLQQVMSANNVVEVLHVDYGKKQFVQVENVKPLASEFFRMPVVTYVCSLHGIVDKGVGWTASQIDYLKSLLLNRTVIAKFQYQSLSEGVHYVTLYGEENTNINKLFELKPKCSLDSDMTLADFAVQKSPSSQKSKISRTTESTHINETYSDLKVNKPVFFTETLTPNSTHMAVVQHVDSPGKFWIQTQRYADEFDLLMNGLGNLYSDPTSTESLIRKPVVGLICAAKAQDGVFYRAAVYKVIDKTAEVYFLDYGNTEVVDSFNLRQLPLRFQQLPAVAVKCSLHGVKPRLKLWEERATLFFSKLVRDRIIDLHVQDKQQDTHIVQLVDPSLDGEKDVSKLLCNAGFAVSEKSIVDYSATRSCGLKTTHASGVFLTGTQPQTPCSSSVVMDSASAFKEYLFPIGSSLEVTVSYIENPNDFWCQKARNAACLEVLMQDIQRFYSHSEFEPLLEAACVARHPETGIWYRALVIQKHQTPHVDVLFIDYGQTKKVAIEDLRKITPAFLKMKGQAFRCSLYNLIHPVLHSSSDWSTEATLEFQEFVDAAASMNVPLKCTIFAVMYDSQKVVFNVVDLETPFQSICNLLVQRRLADRAPSKRSPLPPFRLDTYYYSTHGVKTGCDEKVSITCVKGVNQFFCHLARNSDEVEKLAEKVNFLCHQLEATKCPQTFGTVCFAKYTDGLWYRGQIKSTKPSVVINFVDYGDTLEVDKSDLLPVPIEAGDIMSVPVQAIECGLSDMPEELPCEVDNWFRKFADSHCFTALIVAKEPAGKLILELYDGKTQVNALIKQKFHNEIHKNDASTFKIYGLKSRAAESVEASACKKESSTGPKRDAIDQVPKSRESHAIQRSNDVASKQPQSRWGFSTNGRPEPTRDSGTINNCQKQPELRTSQGNLRHPCTSSKPEVVKPKPQALLKESALPIKSIKPGLEAEVFISHCNSPCSFFVQFATDEDDIYSLVEKLNADQSRCRNIDSSDIHEGDLVCAMFPDDSSWYRAVVRKNTNEKIDVEFVDFGNTAVISSKNVCHLGQSFASFPRYSIHCSVHKLNVDSKDQELAPNFKQVLEQNIEKVICTFVKMSGTMWEVRLDVNGVVLGSVCKDHVKPEIAIPDLKDAASEIKVCTYYKNPDISIGQVITGYTSYIKGPQLFWCQYVAMDKLQEISDMLQNIGNASETTLREDCMPVGSACIALFTEDNLWYRAKVTSKDLDTLSITFVDYGNESKVKIGDVKALPPKLSDVPPHAFDCQLEGFDVSEGFWDETADDAFYELVHDKPLNITIEKMGNSEMPHIVKLDCDGVDINTTMKSHWKTRNPETPPAELFNGAEMASDDDYVASKVNIDSVVTFDTDTDPADNETCTSALEMELSEQENLLSSTGVENEAQIDPLKMATENVTLPITESTVLSETHKKLETITEDEPVLGFTGLSDTNQHAVSKETDVGLPQHSEGASSVTIDSFLMNNTDSQLCIVEEPEAPSYEIIQSNLGCLRRATEKKPVGSECVIWSQVRRSWCTARVLKVSEEATLVLLEKYDSEVVVDPINIFEIMPEKPLQIACIEAAIANDDATKETDATLENSASKLYQTEVSDANGIAVALESEDLNGKEETFIDQMAPNDELAGQPQEEESVSCSAFLEDSKAKHMLVEGAQVHDLVQGLCPDDVESKDPQDDLNTSFEEQNDGAKMSTAVDLLLDFLDTAPRDKVQDVSETDALLEEFNIHVTEDLIVLTSDDGAESDTASDGTLHGDAVAMEVGPDTEESSCFQERSNASDCTSAEDSQVTHLTLKVEDASDDVIFVGVLQESQAVVHEPESEKEKRD</sequence>
<gene type="str">
TDRD6</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-2117</boundaries>
<region_ref type="str">
30086300</region_ref>
<partners type="str">
1) Buc (strictly required)</partners>
<determinants type="str">
1) protein concentration of Buc; 2) protein concentration of Tdrd6</determinants>
<forms type="str">
membrane-less organelles that display amyloid-like features</forms>
<organelles type="str">
mitochondrial cloud; germ plasm; Balbiani body</organelles>
<pmids type="str">
30086300 (research article)</pmids>
<description type="str">
In zebrafish, the Balbiani body (Bb) and the germ plasm (Gp) are intimately linked phase-separated structures essential for germ cell specification and home to many germ-cell specific mRNAs and proteins. Throughout development, these structures occur as a single large aggregate (Bb), which disperses throughout oogenesis and upon fertilization accumulates again into relatively large assemblies (Gp). Formation of the Bb requires Bucky ball (Buc), a protein with prion-like properties. It is found that the multi-tudor domain-containing protein Tdrd6a interacts with Buc via symmetrically dimethylated arginines within its tri-RG motif, affecting its mobility and aggregation properties. Importantly, lack of this regulatory interaction leads to significant defects in germ cell development. Tdrd6a is required for the higher level organization and integrity of Balbiani bodies and of germ plasm mRNPs (PMID:30086300).</description>
<experiment_llps type="str">
In vivo immunodetection assay (immunohistochemistry) and the localization of transgenic Tdrd6a-mCherry fusion protein confirmed that Tdrd6a is expressed in the ovary, where it localizes to nuage and to the Balbiani body (Bb, protein localization). To map physical interactions of Tdrd6a, immunoprecipitation (IP, protein-protein interaction detection assay) was performed with ovary lysates, followed by label-free quantitative mass spectrometry (proteomics), which identified Buc as a strong interactor of Tdrd6a. Loss of Tdrd6a has an effect on the formation of primordial germ cells (PGCs): maternal-zygotic tdrd6a -/- embryos showed a significant reduction in PGC number, irrespective of the genotype of the father. Tdrd6a physically interacts with Gp-residing mRNAs based on RNA-IP followed by sequencing (RIPseq). In tdrd6a mutant oocytes, the Bb often appears to be smaller relative to the entire oocyte, lacking a well-defined edge or even being further distorted (morphology). In the Bb, Buc-eGFP and Tdrd6a form a continuous structure in which Gp mRNAs are embedded (morphology by microscopy). In tdrd6a mutant oocytes, the Buc-eGFP signal is more irregular, however, Gp-transcripts still localize to the Bb (co-localization), indicating that Tdrd6a is not essential for these transcripts to accumulate in the Bb. Electron microscopy (EM) revealed that the electron-dense structures in the Bb display a heterogeneous, fibrillary appearance (morphology). Tdrd6a and Buc interact via symmetrically dimethylated arginines (sDMAs) in the C-terminus of Buc as confirmed by pull-down experiments with modified and unmodified Buc peptides. Expression of Buc in BmN4 transgenic cells results in abundant, cytoplasmic, small granules (particle size and count). In contrast, Tdrd6a displays a ubiquitous cytoplasmic signal (protein localization). Co-transfection results in two possible outcomes: the presence of both Tdrd6a and Buc either results in co-localization in enlarged, cytoplasmic aggregates (morphology) with a broad variety in size or in diffuse cytoplasmic localization of both proteins. Tdrd6a recovers rapidly upon bleaching of Buc-Tdrd6a double-positive granules (FRAP). Interestingly, Buc recovery increases from 35% to 55% in the presence of Tdrd6a. Without Tdrd6a Buc-eGFP cannot be detected in the soluble fraction of BmN4 lysates and is predominantly found in the pellet. In contrast, in the presence of Tdrd6a, significant amounts of Buc-eGFP were soluble. Tdrd6a positively stimulates Buc mobility and solubility and that this can contribute to growth of Buc granules. Tdrd6a and its interaction with arginine-methylated Buc affect the aggregation behavior of Buc-containing structures by stimulating their growth, heterogeneity, and mobility, both in cell culture as well as in vivo (PMID:30086300).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30086300)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-PTM interactions (PMID:30086300)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
regulator of spatial patterns; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</F1R237>
<P0A9A6 type="dict">
<id type="str">
66</id>
<phase_id type="str">
70</phase_id>
<common_name type="str">
FtsZ</common_name>
<name type="str">
Cell division protein FtsZ</name>
<accession type="str">
P0A9A6</accession>
<organism type="str">
Escherichia coli</organism>
<sequence type="str">
MFEPMELTNDAVIKVIGVGGGGGNAVEHMVRERIEGVEFFAVNTDAQALRKTAVGQTIQIGSGITKGLGAGANPEVGRNAADEDRDALRAALEGADMVFIAAGMGGGTGTGAAPVVAEVAKDLGILTVAVVTKPFNFEGKKRMAFAEQGITELSKHVDSLITIPNDKLLKVLGRGISLLDAFGAANDVLKGAVQGIAELITRPGLMNVDFADVRTVMSEMGYAMMGSGVASGEDRAEEAAEMAISSPLLEDIDLSGARGVLVNITAGFDLRLDEFETVGNTIRAFASDNATVVIGTSLDPDMNDELRVTVVATGIGMDKRPEITLVTNKQVQQPVMDRYQQHGMAPLTQEQKPVAKVVNDNAPQTAKEPDYLDIPAFLRKQAD</sequence>
<gene type="str">
FTSZ</gene>
<taxon type="str">
Bacteria</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-383</boundaries>
<region_ref type="str">
30523075</region_ref>
<partners type="str">
1) SlmA (strictly required for LLPS); 2) specific DNA site SBS (not required for LLPS, but promotes it)</partners>
<determinants type="str">
1) protein concentration of FtsZ; 2) protein concentration of SlmA; 3) ionic strength; 4) crowding agent concentration</determinants>
<forms type="str">
condensates</forms>
<organelles type="str">
nuclear body; Ftsz-rich droplets at specific chromosomal DNA sites</organelles>
<pmids type="str">
27725777 (research article), 30523075 (research article)</pmids>
<description type="str">
FtsZ is a soluble GTPase, ancestor of eukaryotic tubulin, that serves as a central element of the division ring in most bacteria. FtsZ reversibly forms condensates in the presence of SlmA, a nucleoid occlusion effector of division site selection, in complex with its specific SlmA-binding sites on the chromosome (SBS). These condensates are consistent with crowding-driven phase-separated droplets. The condensates of FtsZ and SlmA are dynamic, allowing the incorporation of additional protein, the rapid evolution of the integrated FtsZ toward filaments in the presence of GTP, and its recruitment back into the liquid droplets upon GTP depletion. FtsZ SlmA SBS condensates, in which FtsZ remains active for polymerization, were also found in cell-like crowded phase-separated systems revealing their preferential partition into one of the phases, and its accumulation at lipid surfaces (PMID:30523075).</description>
<experiment_llps type="str">
Liquid droplets were observed in vitro (particle size and count) in solutions containing FtsZ labeled with Alexa 647 (FtsZ-Alexa 647) (fluorescent tagging), unlabeled SlmA, and fluorescein-labeled 24-bp oligonucleotide with the consensus sequence SBS (SBS-Fl), in which the two dyes colocalized, independently of the macromolecule used to crowd the solution (Ficoll, PEG or dextran), as revealed by confocal microscopy imaging. These findings were confirmed by turbidity experiment (change in optical properties). Change in protein concentration, change in salt concentration, change in the concentration of a crowding agent affected the formation of condensates (particle size and count by microscopy and change in optical properties). The round structures formed by FtsZ-
SlmA
-SBS were dynamic, a characteristic feature of liquid-like droplets, as revealed by protein capture experiment. Addition of GTP on preformed FtsZ
-SlmA-
SBS condensates induced the formation of FtsZ fibers in which significant colocalization between FtsZ-Alexa 488 and SBS-Alexa 647 was observed by microscopy. Compared with control samples lacking SlmA
-SBS, the fibers were thinner and their lifetime was appreciably shorter, as previously observed in dilute solution. Initially, the fibers coexisted with the round condensates (co-localization), and then, the amount of fibers increased at the expense of the condensates. In open, phase-separated PEG/DNA systems, abundant FtsZ
-SlmA
-SBS condensates were found, mostly distributed in the DNA phase (co-localization), probably because of the preferential partition of the individual components (FtsZ, SlmA, and the SBS) into this phase. (PMID:30523075).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30523075); reversibility (PMID:30523075) </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P0A9A6>
<P0C093 type="dict">
<id type="str">
100</id>
<phase_id type="str">
70</phase_id>
<common_name type="str">
SlmA</common_name>
<name type="str">
Nucleoid occlusion factor SlmA</name>
<accession type="str">
P0C093</accession>
<organism type="str">
Escherichia coli</organism>
<sequence type="str">
MAEKQTAKRNRREEILQSLALMLESSDGSQRITTAKLAASVGVSEAALYRHFPSKTRMFDSLIEFIEDSLITRINLILKDEKDTTARLRLIVLLLLGFGERNPGLTRILTGHALMFEQDRLQGRINQLFERIEAQLRQVLREKRMREGEGYTTDETLLASQILAFCEGMLSRFVRSEFKYRPTDDFDARWPLIAAQLQ</sequence>
<gene type="str">
SLMA</gene>
<taxon type="str">
Bacteria</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-198</boundaries>
<region_ref type="str">
30523075</region_ref>
<partners type="str">
1) FtsZ (strictly required for LLPS); 2) specific DNA site SBS (not required for LLPS, but promotes it)</partners>
<determinants type="str">
1) protein concentration of FtsZ; 2) protein concentration of SlmA; 3) ionic strength; 4) crowding agent concentration</determinants>
<forms type="str">
condensates</forms>
<organelles type="str">
nuclear body; Ftsz-rich droplets at specific chromosomal DNA sites</organelles>
<pmids type="str">
27725777 (research article), 30523075 (research article)</pmids>
<description type="str">
FtsZ is a soluble GTPase, ancestor of eukaryotic tubulin, that serves as a central element of the division ring in most bacteria. FtsZ reversibly forms condensates in the presence of SlmA, a nucleoid occlusion effector of division site selection, in complex with its specific SlmA-binding sites on the chromosome (SBS). These condensates are consistent with crowding-driven phase-separated droplets. The condensates of FtsZ and SlmA are dynamic, allowing the incorporation of additional protein, the rapid evolution of the integrated FtsZ toward filaments in the presence of GTP, and its recruitment back into the liquid droplets upon GTP depletion. FtsZ SlmA SBS condensates, in which FtsZ remains active for polymerization, were also found in cell-like crowded phase-separated systems revealing their preferential partition into one of the phases, and its accumulation at lipid surfaces (PMID:30523075).</description>
<experiment_llps type="str">
Liquid droplets were observed in vitro (particle size and count) in solutions containing FtsZ labeled with Alexa 647 (FtsZ-Alexa 647) (fluorescent tagging), unlabeled SlmA, and fluorescein-labeled 24-bp oligonucleotide with the consensus sequence SBS (SBS-Fl), in which the two dyes colocalized, independently of the macromolecule used to crowd the solution (Ficoll, PEG or dextran), as revealed by confocal microscopy imaging. These findings were confirmed by turbidity experiment (change in optical properties). Change in protein concentration, change in salt concentration, change in the concentration of a crowding agent affected the formation of condensates (particle size and count by microscopy and change in optical properties). The round structures formed by FtsZ-
SlmA
-SBS were dynamic, a characteristic feature of liquid-like droplets, as revealed by protein capture experiment. Addition of GTP on preformed FtsZ
-SlmA-
SBS condensates induced the formation of FtsZ fibers in which significant colocalization between FtsZ-Alexa 488 and SBS-Alexa 647 was observed by microscopy. Compared with control samples lacking SlmA
-SBS, the fibers were thinner and their lifetime was appreciably shorter, as previously observed in dilute solution. Initially, the fibers coexisted with the round condensates (co-localization), and then, the amount of fibers increased at the expense of the condensates. In open, phase-separated PEG/DNA systems, abundant FtsZ
-SlmA
-SBS condensates were found, mostly distributed in the DNA phase (co-localization), probably because of the preferential partition of the individual components (FtsZ, SlmA, and the SBS) into this phase. (PMID:30523075).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30523075); reversibility (PMID:30523075) </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P0C093>
<P22363 type="dict">
<id type="str">
67</id>
<phase_id type="str">
71</phase_id>
<common_name type="str">
Protein P</common_name>
<name type="str">
Phosphoprotein</name>
<accession type="str">
P22363</accession>
<organism type="str">
Rabies virus</organism>
<sequence type="str">
MSKIFVNPSAIRAGLADLEMAEETVDLINRNIEDNQAHLQGEPIEVDNLPEDMKRLHLDDEKSSNLGEMVRVGEGKYREDFQMDEGEDPNLLFQSYLDNVGVQIVRQMRSGERFLKIWSQTVEEIVSYVTVNFPNPPRRSSEDKSTQTTGRELKKETTSAFSQRESQPSKARMVAQVAPGPPALEWSATNEEDDLSVEAEIAHQIAESFSKKYKFPSRSSGIFLYNFEQLKMNLDDIVKEAKNVPGVTRLAHDGSKIPLRCVLGWVALANSKKFQLLVEADKLSKIMQDDLNRYTSC</sequence>
<gene type="str">
P</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
Domains DD (dimerisation), IDD2 and PCTD (N-RNA binding)</segment>
<boundaries type="str">
92-297</boundaries>
<region_ref type="str">
28680096</region_ref>
<partners type="str">
1) protein N (strictly required for LLPS); 2) RNA (maybe required)</partners>
<determinants type="str">
1) salt concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic viral factory; Negri body</organelles>
<pmids type="str">
28680096 (research article)</pmids>
<description type="str">
Replication of Mononegavirales occurs in viral factories which form inclusions in the host-cell cytoplasm. For rabies virus, those inclusions are called Negri bodies (NBs). Viral nucleocapsids are ejected from NBs and transported along microtubules to form either new virions or secondary viral factories. Coexpression of rabies virus N and P proteins results in cytoplasmic inclusions recapitulating NBs properties. This minimal system reveals that an intrinsically disordered domain and the dimerization domain of P are essential for Negri bodies-like structures formation. Since the P dimer-dimer and P dimer - N-RNA interactions are too strong for liquid properties, the liquid-like behaviour is probably delivered by the N-terminal half of the IDD2 domain (residues 132-150). Accordingly, deletion of residues 139-151 led to the disappearance of NB-like droplets. Formation of liquid viral factories by phase separation is common among Mononegavirales and allows specific recruitment and concentration of viral proteins but also the escape to cellular antiviral response.Negative strand RNA viruses, such as rabies virus, induce formation of cytoplasmic inclusions for genome replication (PMID:28680096).</description>
<experiment_llps type="str">
Overexpression of N and P after cell transfection (genetic transformation) leads to the formation of cytoplasmic inclusions in vivo (particle size and count by microscopy). Indeed, in BSR cells constitutively expressing the T7RNA polymerase (BSR-T7/5) and co-transfected by plasmids pTit-P and pTit-N, cytoplasmic spherical inclusions are observed (morphology, particle size and count by microscopy). N-P inclusions formed in this minimal system have the same liquid characteristics by FRAP as Negri bodies (NBs). pTit plasmids allowing the in vivo expression of P deletion mutants were co-transfected with pTit-N and the presence of N-P inclusions was investigated (morphology, particle size and count by microscopy), revealing that the domains DD, IDD2 and PCTD of P are required for NB-likestructures formation. Deletion of residues 139–151 abolished spherical inclusions formation. P and N expressed alone were able to form structures, which recapitulate the properties of NBs in vivo, however it is probable that in such N-P inclusions, N is associated with cellular RNAs and forms N-RNA rings and short RNP-like structures. Several identified partners of P are recruited inside NBs, like focal adhesion kinase FAK and heatshock protein HSP70 (protein co-localization). In vitro studies were not performed so, the requirement for cellular RNAs for NB formation is not elucidated (PMID:28680096).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID:28680096); dynamic movement/reorganization of molecules within the droplet (PMID:28680096); dynamic exchange of molecules with surrounding solvent (PMID:28680096)</experiment_state>
<rna_req type="str">
cellular RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:28680096); protein-RNA interaction (PMID:28680096); electrostatic (cation-anion) interaction (PMID:28680096)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Not known.</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P22363>
<Q8JXF6 type="dict">
<id type="str">
101</id>
<phase_id type="str">
71</phase_id>
<common_name type="str">
Protein N</common_name>
<name type="str">
Nucleoprotein</name>
<accession type="str">
Q8JXF6</accession>
<organism type="str">
Rabies virus</organism>
<sequence type="str">
MDADKIVFKVNNQVVSLKPEIIVDQYEYKYPAIKDLKKPCITLGKAPDLNKAYKSVLSGMNAAKLDPDDVCSYLAAAMQFFEGTCPEDWTSYGILIARKGDRITPNSLVEIKRTDVDGNWALTGGMELTRDPTVSEHASLVGLLLSLYRLSKISGQNTGNYKTNIADRIEQIFETAPFVKIVEHHTLMTTHKMCANWSTIPNFRFLAGTYDMFFSRIEHLYSAIRVGTVVTAYEDCSGLVSFTGFIKQINLTAREAILYFFHKNFEEEIRRMFEPGQETAVPHSYFIHFRSLGLSGKSPYSSNAVGHVFNLIHFVGCYMGQVRSLNATVIAACAPHEMSVLGGYLGEEFFGKGTFERRFFRDEKELQEYEAAELTKTDVALADDGTVNSDDEDYFSGETRSPEAVYTRIMMNGGRLKRSHIRRYVSVSSNHQARPNSFAEFLNKTYSNDS</sequence>
<gene type="str">
N</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-450</boundaries>
<region_ref type="str">
28680096</region_ref>
<partners type="str">
1) P protein (strictly required for LLPS); 2) RNA (maybe required)</partners>
<determinants type="str">
1) salt concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
cytoplasmic viral factory; Negri body</organelles>
<pmids type="str">
28680096 (research article)</pmids>
<description type="str">
Replication of Mononegavirales occurs in viral factories which form inclusions in the host-cell cytoplasm. For rabies virus, those inclusions are called Negri bodies (NBs). Viral nucleocapsids are ejected from NBs and transported along microtubules to form either new virions or secondary viral factories. Coexpression of rabies virus N and P proteins results in cytoplasmic inclusions recapitulating NBs properties. This minimal system reveals that an intrinsically disordered domain and the dimerization domain of P are essential for Negri bodies-like structures formation. Since the P dimer-dimer and P dimer - N-RNA interactions are too strong for liquid properties, the liquid-like behaviour is probably delivered by the N-terminal half of the IDD2 domain (residues 132-150). Accordingly, deletion of residues 139-151 led to the disappearance of NB-like droplets. Formation of liquid viral factories by phase separation is common among Mononegavirales and allows specific recruitment and concentration of viral proteins but also the escape to cellular antiviral response.Negative strand RNA viruses, such as rabies virus, induce formation of cytoplasmic inclusions for genome replication (PMID:28680096).</description>
<experiment_llps type="str">
Overexpression of N and P after cell transfection (genetic transformation) leads to the formation of cytoplasmic inclusions in vivo (particle size and count by microscopy). Indeed, in BSR cells constitutively expressing the T7RNA polymerase (BSR-T7/5) and co-transfected by plasmids pTit-P and pTit-N, cytoplasmic spherical inclusions are observed (morphology, particle size and count by microscopy). N-P inclusions formed in this minimal system have the same liquid characteristics by FRAP as Negri bodies (NBs). pTit plasmids allowing the in vivo expression of P deletion mutants were co-transfected with pTit-N and the presence of N-P inclusions was investigated (morphology, particle size and count by microscopy), revealing that the domains DD, IDD2 and PCTD of P are required for NB-likestructures formation. Deletion of residues 139–151 abolished spherical inclusions formation. P and N expressed alone were able to form structures, which recapitulate the properties of NBs in vivo, however it is probable that in such N-P inclusions, N is associated with cellular RNAs and forms N-RNA rings and short RNP-like structures. Several identified partners of P are recruited inside NBs, like focal adhesion kinase FAK and heatshock protein HSP70 (protein co-localization). In vitro studies were not performed so, the requirement for cellular RNAs for NB formation is not elucidated (PMID:28680096).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID:28680096); dynamic movement/reorganization of molecules within the droplet (PMID:28680096); dynamic exchange of molecules with surrounding solvent (PMID:28680096)</experiment_state>
<rna_req type="str">
cellular RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:28680096); protein-RNA interaction (PMID:28680096); electrostatic (cation-anion) interaction (PMID:28680096)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Not known.</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</Q8JXF6>
<Q9A749 type="dict">
<id type="str">
68</id>
<phase_id type="str">
72</phase_id>
<common_name type="str">
RNase E</common_name>
<name type="str">
Ribonuclease E</name>
<accession type="str">
Q9A749</accession>
<organism type="str">
Caulobacter vibrioides</organism>
<sequence type="str">
MSKKMLIDAAHAEETRVVVVDGTRVEEFDFESQTRKQLRGNIYLAKVTRVEPSLQAAFIEYGGNRHGFLAFNEIHPDYYQIPVADREALMRDDSGDDEDDTPISRRASGGDDEDDVNGGDRAVDDDDDDVEEELARRKRRLMRKYKIQEVIRRRQIMLVQVVKEERGNKGAALTTYLSLAGRYGVLMPNTARGGGISRKITAVTDRKRLKSVVQSLDVPQGMGLIVRTAGAKRTKAEIKRDYEYLLRLWENIRENTLHSIAPALIYEEEDLVKRAIRDMYDKDLDGIWVEGDAGYKEARDFMRMLMPSQAKKVFNYRDPTPLFVKNKIEDHLAQIYSPVVPLRSGGYLVINQTEALVAIDVNSGKATRERNIEATALKTNCEAAEEAARQLRLRDLAGLIVIDFIDMDEAKNNRTVEKVLKDALKDDRARIQMGKISGFGLMEISRQRRRTGVLEGTTHVCEHCEGTGRVRSVESSALAALRAVEAEALKGSGSVILKVSRSVGLYILNEKRDYLQRLLTTHGLFVSVVVDDSLHAGDQEIERTELGERIAVAPPPFVEEDDDFDPNAYDDEEEEDDVILDDEDDTDREDTDDDDATTRKSARDDERGDRKGRRGRRDRNRGRGRRDERDGETESEDEDVVAEGADEDRGEFGDDDEGGRRRRRRGRRGGRRGGREDGDRPTDAFVWIRPRVPFGENVFTWHDPAALVGGGESRRQAPEPRVDAATEAAPRPERAEREERPGRERGRRGRDRGRRQRDEAPVAEMTSVESATVEAAEPFEAPILAPPVIAGPPADVWVELPEVEEAPKKPKRSRARGKKATETSVEAIDTVTEVAAEAPAPETAEPEAVEVAPPAPTVEAAPEPGPVVEAVEEAQPAEPDPNEITAPPEKPRRGWWRR</sequence>
<gene type="str">
RNE</gene>
<taxon type="str">
Bacteria</taxon>
<segment type="str">
C-terminal IDR with alternating blocks of positive and negative charges</segment>
<boundaries type="str">
451-898</boundaries>
<region_ref type="str">
30197298</region_ref>
<partners type="str">
1) RNA (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration of RNase E; 2) ionic strength; 3) salt concentration</determinants>
<forms type="str">
biomolecular condensate</forms>
<organelles type="str">
cytoplasmic ribonucleoprotein granule; bacterial RNP-bodies (BR-bodies)</organelles>
<pmids type="str">
30197298 (research article)</pmids>
<description type="str">
The most common bacterial protein controlling mRNA turnover is RNase E, which is conserved in approximately half of all bacteria. It is shown that the bacterium Caulobacter crescentus Ribonuclease (RNase) E assembles RNP LLPS condensates that are termed bacterial RNP-bodies (BR-bodies), which are multifunctional RNP bodies, similar to eukaryotic P-bodies and stress granules. RNase E requires RNA to assemble a BR-body, and disassembly requires RNA cleavage, suggesting BR-bodies provide localized sites of RNA degradation. The unstructured C-terminal domain of RNase E is both necessary and sufficient to assemble the core of the BR-body, is functionally conserved in related α-proteobacteria, and influences mRNA degradation. BR-bodies are rapidly induced under cellular stresses and provide enhanced cell growth under stress. Caulobacter RNase E is the first bacterial protein identified that forms LLPS condensates, providing an effective strategy for subcellular organization in cells lacking membrane-bound compartments. RNase E recruits RNA degradosome components into BR-bodies (PMID:30197298). </description>
<experiment_llps type="str">
Ccr RNase E-YFP fusion protein localizes into patchy foci within the cytoplasm in vivo in all stages of the cell cycle with significant cell to-cell variability in position, number (0–5/cell), and intensity of foci (particle size and count by microscopy). Cells were treated with high levels of rifampicin (100 mg/mL, change in the concentration of a small molecule) to rapidly deplete cellular mRNAs without disrupting the protein level of RNase E-YFP, which significantly diminished RNase E-YFP fluorescent foci, while the total cell intensity of YFP signal remained similar (particle size and count by microscopy). When the CTD region was deleted from RNase E (mutation), the protein became diffuse throughout the cytoplasm in vivo (protein localization). In contrast, when the NTD was deleted (mutation), robust foci formation was observed (protein localization, particle size and count by microscopy), as with the full-length protein. When the positively charged blocks were deleted from the CTD (mutation), CTD-YFP showed diffuse localization. The intrinsically disordered CTD of Ccr RNase E was able to form LLPS condensates (protein localization, particle size and count by microscopy) in vitro with the condensates being sensitive to ionic strength. In vitro condensate assembly occurs at NaCl concentrations below 200 mM and requires protein concentrations of at least 12.4 μM. Addition of 5–175 mg/mL poly-A RNA at a low concentration (12.4 μM) of CTD-YFP induced in vitro LLPS condensates and broadened the range in salt concentration over which they assemble. RNase E-YFP foci were highly co-localized with Aconitase-Chy or RhlB-CFP foci in vivo, in cells, suggesting that these degradosome proteins are indeed assembled into the BR-bodies. Localization of RhlB-CFP and Aconitase-Chy into cytoplasmic foci were both dependent on the presence of RNase E, as depletion of RNase E from cells led to a complete loss in RhlB or Aconitase foci. Several stresses led to an increase in the number of Ccr RNase E-YFP BR-bodies per cell (particle size and count by microscopy) and a decrease in diffuse RNase E-YFP signal including the addition of ethanol or EDTA, or applying heat shock. (PMID:30197298). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30197298); reversibility (PMID:30197298)</experiment_state>
<rna_req type="str">
cellular RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:30197298); protein-RNA interaction (PMID:30197298)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9A749>
<Q07666 type="dict">
<id type="str">
69</id>
<phase_id type="str">
73</phase_id>
<common_name type="str">
Sam68</common_name>
<name type="str">
KH domain-containing, RNA-binding, signal transduction-associated protein 1</name>
<accession type="str">
Q07666</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MQRRDDPAARMSRSSGRSGSMDPSGAHPSVRQTPSRQPPLPHRSRGGGGGSRGGARASPATQPPPLLPPSATGPDATVGGPAPTPLLPPSATASVKMEPENKYLPELMAEKDSLDPSFTHAMQLLTAEIEKIQKGDSKKDDEENYLDLFSHKNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFIEVFGPPCEAYALMAHAMEEVKKFLVPDMMDDICQEQFLELSYLNGVPEPSRGRGVPVRGRGAAPPPPPVPRGRGVGPPRGALVRGTPVRGAITRGATVTRGVPPPPTVRGAPAPRARTAGIQRIPLPPPPAPETYEEYGYDDTYAEQSYEGYEGYYSQSQGDSEYYDYGHGEVQDSYEAYGQDDWNGTRPSLKAPPARPVKGAYREHPYGRY</sequence>
<gene type="str">
KHDRBS1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
G-rich N-terminal IDR and KH domain</segment>
<boundaries type="str">
1-197</boundaries>
<region_ref type="str">
27377249</region_ref>
<partners type="str">
1) RNA (not only for SNB localization but also for SNB formation)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
Sam68 nuclear bodies (SNBs)</forms>
<organelles type="str">
nuclear body; ribonucleoprotein complex; Sam68 nuclear bodies (SNBs)</organelles>
<pmids type="str">
27377249 (research article)</pmids>
<description type="str">
Sam68 and HNRNPD are essential for the formation of the RNase-sensitive Sam68 nuclear bodies (SNBs). Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures. In case of Sam68 the N-terminal GSG disordered domain and the following KH domain are essential for SNB localization and formation. SNBs are RNase sensitive. In vitro LLPS experiments with these constructs are lacking (PMID:27377249).</description>
<experiment_llps type="str">
In vivo, SNBs disappeared upon a temperature shift from 37 to 32°C for 24 h and reformed when the temperature was returned to 37°C for 3 h (particle size and count by microscopy on change in temperature). Depletion of Sam68 or HNRNPD by RNAi in HeLa cells in vivo resulted in the disappearance of SNBs as detected by immunofluorescence, whereas depletion of the three other proteins (HNRNPL, DBC1, and ZNF346) hardly affected the integrity of SNBs. Based on truncation studies, the GSG domain, particularly the N-terminal-to-KH-domain region (NK region) and the RNA-binding KH domain but not the C-terminal-to-KH-domain region (CK region) in this domain, was required for SNB localization of Sam68. A substantial DBC1 signal was detected when an essential SNB component, either Sam68 or HNRNPD, was knocked down. Furthermore, when HNRNPL was knocked down, the DBC1 signal was detected in nuclear foci distinct from those labeled with Sam68 and HNRNPD (protein localization). Both nuclear foci (the Sam68 substructure and the DBC1 substructure) were sensitive to RNase treatment (enzymatic activity assay). No in vitro results available, LLPS, formation of SNBs may require other factors (PMID:27377249).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:27377249); reversibility of formation and dissolution (PMID:27377249)</experiment_state>
<rna_req type="str">
cellular RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID:27377249) </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q07666>
<Q14103 type="dict">
<id type="str">
70</id>
<phase_id type="str">
74</phase_id>
<common_name type="str">
HNRNPD</common_name>
<name type="str">
Heterogeneous nuclear ribonucleoprotein D0</name>
<accession type="str">
Q14103</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSEEQFGGDGAAAAATAAVGGSAGEQEGAMVAATQGAAAAAGSGAGTGGGTASGGTEGGSAESEGAKIDASKNEEDEGHSNSSPRHSEAATAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQWGSRGGFAGRARGRGGGPSQNWNQGYSNYWNQGYGNYGYNSQGYGGYGGYDYTGYNNYYGYGDYSNQQSGYGKVSRRGGHQNSYKPY</sequence>
<gene type="str">
HNRNPD</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: RRMs and G/Q/Y-rich PLD</segment>
<boundaries type="str">
1-355</boundaries>
<region_ref type="str">
27377249</region_ref>
<partners type="str">
1) RNA (not only for SNB localization but also for SNB formation)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
Sam68 nuclear bodies (SNBs)</forms>
<organelles type="str">
nuclear body; ribonucleoprotein complex; Sam68 nuclear bodies (SNBs)</organelles>
<pmids type="str">
27377249 (research article), 28709000 (research article)</pmids>
<description type="str">
Sam68 and HNRNPD are essential for the formation of the RNase-sensitive Sam68 nuclear bodies (SNBs). Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures. Both the two RRMs (and their intact RNA-binding capability) and the PLD of HNRNPD are required for SNB localization and assembly. The functional PLD is required primarily for Sam68 interaction and for the homodimeric interaction of HNRNPD in SNBs. In vitro LLPS experiments with these constructs are lacking (PMID:27377249).</description>
<experiment_llps type="str">
In vivo, SNBs disappeared upon a temperature shift from 37 to 32°C for 24 h and reformed when the temperature was returned to 37°C for 3 h (particle size and count by microscopy on change in temperature). Depletion of Sam68 or HNRNPD by RNAi in HeLa cells in vivo resulted in the disappearance of SNBs as detected by immunofluorescence, whereas depletion of the three other proteins (HNRNPL, DBC1, and ZNF346) hardly affected the integrity of SNBs. The isoforms of HNRNPD containing exon 7 (p42 and p45) localize in SNBs and function in their formation. A coimmunoprecipitation-based detection assay with FLAG-tagged HNRNPD isoforms indicated that p42 and p45 physically interact with Sam68, HNRNPL, and DBC1. Based on Venus-p45 as the wild-type (WT) Venus-HNRNPD construct, two phenylalanine residues essential for RNA binding in each of RRM1 and RRM2 were mutated to aspartic acid to create mutants RRM1-M (F140D/F142D) and RRM2-M (F225D/F227D), which both failed to localize to SNBs, indicating that RNA binding of HNRNPD through the two RRMs simultaneously is essential for its SNB localization. RRM mutants also almost completely lacked the rescue activity for SNB formation. To examine whether the prion-like property of the HNRNPD prion-like domain is required for SNB formation, the tyrosine residues in the PLD of p45 were mutated to serine to create a partial Y-S mutant (nine tyrosine residues were altered) and a full Y-S mutant (all 18 Tyrs mutated). Both PLD Y-S mutants failed to localize to SNBs and showed significantly reduced rescue activity. FLAG-tagged PLD mutants neither interacted with Sam68 nor cotransfected Venus-tagged p45 itself (physical interaction by coimmunoprecipitation), indicating that the HNRNPD PLD is required for the interaction with Sam68 and for the homodimeric interaction of HNRNPD in SNBs. A substantial DBC1 signal was detected when an essential SNB component (protein localization), either Sam68 or HNRNPD, was knocked down. Furthermore, when HNRNPL was knocked down, the DBC1 signal was detected in nuclear foci distinct from those labeled with Sam68 and HNRNPD (protein localization). Both nuclear foci (the Sam68 substructure and the DBC1 substructure) were sensitive to RNase treatment (enzymatic activity assay). No in vitro results available, LLPS, formation of SNBs may require other factors (PMID:27377249). Confocal fluorescence microscopy of HeLa cells overexpressing N-terminally GFP- fused HNRNPD proteins in vivo showed localization HNRNPD into foci (protein localization), and disappearance of foci on the substitution of tyrosine residues to serines (PMID:28709000).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
temperature-dependence (PMID:27377249); reversibility of formation and dissolution (PMID:27377249)</experiment_state>
<rna_req type="str">
cellular RNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID:27377249); cation-π (cation-pi) interactions (PMID:28709000); π-π (pi-pi) interactions (PMID:28709000)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q14103>
<O43791 type="dict">
<id type="str">
71</id>
<phase_id type="str">
75</phase_id>
<common_name type="str">
SPOP</common_name>
<name type="str">
Speckle-type POZ protein</name>
<accession type="str">
O43791</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSRVPSPPPPAEMSSGPVAESWCYTQIKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLLVSCPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGQNTMNMVKVPECRLADELGGLWENSRFTDCCLCVAGQEFQAHKAILAARSPVFSAMFEHEMEESKKNRVEINDVEPEVFKEMMCFIYTGKAPNLDKMADDLLAAADKYALERLKVMCEDALCSNLSVENAAEILILADLHSADQLKTQAVDFINYHASDVLETSGWKSMVVSHPHLVAEAYRSLASAQCPFLGPPRKRLKQS</sequence>
<gene type="str">
SPOP</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Central region containing the ordered MATH (substrate binding) and BTB domains (dimerization and CUL3 binding)</segment>
<boundaries type="str">
28-359</boundaries>
<region_ref type="str">
30244836</region_ref>
<partners type="str">
1) SPOP subtrates eg. DAXX or androgen receptor (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration of SPOP; 2) substrate concentration; 3) molar ratios SPOP:substrate; 4) presence of cancer mutations (negatively affect LLPS)</determinants>
<forms type="str">
liquid nuclear bodies</forms>
<organelles type="str">
nuclear body; nuclear protein granule; SPOP/DAXX body</organelles>
<pmids type="str">
30244836 (research article)</pmids>
<description type="str">
Mutations in the tumor suppressor SPOP (speckle-type POZ protein) cause prostate, breast and other solid tumors. SPOP is a substrate adaptor of the cullin3-RING ubiquitin ligase and localizes to nuclear speckles. Substrates trigger phase separation of SPOP in vitro and co-localization in membraneless organelles in cells. Substrates include the death-domain-associated protein (DAXX), androgen receptor (AR), and other important signaling cascade effectors, epigenetic modifiers and hormone signaling effectors, these contain multiple SPOP-binding (SB) motifs in their IDRs. Enzymatic activity correlates with cellular co-localization and in vitro mesoscale assembly formation. Disease-associated SPOP-mutations that lead to the accumulation of proto-oncogenic proteins interfere with phase separation and co-localization in membraneless organelles, suggesting that substrate-directed phase separation of this E3 ligase underlies the regulation of ubiquitin-dependent proteostasis (PMID:30244836).</description>
<experiment_llps type="str">
Transiently expressed mCherry-fused SPOP co-localized with GFP-fused DAXX (a SPOP substrate) in largely spherical type of nuclear bodies in vivo (morphology, protein localization) distinct from nuclear speckles, PML bodies, nucleoli, and Cajal bodies, as evidenced by flurescence microscopy. Different expression tags did not influence the co-localization of SPOP and DAXX. The co-expression of the two proteins change their localization, as SPOP localized to nuclear speckles, and DAXX localized to PML bodies when expressed alone. In vitro studies demonstrated that SPOP(28-359) undergoes self-oligomerization (physical interaction), and in the presence of molecular crowders such as Ficoll-70, these oligomers are large enough to be observed by light microscopy (particle size and count). At higher concentrations (change in protein concentration) in vitro DAXX(495-740) forms condensed droplets; however, this tendency is strongly enhanced in the presence of SPOP, and this was the case in the presence of both polymer and protein crowders, as evidenced by fluorescence microscopy of tagged protein constructs (PMID:30244836).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30244836); rheological traits (PMID:30244836); dynamic movement/reorganization of molecules within the droplet assessed using FRAP (PMID:30244836)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:30244836); linear oligomerization/self-association (PMID:27220849); ; </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Bálint Mészáros; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</O43791>
<Q9UER7 type="dict">
<id type="str">
119</id>
<phase_id type="str">
75</phase_id>
<common_name type="str">
DAXX</common_name>
<name type="str">
Death domain-associated protein 6</name>
<accession type="str">
Q9UER7</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MATANSIIVLDDDDEDEAAAQPGPSHPLPNAASPGAEAPSSSEPHGARGSSSSGGKKCYKLENEKLFEEFLELCKMQTADHPEVVPFLYNRQQRAHSLFLASAEFCNILSRVLSRARSRPAKLYVYINELCTVLKAHSAKKKLNLAPAATTSNEPSGNNPPTHLSLDPTNAENTASQSPRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSAYLQEARLKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGPDTFPDYGDVLRAVEKAAARHSLGLPRQQLQLMAQDAFRDVGIRLQERRHLDLIYNFGCHLTDDYRPGVDPALSDPVLARRLRENRSLAMSRLDEVISKYAMLQDKSEEGERKKRRARLQGTSSHSADTPEASLDSGEGPSGMASQGCPSASRAETDDEDDEESDEEEEEEEEEEEEEATDSEEEEDLEQMQEGQEDDEEEDEEEEAAAGKDGDKSPMSSLQISNEKNLEPGKQISRSSGEQQNKGRIVSPSLLSEEPLAPSSIDAESNGEQPEELTLEEESPVSQLFELEIEALPLDTPSSVETDISSSRKQSEEPFTTVLENGAGMVSSTSFNGGVSPHNWGDSGPPCKKSRKEKKQTGSGPLGNSYVERQRSVHEKNGKKICTLPSPPSPLASLAPVADSSTRVDSPSHGLVTSSLCIPSPARLSQTPHSQPPRPGTCKTSVATQCDPEEIIVLSDSD</sequence>
<gene type="str">
DAXX</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal region</segment>
<boundaries type="str">
495-740</boundaries>
<region_ref type="str">
30244836</region_ref>
<partners type="str">
1) SPOP (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration of DAXX; 2) SPOP concentration; 3) molar ratios SPOP:DAXX</determinants>
<forms type="str">
liquid nuclear bodies</forms>
<organelles type="str">
nuclear body; nuclear protein granule; SPOP/DAXX body</organelles>
<pmids type="str">
30244836 (research article)</pmids>
<description type="str">
Mutations in the tumor suppressor SPOP (speckle-type POZ protein) cause prostate, breast and other solid tumors. SPOP is a substrate adaptor of the cullin3-RING ubiquitin ligase and localizes to nuclear speckles. Substrates trigger phase separation of SPOP in vitro and co-localization in membraneless organelles in cells. Substrates include the death-domain-associated protein (DAXX), androgen receptor (AR), and other important signaling cascade effectors, epigenetic modifiers and hormone signaling effectors, these contain multiple SPOP-binding (SB) motifs in their IDRs. Enzymatic activity correlates with cellular co-localization and in vitro mesoscale assembly formation. Disease-associated SPOP-mutations that lead to the accumulation of proto-oncogenic proteins interfere with phase separation and co-localization in membraneless organelles, suggesting that substrate-directed phase separation of this E3 ligase underlies the regulation of ubiquitin-dependent proteostasis (PMID:30244836).</description>
<experiment_llps type="str">
Transiently expressed mCherry-fused SPOP co-localized with GFP-fused DAXX (a SPOP substrate) in largely spherical type of nuclear bodies in vivo (morphology, protein localization) distinct from nuclear speckles, PML bodies, nucleoli, and Cajal bodies, as evidenced by flurescence microscopy. Different expression tags did not influence the co-localization of SPOP and DAXX. The co-expression of the two proteins change their localization, as SPOP localized to nuclear speckles, and DAXX localized to PML bodies when expressed alone. In vitro studies demonstrated that SPOP(28-359) undergoes self-oligomerization (physical interaction), and in the presence of molecular crowders such as Ficoll-70, these oligomers are large enough to be observed by light microscopy (particle size and count). At higher concentrations (change in protein concentration) in vitro DAXX(495-740) forms condensed droplets; however, this tendency is strongly enhanced in the presence of SPOP, and this was the case in the presence of both polymer and protein crowders, as evidenced by fluorescence microscopy of tagged protein constructs (PMID:30244836).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30244836); rheological traits (PMID:30244836); dynamic movement/reorganization of molecules within the droplet assessed using FRAP (PMID:30244836)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:30244836); linear oligomerization/self-association (PMID:27220849); ; </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9UER7>
<P25158-2 type="dict">
<id type="str">
91</id>
<phase_id type="str">
76</phase_id>
<common_name type="str">
Oskar</common_name>
<name type="str">
Isoform C of Maternal effect protein oskar</name>
<accession type="str">
P25158-2</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MTIIESNYISVREEYPDIDSEVRAILLSHAQNGITISSIKSEYRKLTGNPFPLHDNVTDFLLTIPNVTAECSESGKRIFNLKASLKNGHLLDMVLNQKERTSDYSSGAPSLENIPRAPPRYWKNPFKRRALSQLNTSPRTVPKITDEKTKDIATRPVSLHQMANEAAESNWCYQDNWKHLNNFYQQASVNAPKMPVPINIYSPDAPEEPINLAPPGHQPSCRTQSQKTEPTENRHLGIFVHPFNGMNIMKRRHEMTPTPTILTSGTYNDSLLTINSDYDAYLLDFPLMGDDFMLYLARMELKCRFRRHERVLQSGLCVSGLTINGARNRLKRVQLPEGTQIIVNIGSVDIMRGKPLVQIEHDFRLLIKEMHNMRLVPILTNLAPLGNYCHDKVLCDKIYRFNKFIRSECCHLKVIDIHSCLINERGVVRFDCFQASPRQVTGSKEPYLFWNKIGRQRVLQVIETSLEY</sequence>
<gene type="str">
OSKA_DROME</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: Lotus (dimerization, VASA binding) and SGNH domains (RNA-binding) connected by an ID linker</segment>
<boundaries type="str">
1-468</boundaries>
<region_ref type="str">
30260314</region_ref>
<partners type="str">
1) VASA (not required but promotes LLPS)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
phase transitioned condensates</forms>
<organelles type="str">
P granule</organelles>
<pmids type="str">
30260314 (research article)</pmids>
<description type="str">
Germ granules are non-membranous ribonucleoprotein granules deemed the hubs for post-transcriptional gene regulation and functionally linked to germ cell fate across species. Two types of germ granules in the Drosophila embryo are studied: cytoplasmic germ granules that instruct primordial germ cells (PGCs) formation and nuclear germ granules within early PGCs with unknown function. It is shown that cytoplasmic and nuclear germ granules are phase transitioned condensates nucleated by Oskar protein that display liquid as well as hydrogel-like properties. Short, but not Long Osk is necessary and sufficient to instruct the formation of cytoplasmic germ granules in heterologous cell systems independent of other germ plasm proteins. All domains seem to be dispensable for LLPS but at the same time are required to form similar granules as full length Short Oskar. It recruits other germ plasm components. Among these, the core germ plasm protein Vasa, a DEAD-box helicase, Tudor (Tud), and Aubergine (Aub), a Piwi family Pi RNA-binding protein, as well as up to 200 maternally-provided mRNAs. Multiple, independent Oskar protein domains synergize to promote granule phase separation. In the embryo, nuclear germ granules of the phase-separated Oskar promote germ cell divisions thereby increasing PGC number for the next generation (PMID:30260314).</description>
<experiment_llps type="str">
In transgenic flies expressing a GFP-fused Oskar (Osk:GFP) and a Kusabira Orange-fused Vasa (Vasa:KuOr) co-localized within the same granule in vivo (protein localization, microscopy). Cytoplasmic germ granules displayed properties of phase transitioned condensates by FRAP and FLIP. Vasa:KuOr co-localized with Osk:GFP in 95.1% of nuclear germ granules and Vasa:KuOr nuclear granules without Osk:GFP were not observed. Depletion of germ granule components such as Oskar and Vasa prevents the assembly of germ granules during oogenesis in vivo. When transiently overexpressed in S2R+ cells (genetic transformation) not expressing core germ plasm proteins, Short Osk fused at its N-terminus with mCherry (Short mCherry:Osk) organized round, membraneless and often hollow (morphology) nuclear germ granules (particle size and count by microscopy), while Long Osk did not. Short Osk:mCherry formed nuclear granules even in HEK293 cells, so it is able to assemble into nuclear granules in heterologous cell systems independent of other germ plasm proteins. Aliphatic alcohols 1,6 hexanediol and 1,5-pentanediol that disrupt weak hydrophobic interactions and cause rapid disassembly of liquid droplets but not of hydrogels did not dissolve nuclear germ granules formed in S2R+ cells even at high concentrations (particle size and count by microscopy), suggesting a more gel-like state. The size of nuclear granules formed by Osk-DLOTUS, Osk-DL1 and Osk-DL2 mutants was similar to those formed by full length Short Osk, while deletion of the SGNH domain lead to the formation of much larger nuclear granules (particle size and count by microscopy), which lacked the appearance of a hollow core. The ability of Short Osk to homo-dimerize, interact with Vasa, Valois and LASP or bind RNA is dispensable for nuclear granule formation, nor were the LC sequence or the IDR necessary. However, each domain appeared to affect the efficiency of granule formation (particle size and count by microscopy): despite expressing similar amounts of protein, cells with truncated versions contained significantly more diffusely distributed Short Osk (protein localization). No in vitro studies were performed (PMID:30260314).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30260314); dynamic exchange of molecules with surrounding solvent (PMID:30260314); morphological traits (PMID:30260314)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known (PMID:30260314)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
regulator of spatial patterns</functional_class>
<date type="str">
2019-09-11</date>
</P25158-2>
<P08287 type="dict">
<id type="str">
72</id>
<phase_id type="str">
77</phase_id>
<common_name type="str">
Histone H1</common_name>
<name type="str">
Histone H1.11L</name>
<accession type="str">
P08287</accession>
<organism type="str">
Gallus gallus</organism>
<sequence type="str">
MSETAPAPAAEAAPAAAPAPAKAAAKKPKKAAGGAKARKPAGPSVTELITKAVSASKERKGLSLAALKKALAAGGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFRLSKKPGEVKEKAPKKKASAAKPKKPAAKKPAAAAKKPKKAVAVKKSPKKAKKPAASATKKSAKSPKKVTKAVKPKKAVAAKSPAKAKAVKPKAAKPKAAKPKAAKAKKAAAKKK</sequence>
<gene type="str">
H11L_CHICK</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Highly disordered polycationic C-terminal tail</segment>
<boundaries type="str">
115-225</boundaries>
<region_ref type="str">
30301810</region_ref>
<partners type="str">
1) DNA (strictly required for LLPS)</partners>
<determinants type="str">
1) stoichiometry of the components; 2) protein concentration of Histone H1; 3) salt concentration</determinants>
<forms type="str">
phase-separated droplets</forms>
<organelles type="str">
euchromatin</organelles>
<pmids type="str">
30301810 (research article), 30389709 (review)</pmids>
<description type="str">
The highly disordered C-terminal tail (CH1) of Histone H1 condenses internucleosomal linker DNA in chromatin in a way that is still poorly understood. Moreover, CH1 is phosphorylated in a cell cycle-dependent manner that correlates with changes in the chromatin condensation level. In S phase, phosphorylation correlates with a more open chromatin structure that would facilitate replication and transcription and, in M phase, probably enables rearrangement of the condensed chromatin structure (e.g., to allow entry of condensins). The chromatin-condensing properties of H1 are mainly conferred by its ca. 100-residue-long polycationic C-terminal tail, CH1. In chromatin, the tail, which contains several phosphorylation sites, interacts with and condenses internucleosomal linker DNA CH1 remains disordered in the DNA-bound state, despite its nanomolar affinity. Phase-separated droplets (coacervates) form, containing higher-order assemblies of CH1/DNA complexes. Phase-separated condensates form, containing higher-order structures that are highly sensitive to the phosphorylation state of H1, suggesting a mechanism by which condensation of the chromatin fiber and other assemblies might be regulated (PMID:30301810).</description>
<experiment_llps type="str">
The in vitro binding affinity (physical interaction) of CH1 for 36-bp DNA by ITC, at approximately “physiological” ionic strength was Kd=292 nM. When CH1 was added to a solution of 36-bp DNA it became increasingly cloudy (change in optical properties). The DNA-bound polypeptide was highly dynamic as assessed by NMR. Solutions of complexes containing a 1:1 molar ratio of (phosphorylated) CH1-P or CH1:20 bp DNA were both visibly cloudy (change in optical properties). Optical microscopy revealed the presence of micrometer-scale droplets (particle size and count). Addition of salt weakened LLPS. However, long-range order in the coacervate phase was highly phosphorylation- and salt-dependent as assessed by NMR (PMID:30301810).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30301810)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
157|S|phosphorylation|affects|PMID:30301810|CDK2|Notes: Cell cycle-dependent phosphorylation at three serine residues dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate.; 175|S|phosphorylation|affects|PMID:30301810|CDK2|Notes: Cell cycle-dependent phosphorylation at three serine residues dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate.; 193|S|phosphorylation|affects|PMID:30301810|CDK2|Notes: Cell cycle-dependent phosphorylation at three serine residues dramatically alters higher-order structure in the coacervate and reduces partitioning to the coacervate.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:30301810); complex coacervation (PMID:30301810); protein-DNA interaction (PMID:30301810)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</P08287>
<Q5BI67 type="dict">
<id type="str">
73</id>
<phase_id type="str">
78</phase_id>
<common_name type="str">
Sec16</common_name>
<name type="str">
LP14866p</name>
<accession type="str">
Q5BI67</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MLHNNAPWLPPHQQQQQQAPQQHPTPQQQHAMPQQQQTLPAQQQQQQVYASQMFQQHQPNYWPEDQHQQQQQPQSLNYNNYFPGQQQQHPMQQQQLPPQQQLPPQQQQPTQQQHTIQQQLYYPTQQQPQVPAPAEPALDSFDNNNSGGGGGGGRSDGWGDWGDWNDNSNNNNSNGTDGLLEPTGQLLEDSFNVQSSQGSWQAFATSNNVNNNGELPPPANPQSTSLQQQPLNQQSIPLLHQQPQSPPELGQEPELDAIVPPQAFQNQPPTAAPPPTSLTSFSAQMTAVGSPIYAVGASSAHSAGVGASPAPPTGVVAPPAHLAGIGAPPAHLAGVGASPAPSALVGASPAPIIGVGAPPVGAPPVGAPPADATTIAPPAALPPSIVPSSGSNPFKRSTGLNKRVNIMADPAAGAPSPPAPAAAIAPVAPVAPIPPPADQLFGMPAEAHGEGFNLIAAPPVEASLGTPLSAPIPAPIPVPNASLYASPAVPQAFAHLEPDNQEVLSAPNDERAQYLQTSHLSEQLGEGEADQDAGLLPPPGLSRLVLGQPELDSQQQRQVTGATEQPPLNVAQAAALHMQERRADGEDTSDGEQQVRNIQTPPRRVVTGVETNAPSLREQREVVLDGENLEDREAIPPPTLAELPTTSVHHNILPDEAEQLHHNNPPQAMTPLNAQQPHQQQSTLQQQHQQHSTTQQEKKRAAVGRRTTASLDLESDESDEFLQSERERDRERERRDLMEERHSRGRSHSHYPYEGETEDSVRGAAHHETKSLRETHHKRNHDSARSRRHQDPKVERERERDRERDRTWRRRSNKYHSGGEDPDRSYDHSRRYNNSNYEGESDNPEYNHMGDAELDGSGGRSSKTSRHRRSAAEEDFDDYERERNRSRRSTKPQSSAEKSRSSGGRRNYENSGRSARADDGRRRYHDQRNPGAQYPVSATGYVPYGMYEQMSRNPQVYADMYAKFYGQMINSMNAAVSAAASKGGVPAGAGVIPGLMPSAVPVSAAQLVAATSGGSVSGSSEAAMLRERERAAADAAPSTYGGVAGTAGPVTNTAVARPPRRRTPLQFSRPHLVASYAMSLLLKVKPKYAGRGRLRNDVEVAPPRIRDGTSSLLRMYPGPLQGRKLHKDKIISFCKEQIRLGPTKGCTALYATQKKPQGSVTKYRASHALMWHLLILLLRQNGYIADTDVGDLLLENQQEYPYDPSEFEAENEPDADAEQDAAAPADKTVDSDLDSESAAGVTPAEPLAAGAATSSINGADAANAATPLSEQAATDKFRSYVLRGNVEEALQWATDNGLWTHAFFLALYEDRYALTDVAQKFLNRAIKANDPLQTLYQMKSCHTPACVSQLRDEQWGDWRSHLSILVTNKSRQPEYDRSSVVALGDTLFQRGDIYAAHFCYLVAQEEFGRYDSSATELTTLTANVPRLILLGSSHYKHFNEFASNEAIIMTEIYEYARSLFDPKFSIAHFQHYKFLLATRILDYGQHFRCTNYLEQIARHIELKPESYDSNFIQRVCGLAERLRYHDPILINRVSFASPPNATSKDSAAAEEKAWLRQLRSLAYVQPQQEQLQQLQQNQQVQQEQNDIDQQFAEVNKQFRELNMQYESNSNMENTLQPQLPPVDQQPPQQQQQVLSESYQQPTQQYYEPPPQAPTESDPYGQGQPSYYDPNAGQLHYDPNAAQHQYDQQQPQPQPTPSYGQIEPGTEAYQPGQATADPAAVPSGYGYDYWSGTQQPPYGDELQQQTRPAISMPKSKSYGDEDDGGSGGVADPGQKTKPVGSSEAAGKQQASGKQANSGSDLGAPGNKNAGWFGGLWNKLSLKPKNQMILPDDKNPAIVWDKERKCWTNTEGNGDEAESFKPPPKMSDLGMALGGPPAAPIGNAGLGMGLMPVANNAPGSHQSAPLMDQQTPSQPQTYGSPIDYTAAPAPELIPTVPSPAPLSVPSSAPASCREE</sequence>
<gene type="str">
SEC16</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-1953</boundaries>
<region_ref type="str">
25386913</region_ref>
<partners type="str">
1) Sec24AB (strictly required for LLPS); 2) Sec23 (strictly required for LLPS); 3) Sec31 (present in Sec bodies but not required for the formation); 4) Sec24CD (present in Sec bodies but not required for the formation)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
Sec body; cytoplasmic protein granule</organelles>
<pmids type="str">
25386913 (research article), 27874829 (research article)</pmids>
<description type="str">
Sec body formation results from the inhibition of a major anabolic pathway, the protein transport through the secretory pathway, upon amino-acid starvation of Drosophila cells. The inhibition of protein transport through the secretory pathway upon amino-acid starvation is accompanied by the remodeling of ERES and the formation of a type of pro-survival stress assembly with liquid droplet properties, the Sec body, where COPII coat proteins and Sec16 are stored and protected from degradation during the period of stress in a reversible manner. These sec16-positive spherical structures also contain COPII subunits Sec23, the two Sec24 orthologs Sec24AB and Sec24CD, and Sec31. Transport in the early secretory pathway via COPI and COPII vesicle formation is not required for the formation of Sec bodies. Sec24AB and Sec16 are required for Sec body assembly, while Sec24CD is not. The N-terminal LC region of Sec24AB (residues 1-415) plays a key role in recruitment of Sec24 to Sec bodies, but it is not sufficient for their formation. Starvation leads to ERES component stabilization that is inhibited when Sec bodies do not form. Therefore, Sec body formation is instrumental to efficient resumption of protein transport through the secretory pathway that contributes to cell survival and growth after re-feeding (PMID:25386913). dPARP16 is an enzyme necessary and sufficient to catalyse MARylation and Sec body formation during amino-acid starvation. The ERES component Sec16 gets MARylated by dPARP16 on its C-terminus in an amino-acid starvation specific manner. This event initiates the formation of the Sec bodies. dPARP16 catalytic activity is necessary and sufficient for both amino-acid starvation induced mono-ADP-ribosylation and subsequent Sec body formation (PMID:27874829).</description>
<experiment_llps type="str">
When Sec24AB-depleted cells (by RNA interference) are starved, the normal Sec body formation is impaired (particle size and count by microscopy), Sec23 depletion also results in the same in vivo phenotype. Sec24CD depletion (by RNA interference) did not lead to the same phenotype as Sec24AB depletion and Sec bodies form seemingly normally (particle size and count by microscopy) in vivo. The GFP-fused LC region of Sec24AB (residues 1-415) is largely recruited to ERES under normal growth conditions in vivo although not as efficiently as full-length Sec24AB (particle size and count by microscopy). Under in vivo starvation conditions, it localizes to Sec bodies (protein localization) as full-length Sec24AB and seems to lead to their enlargement. Conversely, the non-LC region of Sec24AB is mostly cytoplasmic and remains largely so upon starvation, although a small pool is recruited to the Sec bodies (particle size and count by microscopy). This shows that the N-terminal LC region of Sec24AB plays a key role in recruitment of Sec24 to Sec bodies (PMID:25386913). Amino-acid starvation leads to the formation of mono ADP-ribosylation (MARylation) spots visualised with GFP-MAD in vivo (particle size and count by microscopy). PARPs were tested for their role in GFP-MAD spot formation (other PTMs) and Sec-body formation upon amino-acid starvation and showed that those strictly depends on dPARP16 in vivo (particle size and count) as dPARP16 depletion by RNA interference completely prevents their formation as does the expression of a catalytic mutant or a mutant lacking the membrane anchoring region of dPARP16. A significant number of Sec bodies (Sec16 marker) are formed adjacent to, or overlapping with, GFP-MAD spots (protein co-localization). When cherry-MAD and Sec16-GFP-CAAX (fusion protein) are co-transfected in S2 cells (genetic transformation) in growing conditions, the cherry-MAD remains diffuse (protein localization). However, it strongly co-localises with Sec16-GFP-CAAX at the plasma membrane upon amino-acid starvation (protein localization, protein co-lacalization). Upon amino-acid starvation, the the SRCD (Starvation Response Conserved Domain; residues 1805–1848) within the C-terminus of Sec16 gets MARylated by dPARP16 that is a key event for in vivo Sec body formation (PMID:27874829).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:25386913); dynamic exchange of molecules with surrounding solvent (PMID:25386913); morphological traits (PMID:25386913); reversibility of formation and dissolution (PMID:25386913)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
1805-1848|EDK|mono ADP-ribosylation|enables|PMID:27874829|PARP16|Notes: mono ADP-ribosylation of Sec16 by dPARP16 is activated by amino-acid starvation and it is critical for Sec body formation.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q5BI67>
<A1Z813 type="dict">
<id type="str">
102</id>
<phase_id type="str">
78</phase_id>
<common_name type="str">
Sec24AB</common_name>
<name type="str">
Sec24AB ortholog, isoform A</name>
<accession type="str">
A1Z813</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MSTYNPNFVPPAHAPMPLNGNNFVNGVQGSVQQQPGPPPGQQYIPQKQPQQFQQPPPAAAFPGAGAPGNVPPPQQFNSGITNQFLPPTSGAATPLQQLPPSTLPPHLRPPAANGPPLTNGSNGASSANSSRTASPRPVGAAPQYAQGPIAAALNNPPLASGLRPSPQPTHQSLANLTSNLENLNLNTTRANGGTSILPQPQTQQQYAPTVTQKDGRGVASAQTGPPQFNDANSLLAASGVAAALVPNAMATPFSGQKPPNLAPNPAKMFGSASMAGRPTPAGQRIPYGVPPPTNPEQQSQQNNNLQNAPPPPRVGAVWPPSLPNVAAPGAQPMMPPAQQTPQTYPYSQVYQPGPQQQPPPPQSAVQPPPPGMFGTQPTGAPLQYQAQAPPQAYGQHPQQAPQTAPGGPYGTTAPLNVAQQGFSRLWGQDTIDLMQNRHILTPATLPPPKVVLHNQFHESINCSPSIMRCTLTKIPESNSLLQKSRLPLGIVIHPFRDVNSLPVIQCINIVRCRLCRTYINPFVYFVDSKMWKCNLCYRVNELPDDFQFDPATKTYGDVTRRPEVRSSTIEFIAPSEYMLRPPQPAMYLFLFDVSIIAQQSGYLEAACAVLNRHLDEMPGDARTQVGFICFDSFVHFYSMAEGLNQPHEMTLLDIEDPFLPRPDSLLVNLKECKELVRDLLKQLPKRFAHTHDPGSALGAALQVAFKLMQASGGRITVFQSCLPNKGPGALEPREDPNNRSAKDVAHLNPATDFYKRFALECSGYQIACDLFLMNQQYSDMATISGISKHSGGCVHHFPLYQKTKPHMVESFRSCFKRYLTRKIGFEAVMRIRCTRGLQVHTFHGNFFVRSTDLLSLPNVNPDAGYGMQISYEESLTDAKTICFQAALLYTNSEGERRIRVHTVCLPVTASLPEVMHSADTEAIIGLLSKMAVDRSVASNLSDARDAFINATIDVYNAFKIAQNLPSGQSGQLIAPRSLALLPLYILALLKHPAFRVGTSTRLDDRVYAMDCMKTLPLDQLMKYVYPELYKIDALIYHARNSNISSNQDDDEDEDEPLPELPRLQLSAEHLDSRSIFLMDCGTLIMIYVGLNVPPDVLEAVLGISSTAELGDYVYGLPNVVSNENDVLKRFILRLNYDKPYSALVQIIRDTSTAKGQFTERLTDDRSESSLSYYEFLQHIRAQVK</sequence>
<gene type="str">
SEC24AB</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
LC region with polar and P-rich blocks</segment>
<boundaries type="str">
1-415</boundaries>
<region_ref type="str">
25386913</region_ref>
<partners type="str">
1) Sec16 (strictly required for LLPS); 2) Sec23 (strictly required for LLPS); 3) Sec31 (present in Sec bodies but not required for the formation); 4) Sec24CD (present in Sec bodies but not required for the formation)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
Sec body; cytoplasmic protein granule</organelles>
<pmids type="str">
25386913 (research article), 27874829 (research article)</pmids>
<description type="str">
Sec body formation results from the inhibition of a major anabolic pathway, the protein transport through the secretory pathway, upon amino-acid starvation of Drosophila cells. The inhibition of protein transport through the secretory pathway upon amino-acid starvation is accompanied by the remodeling of ERES and the formation of a type of pro-survival stress assembly with liquid droplet properties, the Sec body, where COPII coat proteins and Sec16 are stored and protected from degradation during the period of stress in a reversible manner. These sec16-positive spherical structures also contain COPII subunits Sec23, the two Sec24 orthologs Sec24AB and Sec24CD, and Sec31. Transport in the early secretory pathway via COPI and COPII vesicle formation is not required for the formation of Sec bodies. Sec24AB and Sec16 are required for Sec body assembly, while Sec24CD is not. The N-terminal LC region of Sec24AB (residues 1-415) plays a key role in recruitment of Sec24 to Sec bodies, but it is not sufficient for their formation. Starvation leads to ERES component stabilization that is inhibited when Sec bodies do not form. Therefore, Sec body formation is instrumental to efficient resumption of protein transport through the secretory pathway that contributes to cell survival and growth after re-feeding (PMID:25386913). dPARP16 is an enzyme necessary and sufficient to catalyse MARylation and Sec body formation during amino-acid starvation. The ERES component Sec16 gets MARylated by dPARP16 on its C-terminus in an amino-acid starvation specific manner. This event initiates the formation of the Sec bodies. dPARP16 catalytic activity is necessary and sufficient for both amino-acid starvation induced mono-ADP-ribosylation and subsequent Sec body formation (PMID:27874829).</description>
<experiment_llps type="str">
When Sec24AB-depleted cells (by RNA interference) are starved, the normal Sec body formation is impaired (particle size and count by microscopy), Sec23 depletion also results in the same in vivo phenotype. Sec24CD depletion (by RNA interference) did not lead to the same phenotype as Sec24AB depletion and Sec bodies form seemingly normally (particle size and count by microscopy) in vivo. The GFP-fused LC region of Sec24AB (residues 1-415) is largely recruited to ERES under normal growth conditions in vivo although not as efficiently as full-length Sec24AB (particle size and count by microscopy). Under in vivo starvation conditions, it localizes to Sec bodies (protein localization) as full-length Sec24AB and seems to lead to their enlargement. Conversely, the non-LC region of Sec24AB is mostly cytoplasmic and remains largely so upon starvation, although a small pool is recruited to the Sec bodies (particle size and count by microscopy). This shows that the N-terminal LC region of Sec24AB plays a key role in recruitment of Sec24 to Sec bodies (PMID:25386913). Amino-acid starvation leads to the formation of mono ADP-ribosylation (MARylation) spots visualised with GFP-MAD in vivo (particle size and count by microscopy). PARPs were tested for their role in GFP-MAD spot formation (other PTMs) and Sec-body formation upon amino-acid starvation and showed that those strictly depends on dPARP16 in vivo (particle size and count) as dPARP16 depletion by RNA interference completely prevents their formation as does the expression of a catalytic mutant or a mutant lacking the membrane anchoring region of dPARP16. A significant number of Sec bodies (Sec16 marker) are formed adjacent to, or overlapping with, GFP-MAD spots (protein co-localization). When cherry-MAD and Sec16-GFP-CAAX (fusion protein) are co-transfected in S2 cells (genetic transformation) in growing conditions, the cherry-MAD remains diffuse (protein localization). However, it strongly co-localises with Sec16-GFP-CAAX at the plasma membrane upon amino-acid starvation (protein localization, protein co-lacalization). Upon amino-acid starvation, the the SRCD (Starvation Response Conserved Domain; residues 1805–1848) within the C-terminus of Sec16 gets MARylated by dPARP16 that is a key event for in vivo Sec body formation (PMID:27874829).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:25386913); dynamic exchange of molecules with surrounding solvent (PMID:25386913); morphological traits (PMID:25386913); reversibility of formation and dissolution (PMID:25386913)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</A1Z813>
<Q9VNF8 type="dict">
<id type="str">
103</id>
<phase_id type="str">
78</phase_id>
<common_name type="str">
Sec23</common_name>
<name type="str">
Secretory 23, isoform A</name>
<accession type="str">
Q9VNF8</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MTTYEEFIQQNEDRDGVRLTWNVWPSSRIEASRLVVPLACLYQPLKERPDLPPIQYEPVLCTRSNCRAILNPLCQVDYRAKLWVCNFCFQRNPFPPQYAAISEQHQPAELIPGFSTIEYTITRAPTMPPVFIFLVDTCMDEEELDALKDSLQMSLSLLPTNALVGLITFGKMIQVHELGAEGCSKSYVFRGTKDLTAKQVQDMLGIGRGAAPGPQQQQHLPGQPAGAAAPVPPAHRFLQPIGQCDAALGDLLSELQRDPWPVPQGKRYLRSTGAALSIAVGLLECTYPNTGGRIMTFVGGPCSQGPGQVVDDELKHPIRSHHDIHKDNVRFMKKAIKHYDALALRAATNGHSVDIYSCALDQTGLLEMKQLCNSTGGHMVMGDSFNSSLFKQTFQRVFARDGRNDLKMAFNATLEVKCSRELKISGGIGSCVSLNVKSPSVSDVEIGMGNTVQWKLCTLNPSSTVAYFFEVVNQHAAPIPQGGRGCIQFITQYQHPSGQRRIRVTTLARNWADATSNVHHISAGFDQEAAAVLMARMVVYRAETDEGPDILRWVDRQLIRLCQKFGEYSKDDPNSFRLSQNFSLFPQFMYHLRRSQFLQVFNNSPDETTFYRHMLMREDLTQSLIMIQPILYSYSFNGPPEPVLLDTASIQADRILLMDTFFQILIYHGETIAQWRALKYQDMPEYENFKQLLQAPVDDAQEILQTRFPMPRYIDTEHGGSQARFLLSKVNPSQTHNNMYAYGQDGGAPVLTDDVSLQLFMEHLKKLAVSTTT</sequence>
<gene type="str">
SEC23</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-773</boundaries>
<region_ref type="str">
25386913</region_ref>
<partners type="str">
1) Sec16 (strictly required for LLPS); 2) Sec24AB (strictly required for LLPS); 3) Sec31 (present in Sec bodies but not required); 4) Sec24CD (present in Sec bodies but not required)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
Sec body; cytoplasmic protein granule</organelles>
<pmids type="str">
25386913 (research article), 27874829 (research article)</pmids>
<description type="str">
Sec body formation results from the inhibition of a major anabolic pathway, the protein transport through the secretory pathway, upon amino-acid starvation of Drosophila cells. The inhibition of protein transport through the secretory pathway upon amino-acid starvation is accompanied by the remodeling of ERES and the formation of a type of pro-survival stress assembly with liquid droplet properties, the Sec body, where COPII coat proteins and Sec16 are stored and protected from degradation during the period of stress in a reversible manner. These sec16-positive spherical structures also contain COPII subunits Sec23, the two Sec24 orthologs Sec24AB and Sec24CD, and Sec31. Transport in the early secretory pathway via COPI and COPII vesicle formation is not required for the formation of Sec bodies. Sec24AB and Sec16 are required for Sec body assembly, while Sec24CD is not. The N-terminal LC region of Sec24AB (residues 1-415) plays a key role in recruitment of Sec24 to Sec bodies, but it is not sufficient for their formation. Starvation leads to ERES component stabilization that is inhibited when Sec bodies do not form. Therefore, Sec body formation is instrumental to efficient resumption of protein transport through the secretory pathway that contributes to cell survival and growth after re-feeding (PMID:25386913). dPARP16 is an enzyme necessary and sufficient to catalyse MARylation and Sec body formation during amino-acid starvation. The ERES component Sec16 gets MARylated by dPARP16 on its C-terminus in an amino-acid starvation specific manner. This event initiates the formation of the Sec bodies. dPARP16 catalytic activity is necessary and sufficient for both amino-acid starvation induced mono-ADP-ribosylation and subsequent Sec body formation (PMID:27874829).</description>
<experiment_llps type="str">
When Sec24AB-depleted cells (by RNA interference) are starved, the normal Sec body formation is impaired (particle size and count by microscopy), Sec23 depletion also results in the same in vivo phenotype. Sec24CD depletion (by RNA interference) did not lead to the same phenotype as Sec24AB depletion and Sec bodies form seemingly normally (particle size and count by microscopy) in vivo. The GFP-fused LC region of Sec24AB (residues 1-415) is largely recruited to ERES under normal growth conditions in vivo although not as efficiently as full-length Sec24AB (particle size and count by microscopy). Under in vivo starvation conditions, it localizes to Sec bodies (protein localization) as full-length Sec24AB and seems to lead to their enlargement. Conversely, the non-LC region of Sec24AB is mostly cytoplasmic and remains largely so upon starvation, although a small pool is recruited to the Sec bodies (particle size and count by microscopy). This shows that the N-terminal LC region of Sec24AB plays a key role in recruitment of Sec24 to Sec bodies (PMID:25386913). Amino-acid starvation leads to the formation of mono ADP-ribosylation (MARylation) spots visualised with GFP-MAD in vivo (particle size and count by microscopy). PARPs were tested for their role in GFP-MAD spot formation (other PTMs) and Sec-body formation upon amino-acid starvation and showed that those strictly depends on dPARP16 in vivo (particle size and count) as dPARP16 depletion by RNA interference completely prevents their formation as does the expression of a catalytic mutant or a mutant lacking the membrane anchoring region of dPARP16. A significant number of Sec bodies (Sec16 marker) are formed adjacent to, or overlapping with, GFP-MAD spots (protein co-localization). When cherry-MAD and Sec16-GFP-CAAX (fusion protein) are co-transfected in S2 cells (genetic transformation) in growing conditions, the cherry-MAD remains diffuse (protein localization). However, it strongly co-localises with Sec16-GFP-CAAX at the plasma membrane upon amino-acid starvation (protein localization, protein co-lacalization). Upon amino-acid starvation, the the SRCD (Starvation Response Conserved Domain; residues 1805–1848) within the C-terminus of Sec16 gets MARylated by dPARP16 that is a key event for in vivo Sec body formation (PMID:27874829).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:25386913); dynamic exchange of molecules with surrounding solvent (PMID:25386913); morphological traits (PMID:25386913); reversibility of formation and dissolution (PMID:25386913)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q9VNF8>
<P24928 type="dict">
<id type="str">
74</id>
<phase_id type="str">
79</phase_id>
<common_name type="str">
RPB1</common_name>
<name type="str">
DNA-directed RNA polymerase II subunit RPB1</name>
<accession type="str">
P24928</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPASPKYTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN</sequence>
<gene type="str">
POLR2A</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal tail with 52 heptade repeats of YSPTSPS</segment>
<boundaries type="str">
1593-1960</boundaries>
<region_ref type="str">
30127355</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) phosphorylation state; 2) valency of CTD</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
RNA polymerase II, holoenzyme; POLII clusters</organelles>
<pmids type="str">
29849146 (research article), 29930094 (research article), 30127355 (research article)</pmids>
<description type="str">
The largest subunit of Pol II, RPB1, contains a C-terminal low-complexity domain, CTD, that is critical for pre-mRNA synthesis and co-transcriptional processing. The CTD is conserved from humans to fungi, but differs in the number of its heptapeptide repeats, with the consensus sequence YSPTSPS. Truncating the CTD of RPB1 in S. cerevisiae to fewer than 13 repeats leads to growth defects, and a minimum of eight repeats is required for yeast viability. The CTD serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Assembly of the preinitiation complex at Pol II promoters requires an unphosphorylated CTD and that subsequent CTD phosphorylation at S5 CTD residues by the cyclin-dependent kinase 7 (CDK7) in transcription factor IIH (TFIIH) stimulates the transition of Pol II into active elongation. Therefore, phosphorylation at S5 is incompatible with CTD phase separation and transfers the CTD from the highly concentrated state within droplets to the dispersed pool (PMID:30127355). Phase separated condensates formed by the LC domains of FUS, EWS and TAF15 when they are translocated onto a variety of different DNA-binding domains in oncogenic fusion proteins directly bind the C-terminal domain (CTD) of RNA polymerase II in a manner reversible by phosphorylation of the iterated, heptad repeats of the CTD (PMID:24267890, PMID:28945358). Mediator and Pol II, both of which can form small transient and large stable clusters in living embryonic stem cells, are co-localized in the stable clusters, which associate with chromatin, have properties of phase-separated condensates, and are sensitive to transcriptional inhibitors. Large clusters of Mediator, recruited by transcription factors at large or clustered enhancer elements probably interact with large Pol II clusters in transcriptional condensates in vivo (PMID:29930094).</description>
<experiment_llps type="str">
In vitro differential interference contrast (DIC) microscopy revealed the formation of micrometer-sized droplets (particle size and count) at a concentration of 20 μM MBP-fused human Pol II CTD in the presence of 5–10% of dextran. Fluorescence microscopy demonstrated that MBP-hCTD molecules were strongly concentrated within the droplet interior compared to the surrounding milieu (protein localization). At higher dextran concentration (16%), droplets could be detected at a concentration of 5 μM MBP-hCTD and the number of droplets increased with increasing protein concentration. hCTD also underwent LLPS after cleavage of the maltose-binding protein (MBP) tag, and droplet formation was robust against changes in ionic strength and against incubation of the sample for 1 h at different temperatures (particle size and count by microscopy). As expected for such interactions, liquid phase separation of yCTD and hCTD was counteracted by addition of 5–10% 1,6-hexanediol. The length of CTD influences the stability and dynamics of LLPS droplets, with a longer CTD (mutation) leading to stronger CTD–CTD interactions and less dynamic droplets (morphology), and also affects POLII clustering (particle size and count by microscopy). Using two engineered human cell lines that express a fluorescent Dendra2-tagged version of RPB1 (creation of a fusion protein), cells with the truncated, yeast-like CTD (25R) showed less Pol II clustering in vivo (particle size and count by microscopy) than cells with full-length human CTD (52R). CDK7-phosphorylated hCTD was no longer able to form droplets. In addition, phosphorylation of preformed hCTD droplets by human CDK7 caused gradual shrinking and ultimately disappearance of hCTD droplets (particle size and count by microscopy) (PMID:30127355).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30127355); morphological traits (PMID:30127355); sensitivity to 1,6-hexanediol (PMID:30127355)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
1593-1960|S|hyperphosphorylation|abolishes|PMID:30127355|CDK7|Notes: Phosphorylation of the 5th S residues in the YSPTSPS heptide repeates by CDK7 (protein kinase subunit of transcription factor IIH (TFIIH)) abolishes phase separation ability and thus liberates POLII from the pre-initiation complex for transcription elongation.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P24928>
<P04050 type="dict">
<id type="str">
75</id>
<phase_id type="str">
80</phase_id>
<common_name type="str">
RPB1</common_name>
<name type="str">
DNA-directed RNA polymerase II subunit RPB1</name>
<accession type="str">
P04050</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR</sequence>
<gene type="str">
RPO21</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal tail with 26 heptade repeats of YSPTSPS</segment>
<boundaries type="str">
1542-1733 </boundaries>
<region_ref type="str">
30127355</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) phosphorylation state; 2) valency of CTD</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
RNA polymerase II, holoenzyme; POLII clusters</organelles>
<pmids type="str">
30127355 (research article)</pmids>
<description type="str">
The largest subunit of Pol II, RPB1, contains a C-terminal low-complexity domain, CTD, that is critical for pre-mRNA synthesis and co-transcriptional processing. The CTD is conserved from humans to fungi, but differs in the number of its heptapeptide repeats, with the consensus sequence YSPTSPS. Truncating the CTD of RPB1 in S. cerevisiae to fewer than 13 repeats leads to growth defects, and a minimum of eight repeats is required for yeast viability. The CTD serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Like the human CTD, the shorter yeast CTD formed droplets in a concentration-dependent manner. Phosphorylation of yeast CTD by the yeast TFIIH kinase subcomplex inhibited phase separation (PMID:30127355).</description>
<experiment_llps type="str">
Protein concentration-dependent liquid phase separation of glutathione S-transferase (GST)-tagged yCTD (GST-yCTD fusion protein) was observed in the presence of 16% dextran in vitro (particle size and count by microscopy). In vitro formation of yeast CTD droplets was also resistant against changes in ionic strength and temperature (particle size and count by microscopy). As expected for such interactions, liquid phase separation of yCTD and hCTD was counteracted by addition of 5–10% 1,6-hexanediol in vitro (particle size and count by microscopy). When fluorescently labeled Pol II was added to preformed CTD droplets at a concentration of 0.02 μM in vitro, Pol II located to CTD droplets (protein co-localization) as assessed by fluorescence microscopy. Phosphorylation of yCTD by the yeast TFIIH kinase subcomplex inhibited phase separation (particle size and count by microscopy) (PMID:30127355).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30127355); morphological traits (PMID:30127355); sensitivity to 1,6-hexanediol (PMID:30127355)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
1542-1733|S|hyperphosphorylation|abolishes|PMID:30127355|KIN28|Notes: Phosphorylation of the 5th S residues in the YSPTSPS heptide repeates by KIN28 (a subunit of transcription factor IIH (TFIIH)) abolishes phase separation ability and thus liberates POLII from the pre-initiation complex for transcription elongation.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P04050>
<O60563 type="dict">
<id type="str">
76</id>
<phase_id type="str">
81</phase_id>
<common_name type="str">
Cyclin-T1, CYCT1</common_name>
<name type="str">
Cyclin-T1</name>
<accession type="str">
O60563</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEGERKNNNKRWYFTREQLENSPSRRFGVDPDKELSYRQQAANLLQDMGQRLNVSQLTINTAIVYMHRFYMIQSFTQFPGNSVAPAALFLAAKVEEQPKKLEHVIKVAHTCLHPQESLPDTRSEAYLQQVQDLVILESIILQTLGFELTIDHPHTHVVKCTQLVRASKDLAQTSYFMATNSLHLTTFSLQYTPPVVACVCIHLACKWSNWEIPVSTDGKHWWEYVDATVTLELLDELTHEFLQILEKTPNRLKRIWNWRACEAAKKTKADDRGTDEKTSEQTILNMISQSSSDTTIAGLMSMSTSTTSAVPSLPVSEESSSNLTSVEMLPGKRWLSSQPSFKLEPTQGHRTSENLALTGVDHSLPQDGSNAFISQKQNSKSVPSAKVSLKEYRAKHAEELAAQKRQLENMEANVKSQYAYAAQNLLSHHDSHSSVILKMPIEGSENPERPFLEKADKTALKMRIPVAGGDKAASSKPEEIKMRIKVHAAADKHNSVEDSVTKSREHKEKHKTHPSNHHHHHNHHSHKHSHSQLPVGTGNKRPGDPKHSSQTSNLAHKTYSLSSSFSSSSSTRKRGPSEETGGAVFDHPAKIAKSTKSSSLNFSFPSLPTMGQMPGHSSDTSGLSFSQPSCKTRVPHSKLDKGPTGANGHNTTQTIDYQDTVNMLHSLLSAQGVQPTQPTAFEFVRPYSDYLNPRSGGISSRSGNTDKPRPPPLPSEPPPPLPPLPK</sequence>
<gene type="str">
CCNT1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
IDR with H-rich region (HRD)</segment>
<boundaries type="str">
462-654</boundaries>
<region_ref type="str">
29849146</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) salt concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
nuclear speckle</organelles>
<pmids type="str">
29849146 (research article), 30663929 (review)</pmids>
<description type="str">
The phase-separated droplets and speckles compartmentalize the kinase and substrate to enable highly efficient reactions, which results in the hyperphosphorylation of the POLII CTD and robust transcriptional elongation and RNA processing. Phase separation being induced by CYCT1 of P-TEFb (a well-defined transcription elongation factor) and DYRK1A (a probable gene-specific elongation factor) expands the regulatory roles of phase separation to the next stage of the transcription cycle. The histidine-rich domain markedly enhances the binding of P-TEFb to the POLII CTD and functional engagement with target genes in cells. Furthermore, some key initiation and elongation factors that phase separate should no longer be viewed as passive passengers waiting to be picked up by the CTD. Rather, they have active roles in recruiting Pol II through multivalent interactions to their droplets and/or speckles that function as hubs where much of transcription and RNA processing is dynamically controlled (PMID:29849146).</description>
<experiment_llps type="str">
Wild-type GFP-fused T1-IDR spontaneously formed micrometre-sized (particle size and count), spherical droplets (morphology) in vitro when studied by microscopy, whereas GFP–T1-IDRΔHRD (mutation) produced only a low level of irregular aggregates (particle size and count, morphology). Mirroring its disruption of the GFP–T1-IDR droplets in vitro, single-particle tracking in U2OS cells of Halo-tagged wild-type CYCT1 and CYCT1ΔHRD proteins at 95 Hz showed that CYCT1ΔHRD diffused faster and showed a smaller bound fraction (8.8%) than did wild-type CYCT1 (13.0%). Also, wild-type CYCT1–Flag formed nuclear speckle-like droplets within Hela cells in vivo, while CYCT1ΔHRD–Flag did not as examined by indirect immunofluorescence staining with anti-Flag monoclonal antibody. 1,6-hexanediol also quickly dissembled the CYCT1 nuclear speckles. Although the POLII CTD itself is a low-complexity sequence, recombinant mCherry-fused CTD23 alone did not phase separate, but it was readily incorporated into droplets when incubated together with GFP–T1-IDR (protein co-localization). Pre-phosphorylation by CAK not only enhanced the incorporation of mCherry–CTD into the GFP–T1-IDR droplets (protein co-localization), but also promoted phase separation overall by producing bigger and brighter droplets (particle size and count) when assessed by microscopy. The hyperphosphorylation of POLII CTD by P-TEFb is promoted by the CYCT1 IDR (other change in phenotype/functional readout), which forms phase-separated droplets and/or speckles in a histidine-rich domain, HRD-dependent manner and recruits the CTD into these compartments (protein co-localization). (PMID:29849146).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29849146); morphological traits (PMID:29849146); sensitivity to 1,6-hexanediol (PMID:29849146)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</O60563>
<Q13627 type="dict">
<id type="str">
77</id>
<phase_id type="str">
82</phase_id>
<common_name type="str">
DYRK1A</common_name>
<name type="str">
Dual specificity tyrosine-phosphorylation-regulated kinase 1A</name>
<accession type="str">
Q13627</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MHTGGETSACKPSSVRLAPSFSFHAAGLQMAGQMPHSHQYSDRRQPNISDQQVSALSYSDQIQQPLTNQVMPDIVMLQRRMPQTFRDPATAPLRKLSVDLIKTYKHINEVYYAKKKRRHQQGQGDDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTSNSVSTSPAMEQSQSSGTTSSTSSSSGGSSGTSNSGRARSDPTHQHRHSGGHFTAAVQAMDCETHSPQVRQQFPAPLGWSGTEAPTQVTVETHPVQETTFHVAPQQNALHHHHGNSSHHHHHHHHHHHHHGQQALGNRTRPRVYNSPTNSSSTQDSMEVGHSHHSMTSLSSSTTSSSTSSSSTGNQGNQAYQNRPVAANTLDFGQNGAMDVNLTVYSNPRQETGIAGHPTYQFSANTGPAHYMTEGHLTMRQGADREESPMTGVCVQQSPVASS</sequence>
<gene type="str">
DYRK1A</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
IDR with H-rich region (HRD)</segment>
<boundaries type="str">
491-686</boundaries>
<region_ref type="str">
29849146</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) salt concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
nuclear speckle</organelles>
<pmids type="str">
29849146 (research article)</pmids>
<description type="str">
The phase-separated droplets and speckles compartmentalize the kinase and substrate to enable highly efficient reactions, which results in the hyperphosphorylation of the CTD and robust transcriptional elongation and RNA processing. Phase separation being induced by CYCT1 of P-TEFb (a well-defined transcription elongation factor) and DYRK1A (a probable gene-specific elongation factor) expands the regulatory roles of phase separation to the next stage of the transcription cycle. Some key initiation and elongation factors that phase separate should no longer be viewed as passive passengers waiting to be picked up by the CTD. Rather, they have active roles in recruiting Pol II through multivalent interactions to their droplets and/or speckles that function as hubs where much of transcription and RNA processing is dynamically controlled (PMID:29849146).</description>
<experiment_llps type="str">
The GFP fusion of the DYRK1A IDR (amino acids 491–686) formed droplets (protein localization) in vitro in an histidine-rich domain, HRD-dependent manner as assessed by microscopy. The deletion of the HRD causes DYRK1A to decrease physical interaction with RNA Pol II, but not DCAF7 as shown by co-immunoprecipitation assay (PMID:29849146).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:29849146)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q13627>
<P03520 type="dict">
<id type="str">
78</id>
<phase_id type="str">
83</phase_id>
<common_name type="str">
Protein P</common_name>
<name type="str">
Phosphoprotein</name>
<accession type="str">
P03520</accession>
<organism type="str">
Vesicular stomatitis Indiana virus</organism>
<sequence type="str">
MDNLTKVREYLKSYSRLDQAVGEIDEIEAQRAEKSNYELFQEDGVEEHTKPSYFQAADDSDTESEPEIEDNQGLYAQDPEAEQVEGFIQGPLDDYADEEVDVVFTSDWKPPELESDEHGKTLRLTSPEGLSGEQKSQWLSTIKAVVQSAKYWNLAECTFEASGEGVIMKERQITPDVYKVTPVMNTHPSQSEAVSDVWSLSKTSMTFQPKKASLQPLTISLDELFSSRGEFISVGGDGRMSHKEAILLGLRYKKLYNQARVKYSL</sequence>
<gene type="str">
P</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-265</boundaries>
<region_ref type="str">
30181255</region_ref>
<partners type="str">
1) Nucleoprotein; 2) RNA-directed RNA polymerase L</partners>
<determinants type="str">
1) temperature</determinants>
<forms type="str">
inclusions, liquid(-like) compartments, viroplasm</forms>
<organelles type="str">
cytoplasmic viral factory; viroplasm</organelles>
<pmids type="str">
30181255 (research article)</pmids>
<description type="str">
RNA viruses that replicate in the cell cytoplasm typically concentrate their replication machinery within specialized compartments. This concentration favors enzymatic reactions and shields viral RNA from detection by cytosolic pattern recognition receptors. Nonsegmented negative-strand (NNS) RNA viruses, which include some of the most significant human, animal, and plant pathogens extant, form inclusions that are sites of RNA synthesis and are not circumscribed by a membrane (viroplasm). The viroplasm shares similarities with cellular protein/RNA structures such as P granules and nucleoli, which are phase-separated liquid compartments. Replication compartments of vesicular stomatitis virus (VSV) have the properties of liquid-like compartments that form by phase separation. The N-RNA:P-L complex is sufficient for transcription of viral mRNA in vitro (PMID:30181255).</description>
<experiment_llps type="str">
Both, the depletion of specific viral proteins using peptide-conjugated morpholino oligomers (PPMOs) and expression of the individual viral proteins of the replication machinery in cells (change in protein concentration) demonstrates that the 3 viral proteins required for replication (P, N and L) are sufficient to drive cytoplasmic phase separation in vivo (protein localization, particle size and count, microscopy). The viral genomic RNA, or the catalytic activity of the L-encoded RNA-dependent RNA polymerase (RdRp) (studied by using a catalytically inactive mutant), is not required for formation of the phase-separated viroplasm (PMID:30181255).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30181255); dynamic exchange of molecules with surrounding solvent (PMID:30181255); morphological traits (PMID:30181255); rheological traits (PMID:30181255)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa; Orsolya Kovács</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P03520>
<P03521 type="dict">
<id type="str">
104</id>
<phase_id type="str">
83</phase_id>
<common_name type="str">
Protein N</common_name>
<name type="str">
Nucleoprotein</name>
<accession type="str">
P03521</accession>
<organism type="str">
Vesicular stomatitis Indiana virus</organism>
<sequence type="str">
MSVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINTTKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDIRGKLDKDWSSFGINIGKAGDTIGIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKKLMDGLTNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTIVSRFKDCAALATFGHLCKITGMSTEDVTTWILNREVADEMVQMMLPGQEIDKADSYMPYLIDFGLSSKSPYSSVKNPAFHFWGQLTALLLRSTRARNARQPDDIEYTSLTTAGLLYAYAVGSSADLAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPDMMQYAKRAVMSLQGLREKTIGKYAKSEFDK</sequence>
<gene type="str">
N</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-422</boundaries>
<region_ref type="str">
30181255</region_ref>
<partners type="str">
1) P protein; 2) RNA-directed RNA polymerase L</partners>
<determinants type="str">
1) temperature</determinants>
<forms type="str">
inclusions,; liquid(-like) compartments, viroplasm</forms>
<organelles type="str">
cytoplasmic viral factory; viroplasm</organelles>
<pmids type="str">
30181255 (research article)</pmids>
<description type="str">
RNA viruses that replicate in the cell cytoplasm typically concentrate their replication machinery within specialized compartments. This concentration favors enzymatic reactions and shields viral RNA from detection by cytosolic pattern recognition receptors. Nonsegmented negative-strand (NNS) RNA viruses, which include some of the most significant human, animal, and plant pathogens extant, form inclusions that are sites of RNA synthesis and are not circumscribed by a membrane (viroplasm). The viroplasm shares similarities with cellular protein/RNA structures such as P granules and nucleoli, which are phase-separated liquid compartments. Replication compartments of vesicular stomatitis virus (VSV) have the properties of liquid-like compartments that form by phase separation. The N-RNA:P-L complex is sufficient for transcription of viral mRNA in vitro (PMID:30181255).</description>
<experiment_llps type="str">
Both, the depletion of specific viral proteins using peptide-conjugated morpholino oligomers (PPMOs) and expression of the individual viral proteins of the replication machinery in cells (change in protein concentration) demonstrates that the 3 viral proteins required for replication (P, N and L) are sufficient to drive cytoplasmic phase separation in vivo (protein localization, particle size and count, microscopy). The viral genomic RNA, or the catalytic activity of the L-encoded RNA-dependent RNA polymerase (RdRp) (studied by using a catalytically inactive mutant), is not required for formation of the phase-separated viroplasm (PMID:30181255).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30181255); dynamic exchange of molecules with surrounding solvent (PMID:30181255); morphological traits (PMID:30181255);  rheological traits (PMID:30181255)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P03521>
<P03523 type="dict">
<id type="str">
105</id>
<phase_id type="str">
83</phase_id>
<common_name type="str">
Protein L</common_name>
<name type="str">
RNA-directed RNA polymerase L</name>
<accession type="str">
P03523</accession>
<organism type="str">
Vesicular stomatitis Indiana virus</organism>
<sequence type="str">
MEVHDFETDEFNDFNEDDYATREFLNPDERMTYLNHADYNLNSPLISDDIDNLIRKFNSLPIPSMWDSKNWDGVLEMLTSCQANPISTSQMHKWMGSWLMSDNHDASQGYSFLHEVDKEAEITFDVVETFIRGWGNKPIEYIKKERWTDSFKILAYLCQKFLDLHKLTLILNAVSEVELLNLARTFKGKVRRSSHGTNICRIRVPSLGPTFISEGWAYFKKLDILMDPNFLLMVKDVIIGRMQTVLSMVCRIDNLFSEQDIFSLLNIYRIGDKIVERQGNFSYDLIKMVEPICNLKLMKLARESRPLVPQFPHFENHIKTSVDEGAKIDRGIRFLHDQIMSVKTVDLTLVIYGSFRHWGHPFIDYYTGLEKLHSQVTMKKDIDVSYAKALASDLARIVLFQQFNDHKKWFVNGDLLPHDHPFKSHVKENTWPTAAQVQDFGDKWHELPLIKCFEIPDLLDPSIIYSHKSHSMNRSEVLKHVRMNPNTPIPSKKVLQTMLDTKATNWKEFLKEIDEKGLDDDDLIIGLKGKERELKLAGRFFSLMSWKFPEYFVITEYLIKTHFVPMFKGLTMADDLTAVIKKMLDSSSGQGLKSYEAICIANHIDYEKWNNHQRKLSNGPVFRVMGQFLGYPSLIERTHEFFEKSLIYYNGRPDLMRVHNNTLINSTSQPVCWQGQEGGLEGLRQKGWTILNLLVIQREAKIRNTAVKVLAQGDNQVICTQYKTKKSRNVVELQGALNQMVSNNEKIMTAIKIGTGKLGLLINDDETMQSADYLNYGKIPIFRGVIRGLETKRWSRVTCVTNDQIPTCANIMSSVSTNALTVAHFAENPINAMIQYNYFGTFARLLLMMHDPALRQSLYEVQDKIPGLHSSTFKYAMLYLDPSIGGVSGMSLSRFLIRAFPDPVTESLSSWRFIHVHARSEHLKEMSAVFGNPEIAKFRITHIDKLVEDPTSLNIAMGMSPANLLKTEVKKCLIESRQTIRNQVIKDATIYLYHEEDRLRSFLWSINPLFPRFLSEFKSGTFLGVPDGLISLFQNSRTIRNSFKKKYHRELDDLIVRSEVSSLTHLGKLHLRRGSCKMWTCSATHADTLRYKSWGRTVIGTTVPHPLEMLGPQHRKETPCAPCNTSGFNYVSVHCPDGIHDVFSSRGPLPAYLGSKTSESTSILQPWERESKVPLIKRATRLRDAISWFVEPDSKLAMTILSNIHSLTGEEWTKRQHGFKRTGSALHRFSTSRMSHGGFASQSTAALTRLMATTDTMRDLGDQNFDFLFQATLLYAQITTTVARDGWITSCTDHYHIACKSCLRPIEEITLDSSMDYTPPDVSHVLKTWRNGEGSWGQEIKQIYPLEANWKNLAPAEQSYQVGRCIGFLYGDLAYRKSTHAEDSSLFPLSIQGRIRGRGFLKGLLDGLMRASCCQVIHRRSLAHLKRPANAVYGGLIYLIDKLSVSPPFLSLTRSGPIRDELETIPHKIPTSYPTSNRDMGVIVRNYFKYQCRLIEKGKYRSHYSQLWLFSDVLSIDFIGPFSISTTLLQILYKPFLSGKDKNELRELANLSSLLRSGEGWEDIHVKFFTKDILLCPEEIRHACKFGIPKDNNKDMSYPPWGRESRGTITTIPVYYTTTPYPKMLEMPPRIQNPLLSGIRLGQLPTGAHYKIRSILHGMGIHYRDFLSCGDGSGGMTAALLRENVHSRGIFNSLLELSGSVMRGASPEPPSALETLGGDKSRCVNGETCWEYPSDLCDPRTWDYFLRLKAGLGLQIDLIVMDMEVRDSSTSLKIETNVRNYVHRILDEQGVLIYKTYGTYICESEKNAVTILGPMFKTVDLVQTEFSSSQTSEVYMVCKGLKKLIDEPNPDWSSINESWKNLYAFQSSEQEFARAKKVSTYFTLTGIPSQFIPDPFVNIETMLQIFGVPTGVSHAAALKSSDRPADLLTISLFYMAIISYYNINHIRVGPIPPNPPSDGIAQNVGIAITGISFWLSLMEKDIPLYQQCLAVIQQSFPIRWEAVSVKGGYKQKWSTRGDGLPKDTRISDSLAPIGNWIRSLELVRNQVRLNPFNEILFNQLCRTVDNHLKWSNLRRNTGMIEWINRRISKEDRSILMLKSDLHEENSWRD</sequence>
<gene type="str">
L</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-2109</boundaries>
<region_ref type="str">
30181255</region_ref>
<partners type="str">
1) P protein; 2) Nucleoprotein</partners>
<determinants type="str">
1) temperature</determinants>
<forms type="str">
inclusions,; liquid(-like) compartments, viroplasm</forms>
<organelles type="str">
cytoplasmic viral factory; viroplasm</organelles>
<pmids type="str">
30181255 (research article)</pmids>
<description type="str">
RNA viruses that replicate in the cell cytoplasm typically concentrate their replication machinery within specialized compartments. This concentration favors enzymatic reactions and shields viral RNA from detection by cytosolic pattern recognition receptors. Nonsegmented negative-strand (NNS) RNA viruses, which include some of the most significant human, animal, and plant pathogens extant, form inclusions that are sites of RNA synthesis and are not circumscribed by a membrane (viroplasm). The viroplasm shares similarities with cellular protein/RNA structures such as P granules and nucleoli, which are phase-separated liquid compartments. Replication compartments of vesicular stomatitis virus (VSV) have the properties of liquid-like compartments that form by phase separation. The N-RNA:P-L complex is sufficient for transcription of viral mRNA in vitro (PMID:30181255).</description>
<experiment_llps type="str">
Both, the depletion of specific viral proteins using peptide-conjugated morpholino oligomers (PPMOs) and expression of the individual viral proteins of the replication machinery in cells (change in protein concentration) demonstrates that the 3 viral proteins required for replication (P, N and L) are sufficient to drive cytoplasmic phase separation in vivo (protein localization, particle size and count, microscopy). The viral genomic RNA, or the catalytic activity of the L-encoded RNA-dependent RNA polymerase (RdRp) (studied by using a catalytically inactive mutant), is not required for formation of the phase-separated viroplasm (PMID:30181255).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30181255); dynamic exchange of molecules with surrounding solvent (PMID:30181255); morphological traits (PMID:30181255); rheological traits (PMID:30181255)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P03523>
<P04156 type="dict">
<id type="str">
106</id>
<phase_id type="str">
85</phase_id>
<common_name type="str">
PrP</common_name>
<name type="str">
Major prion protein</name>
<accession type="str">
P04156</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG</sequence>
<gene type="str">
PRNP</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Prion domain with induced unfolding of alpha-helical Thr residues, induced alpha helix folding of Gly and Ala residues</segment>
<boundaries type="str">
23-111</boundaries>
<region_ref type="str">
30401430</region_ref>
<partners type="str">
1) Amiloid-beta oligomer (strictly required for LLPS); 2) Metabotropic glutamate receptor 5 (mGluR5) (not strictly required) </partners>
<determinants type="str">
1) crowding agent concentration; 2) stoichiometry of the components; 3) pH; 4) salt concentration</determinants>
<forms type="str">
Aβo/PrP hydrogels</forms>
<organelles type="str">
cytoplasmic protein granule</organelles>
<pmids type="str">
30401430 (research article)</pmids>
<description type="str">
PrP^C creates a hydrogel in crowded phisiological conditions with ~12- or ~50-mer Amiloid beta oligomers (Aβo). In the hydrogel PrP^C is moderately to highly mobile, depending on the ratio of Aβo to PrP^C. Aβo seems to be highly coordinated in the gel, and does not show mobility. Major secondary structure changes are observed for hydrogel PrP^C. In monomeric PrP^C, the 40 Gly of the N-term and the six Ala of the linker region (aa 113–120) are unstructured. The vast majority of these residues exhibit a-helical character in the hydrogel. This conformational shift spans PrP^C regions for mGluR5 and Aβo interaction. PrP^C regions 23-51, and 91-111 bind to Aβo (PMID:30401430).</description>
<experiment_llps type="str">
To further illustrate dynamic exchange of hydrogel PrPC in vitro, Alexa 568-tagged PrPC (fluorescent tagging) was added to hydrogels containing PrP-FAM or Aβo-FAM. Alexa 568 PrPC readily enters FAM-Aβo/PrP hydrogels, resulting in orange signal (co-localization). For PrP-FAM hydrogels, PrP-Alexa 568 incorporation decreases FAM signal, while for Aβo-FAM hydrogels there is no change (co-localization). Thus, FRAP shows high PrPC diffusivity within hydrogels. Both FRAP and ssNMR demonstrate that Aβo is held fixed in hydrogels, unable to either rotate or translate detectably (morphology). In vivo: unidentified cellular constituents or PrP^C glycosylation may stabilize cellular hydrogel (PMID:30401430).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic exchange of molecules with surrounding solvent (PMID:30401430); reversibility of formation and dissolution (PMID:30401430)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known (PMID:30401430)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Tamás Horváth</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</P04156>
<P05067 type="dict">
<id type="str">
107</id>
<phase_id type="str">
85</phase_id>
<common_name type="str">
Amyloid-beta oligomer</common_name>
<name type="str">
Amyloid-beta A4 protein</name>
<accession type="str">
P05067</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN</sequence>
<gene type="str">
APP</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Amyloid-forming region</segment>
<boundaries type="str">
672-713</boundaries>
<region_ref type="str">
30401430</region_ref>
<partners type="str">
1) PrP^C (strictly required for LLPS); 2) Metabotropic glutamate receptor 5 (mGluR5) (not strictly required)</partners>
<determinants type="str">
1) crowding agent concentration; 2) stoichiometry of the components; 3) pH; 4) salt concentration</determinants>
<forms type="str">
Aβo/PrP hydrogels</forms>
<organelles type="str">
cytoplasmic protein granule</organelles>
<pmids type="str">
30401430 (research article)</pmids>
<description type="str">
PrP^C creates a hydrogel in crowded phisiological conditions with ~12- or ~50-mer Amiloid beta oligomers (Aβo). In the hydrogel PrP^C is moderately to highly mobile, depending on the ratio of Aβo to PrP^C. Aβo seems to be highly coordinated in the gel, and does not show mobility. Major secondary structure changes are observed for hydrogel PrP^C. In monomeric PrP^C, the 40 Gly of the N-term and the six Ala of the linker region (aa 113–120) are unstructured. The vast majority of these residues exhibit a-helical character in the hydrogel. This conformational shift spans PrP^C regions for mGluR5 and Aβo interaction. PrP^C regions 23-51, and 91-111 bind to Aβo (PMID:30401430).</description>
<experiment_llps type="str">
To further illustrate dynamic exchange of hydrogel PrPC in vitro, Alexa 568-tagged PrPC (fluorescent tagging) was added to hydrogels containing PrP-FAM or Aβo-FAM. Alexa 568 PrPC readily enters FAM-Aβo/PrP hydrogels, resulting in orange signal (co-localization). For PrP-FAM hydrogels, PrP-Alexa 568 incorporation decreases FAM signal, while for Aβo-FAM hydrogels there is no change (co-localization). Thus, FRAP shows high PrPC diffusivity within hydrogels. Both FRAP and ssNMR demonstrate that Aβo is held fixed in hydrogels, unable to either rotate or translate detectably (morphology). In vivo: unidentified cellular constituents or PrP^C glycosylation may stabilize cellular hydrogel (PMID:30401430).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic exchange of molecules with surrounding solvent (PMID:30401430); reversibility of formation and dissolution (PMID:30401430)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known (PMID:30401430)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Tamás Horváth</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</P05067>
<Q500V5 type="dict">
<id type="str">
79</id>
<phase_id type="str">
86</phase_id>
<common_name type="str">
ADCP1</common_name>
<name type="str">
Agenet domain-containing protein</name>
<accession type="str">
Q500V5</accession>
<organism type="str">
Arabidopsis thaliana</organism>
<sequence type="str">
MLRPRRSLGVSSPAKQRKKAAPKNSMATRANRKRLPSYLKPGSAVEISSDEIGFRGSWYMGKVITIPSSSDKDSVKCQVEYTTLFFDKEGTKPLKEVVDMSQLRPPAPPMSEIEKKKKIVVGEEVDAFYNDGWWEGDVTEVLDDGKFSVFFRSSKEQIRFRKDELRFHREWVDGAWKPPLEETEEEEDESEEDKLDDSEDEEDILARVDLETTRAIAKQMFSSGTVVEVSSDEEGFQGCWFAAKVVEPVGEDKFLVEYRDLREKDGIEPLKEETDFLHIRPPPPRDEDIDFAVGDKINAFYNDGWWVGVVIDGMKHGTVGIYFRQSQEKMRFGRQGLRLHKDWVDGTWQLPLKGGKIKREKTVSCNRNVRPKKATEKQAFSIGTPIEVSPEEEGFEDSWFLAKLIEYRGKDKCLVEYDNLKAEDGKEPLREEVNVSRIRPLPLESVMVSPFERHDKVNALYNDGWWVGVIRKVLAKSSYLVLFKNTQELLKFHHSQLRLHQEWIDGKWITSFKSQKV</sequence>
<gene type="str">
AT1G09320</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal Aganet domains 3-6</segment>
<boundaries type="str">
180-517</boundaries>
<region_ref type="str">
30425322</region_ref>
<partners type="str">
1) H3K9me DNA (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration of ADCP1; 2) chromatin marks; 3) phosphorylation state of H3S10</determinants>
<forms type="str">
heterochromatin</forms>
<organelles type="str">
heterochromatin</organelles>
<pmids type="str">
30425322 (research article)</pmids>
<description type="str">
ADCP1 is an H3K9me2-specific chromatin state reader with tandem Agenet domains. ADCP1 is directly associated with heterochromatic regions, moreover it is required for maintaining the heterochromatin patterning in the nuclei, and this function likely depends on its binding ability to H3K9me2. Also, ADCP1 is required for the maintenance of H3K9me2 and CHG/CHH methylation levels in vivo. ADCP1 plays an important role in transcriptional silencing of TEs through modulating the level of DNA and H3K9 methylation. ADCP1 forms DNA-rich puncta with H3K9me3 DNA but not with native DNA in vitro. Puncta formation is H3K9me recognition-dependent as a reader pocket mutant ADCP1 failed to form puncta with H3K9me3 DNA. Several lines of evidence suggest that the puncta formation by ADCP1/H3K9me3 DNA is due to phase separation (PMID:30425322).</description>
<experiment_llps type="str">
In vitro, the binding affinities of H3K9me1 and H3K9me3 peptides to ADCP1 were in the same range of the H3K9me2 peptide despite some slight preference for H3K9me2 (protein-protein interaction detection with ITC and SPR), thus, ADCP1 is an H3K9me2 reader and does not strictly discriminate on the basis of the methylation states, this physical interaction was also evidenced by X-ray crystallography. Protein phosphorylation of H3S10 weakened the binding affinity of ADCP1 to H3K9me2 peptide (protein-protein interaction detection assay). Results from in vivo immunostaining of GFP-fused ADCP1 complementation plants with anti-GFP antibody (immunodetection assay) showed that ADCP1 strongly co-localized with heterochromatin mark H3K9me2, mainly within the heterochromatin regions. ADCP1 forms DNA-rich puncta with H3K9me3 DNA but not with native DNA in vitro. Puncta formation is H3K9me recognition-dependent as a reader pocket mutant ADCP1 failed to form puncta with H3K9me3 DNA (microscopy)(PMID:30425322).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30425322); dynamic exchange of molecules with surrounding solvent(PMID:30425322); morphological traits (PMID:30425322)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-PTM interactions (PMID:30425322)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</Q500V5>
<Q14781 type="dict">
<id type="str">
80</id>
<phase_id type="str">
87</phase_id>
<common_name type="str">
CBX2</common_name>
<name type="str">
Chromobox protein homolog 2</name>
<accession type="str">
Q14781</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEELSSVGEQVFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQKKEHEKEVQNRKRGKRPRGRPRKLTAMSSCSRRSKLKEPDAPSKSKSSSSSSSSTSSSSSSDEEDDSDLDAKRGPRGRETHPVPQKKAQILVAKPELKDPIRKKRGRKPLPPEQKATRRPVSLAKVLKTARKDLGAPASKLPPPLSAPVAGLAALKAHAKEACGGPSAMATPENLASLMKGMASSPGRGGISWQSSIVHYMNRMTQSQAQAASRLALKAQATNKCGLGLDLKVRTQKGELGMSPPGSKIPKAPSGGAVEQKVGNTGGPPHTHGASRVPAGCPGPQPAPTQELSLQVLDLQSVKNGMPGVGLLARHATATKGVPATNPAPGKGTGSGLIGASGATMPTDTSKSEKLASRAVAPPTPASKRDCVKGSATPSGQESRTAPGEARKAATLPEMSAGEESSSSDSDPDSASPPSTGQNPSVSVQTSQDWKPTRSLIEHVFVTDVTANLITVTVKESPTSVGFFNLRHY</sequence>
<gene type="str">
CBX2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: AT-hook, phosphorylable S-tract, IDR with positive charges </segment>
<boundaries type="str">
1-532</boundaries>
<region_ref type="str">
30514760</region_ref>
<partners type="str">
1) DNA with H3K27me3 (not required)</partners>
<determinants type="str">
1) protein concentration of CBX2; 2) salt concentration</determinants>
<forms type="str">
liquid droplets, condensates</forms>
<organelles type="str">
PcG protein complex; euchromatin; heterochromatin; PcG chromatin condensates</organelles>
<pmids type="str">
30514760 (research article), 31171700 (research article)</pmids>
<description type="str">
The Polycomb-repressive complex 1 (PRC1) family complexes are central to maintaining the repression of genes whose expression would generate inappropriately specified cells. PRC1 protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. CBX2 acts as a scaffold, while other subunits of CBX2-PRC1 are clients. However, the absence of CBX2-PRC1 subunits leading to irregular shapes of CBX2 condensates suggests that the trimeric client has critical roles in regulating the material properties of CBX2-PRC1 condensates as well as the assembly of PcG condensates. CBX2 condensates colocalize CBX2-PRC1 subunits and H3K27m3-marked chromatin regions. CBX2 dynamically exchanges with the surrounding environment within condensates and has liquid-like properties. CBX2 can undergo LLPS to form condensates in vitro. CBX2 condensates can concentrate DNA and nucleosomes in vitro. CBX2 contains a high content of Lys and Arg. Conserved residues (positive-negative charge patterns) within the IDR that are critical for the LLPS of CBX2. Perturbation of these charged clusters reduces the phase separation of CBX2 both in vitro and in vivo. H3K27me3 contributes little to the formation of CBX2 condensates in living cells (PMID:30514760). Reconstituted PRC1 readily phase-separates into droplets in vitro at low concentrations and physiological salt conditions. Point mutationsin an internal domain of Cbx2 eliminate phase separation. These same point mutations eliminate the formation of puncta in cells and have been shown previously to eliminate nucleosome compaction in vitro and generate axial patterning defects in mice (PMID:31171700).</description>
<experiment_llps type="str">
Overexpressing YFP-Cbx2 and HaloTag (HT)-Cbx2 (fusion proteins) in transgenic PGK12.1 mouse embryonic stem cells in vivo and examining them by fluorescence live-cell imaging showed that both YFP-CBX2 and HT-CBX2 formed condensates in living wild-type mES (particle size and count) cells and that the CBX2 condensates exhibit liquid-like properties (FRAP). Under the basal expression, the protein level of YFP-CBX2 was similar to that of the endogenous protein CBX2, the distribution of YFP-CBX2 and HT-CBX2 in Cbx2-/- mES cells was similar to that in wild-type mES cells (particle size and count by microscopy). YFP-CBX2 condensates colocalized with condensates of other PRC1 complex subunits RING1B and PHC1 in vivo. Immunofluorescence of H3K27me3 and YFP-CBX2 showed that CBX2 condensates colocalize with chromatin with the dense H3K27me3 mark suggesting that PcG-targeted genes are recruited to CBX2 condensates, or vice versa. CBX2 condensates were protein concentration-dependent. Recombinant GST-CBX2-FLAG (GST-CBX2) did not undergo LLPS in vitro at high salt concentration or in the presence of glutathione. After dialyzing the high salt of GST-CBX2 fusion to 140 mM NaCl at 4 °C overnight and transferring 10 μl of sample to coverslip CBX2 condensates with a size of a few hundred nanometers were observed by DIC microscopy. So did FLAG-CBX2. In vitro phase separation of CBX2 was protein concentration-dependent. In vitro treatment of CBX2 condensates with increasing concentrations of NaCl and Triton X-100 caused a reduction in the number of CBX2 condensates (particle size and count by microscopy). Fluorescent dye-labelled 24-bp double-stranded DNA and similarly labeled nucleosomes did not form condensates, however, in the presence of CBX2, DNA was concentrated and CBX2 condensates colocalized with the concentrated DNA or nucleosomes. Site-directed mutagenesis studies demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region for compaction of chromatin in vitro, promote the condensate formation both in vitro and in vivo. Genetic engineering studies implied that trimethylation of Lys-27 at histone H3 (H3K27me3), a marker of heterochromatin formation produced by PRC2, had minimal effects on the CBX2 condensate formation (particle size and count) (PMID:30514760). EGFP-CBX2+ RING1b could form dense spherical droplets in the presence of volume excluder that increased in size as a function of concentration and could fuse with each other (particle size and count bz microscopy). Mutational studies suggested that the positive charges within the CBX2 LCDR are critical for phase separation in vitro in addition to the previously described roles in chromatin compaction and proper axial patterning in vivo, in mice. At higher salt concentration, the preformed droplets drastically reduced in number and size (particle size and count by microscopy). Reducing the salt concentration to 100 mM KCl resulted in reformation of droplets. In vivo results recapitulated the findings of in vitro assays and underscore the importance of positively charged residues in the CBX2 LCDR for PRC1 phase separation (PMID:31171700).  ; </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30514760); dynamic exchange of molecules with surrounding solvent (PMID:30514760, PMID:31171700); sensitivity to 1,6-hexanediol (PMID:30514760, PMID:31171700); reversibility of formation and dissolution (PMID:31171700)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
101-480|S|phosphorylation|promotes|PMID:31171700|CK2|Notes:The results from CK2 overexpression and from mutations in the serine-rich patch are consistent with a role for phosphorylation in generating the negative charge necessary for phase separation.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:30514760) </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir; biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</Q14781>
<Q02794 type="dict">
<id type="str">
81</id>
<phase_id type="str">
88</phase_id>
<common_name type="str">
Std1</common_name>
<name type="str">
Protein STD1</name>
<accession type="str">
Q02794</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MFVSPPPATARNQVLGKRKSKRHDENPKNVQPNADTEMTNSVPSIGFNSNLPHNNQEINTPNHYNLSSNSGNVRSNNNFVTTPPEYADRARIEIIKRLLPTAGTKPMEVNSNTAENANIQHINTPDSQSFVSDHSSSYESSIFSQPSTALTDITTGSSLIDTKTPKFVTEVTLEDALPKTFYDMYSPEVLMSDPANILYNGRPKFTKRELLDWDLNDIRSLLIVEQLRPEWGSQLPTVVTSGINLPQFRLQLLPLSSSDEFIIATLVNSDLYIEANLDRNFKLTSAKYTVASARKRHEEMTGSKEPIMRLSKPEWRNIIENYLLNVAVEAQCRYDFKQKRSEYKRWKLLNSNLKRPDMPPPSLIPHGFKIHDCTNSGSLLKKALMKNLQLKNYKNDAKTLGAGTQKNVVNKVSLTSEERAAIWFQCQTQVYQRLGLDWKPDGMS</sequence>
<gene type="str">
STD1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-rich N-terminal IDR</segment>
<boundaries type="str">
1-78</boundaries>
<region_ref type="str">
29249654</region_ref>
<partners type="str">
1) Hsp104 (strictly required for LLPS); 2) Sip5 (negative regulator)</partners>
<determinants type="str">
1) Hsp104 activity; 2) phosphorylation state of Sip5; 3) nutrient supply</determinants>
<forms type="str">
liquid-like puncta</forms>
<organelles type="str">
cytoplasmic protein granule; Std1 bodies</organelles>
<pmids type="str">
29249654 (research article), 29322248 (review)</pmids>
<description type="str">
Glucose metabolism in yeast is regulated by controlled localization of the Std1 protein into dynamic, reversible bodies under non-pathological conditions. The sequences of Std1 and its non-puncta forming paralog Mth1 are very similar, with the exception of the N-terminal region, which in Std1 includes 15 asparagines between amino acids 26 and 78. Std1(1–78) forms puncta in sip5Δ cells that colocalize with Hsp104. Thus, the asparagine-rich domain of Std1 is necessary and sufficient for Std1 puncta formation. Sip5 and Snf1 interact with distinct regions of Std1, with Snf1 binding Std1(340–424) and Sip5 interacting with Std1(1–78) and preventing Std1 self-interactions. The Sip5-Std1(1–78) interaction is inhibited by phosphorylation of Sip5 at S236 by the Vhs1 kinase, triggering the release of Snf1 and Std1 accretion. Sequestration of Std1 into puncta requires Hsp104 activity and is sufficient to prevent its corepressor function. One role of reversible Std1 puncta formation is to provide a rapid source of Std1 upon encounter of poor carbonsources (PMID:29249654).</description>
<experiment_llps type="str">
In wild-type cells, in vivo Std1-GFP (fusion protein) localizes—under respiration conditions—to the cytoplasm with an enrichment in the nucleus as assessed by microscopy. When grown in glucose-containing medium (perturbation of the cell environment to induce phenotypic changes), Std1 additionally localizes to puncta in approximately 50% of the cells. Knocking out of SIP5 results in 90% of cells exhibiting Std1 puncta under both fermentation and respiration conditions. The Std1 puncta do not colocalize with the nucleolus, spindle-pole bodies or Hsp42 in vivo, but GFP-Std1 does colocalize with the Hsp104 chaperone as assessed by microscopy. Puncta formation also occurs in vivo when Vhs1 kinase is overexpressed or in a Sip5 S236D phosphomimetic mutant, and is prevented by the Sip5 S236A non-phosphorylable mutation. Std1(78–444) does not form puncta in Sip5Δ cells (knock-out) in vivo, while Std1(1–78) does (mutation, microscopy), thus, the N-terminal asparagine-rich domain of Std1 is necessary and sufficient for Std1 puncta formation. Knocking out HSP104 (change in protein concentration) prevents Std1 puncta formation in vivo when cells are treated with glucose or when SIP5 is deleted (perturbation of the cell environment to induce phenotypic changes). Std1 puncta are not amyloidic but when galactose-grown sip5Δ cells are treated with 1-6 hexanediol, the Std1 puncta are dissolved (particle size and count) and Std1 relocalizes to the cell periphery (protein localization) (PMID:29249654).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
sensitivity to 1,6-hexanediol (PMID:29249654); reversibility of formation and dissolution (PMID:29249654); dynamic movement/reorganization of molecules within the droplet (PMID:29249654)</experiment_state>
<rna_req type="str">
Not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
simple coacervation of hydrophobic residues (PMID:29249654)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
sensor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q02794>
<P38996 type="dict">
<id type="str">
82</id>
<phase_id type="str">
89</phase_id>
<common_name type="str">
Nab3</common_name>
<name type="str">
Nuclear polyadenylated RNA-binding protein 3</name>
<accession type="str">
P38996</accession>
<organism type="str">
Saccharomyces cerevisiae</organism>
<sequence type="str">
MSDENHNSDVQDIPSPELSVDSNSNENELMNNSSADDGIEFDAPEEEREAEREEENEEQHELEDVNDEEEEDKEEKGEENGEVINTEEEEEEEHQQKGGNDDDDDDNEEEEEEEEDDDDDDDDDDDDEEEEEEEEEEGNDNSSVGSDSAAEDGEDEEDKKDKTKDKEVELRRETLEKEQKDVDEAIKKITREENDNTHFPTNMENVNYDLLQKQVKYIMDSNMLNLPQFQHLPQEEKMSAILAMLNSNSDTALSVPPHDSTISTTASASATSGARSNDQRKPPLSDAQRRMRFPRADLSKPITEEEHDRYAAYLHGENKITEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHGDHGTNSSSTFISSAKRPFQTESGDMYNDDNGAGYKKSRRHTVSCNIFVKRTADRTYAIEVFNRFRDGTGLETDMIFLKPRMELGKLINDAAYNGVWGVVLVNKTHNVDVQTFYKGSQGETKFDEYISISADDAVAIFNNIKNNRNNSRPTDYRAMSHQQNIYGAPPLPVPNGPAVGPPPQTNYYQGYSMPPPQQQQQQPYGNYGMPPPSHDQGYGSQPPIPMNQSYGRYQTSIPPPPPQQQIPQGYGRYQAGPPPQPPSQTPMDQQQLLSAIQNLPPNVVSNLLSMAQQQQQQPHAQQQLVGLIQSMQGQAPQQQQQQLGGYSSMNSSSPPPMSTNYNGQNISAKPSAPPMSHQPPPPQQQQQQQQQQQQQQQQPAGNNVQSLLDSLAKLQK</sequence>
<gene type="str">
NAB3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
RNA recognition motif (RRM); prion-like domain (PrLD)</segment>
<boundaries type="str">
329-404; 568-793</boundaries>
<region_ref type="str">
30557374</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) glucose availability</determinants>
<forms type="str">
granules</forms>
<organelles type="str">
nuclear body</organelles>
<pmids type="str">
30557374 (research article)</pmids>
<description type="str">
In yeast, transcription by RNA polymerase II can be terminated by the Nrd1-Nab3-Sen1 (NNS) pathway which primarily generates short noncoding transcripts. The NNS termination pathway contains Nrd1 and Nab3, essential RNA-binding proteins with canonical RNA recognition motifs (RRMs). Changes in the transcriptome following glucose-deprivation are mediated in part by the NNS pathway. The yeast transcription termination factor, Nab3, is targeted to intranuclear granules in response to glucose starvation by Nab3’s proline/glutamine-rich, prion-like domain (PrLD) which can assemble into amyloid in vitro (PMID:25611193). Localization to the granule is reversible and sensitive to the chemical probe 1,6 hexanediol suggesting condensation is driven by phase separation. Nab3’s RNA recognition motif is also required for localization as seen for other PrLD-containing RNA-binding proteins that phase separate. Although the PrLD is necessary, it is not sufficient to localize to the granule (PMID:30557374).</description>
<experiment_llps type="str">
N-terminally GFP-fused Nab3 variants were introduced into cells. Since many of the mutations are lethal, cells also expressed untagged Nab3 on a differently marked CEN plasmid. All Nab3 variants were expressed from the endogenous NAB3 promoter in a strain deleted for chromosomal NAB3 (knock-out). Imaging via confocal microscopy showed that GFP-tagged wild type Nab3 exhibited a pan-nuclear distribution (protein localization) in glucose rich conditions in vivo (perturbation of the cell environment to induce phenotypic changes). In glucose starved cells, Nab3 localized to a granule in the population in which GFP-Nab3 was expressed.; Glucose starved cells with formed nuclear granules were treated with 1,6-hexanediol which caused a virtually complete loss of granules from cells (particle size and count by microscopy), similar to that seen for yeast P-bodies. The observations made by the employed microfluidics chamber were consistent with the results seen above using confocal microscopy. The microfluidics chamber holds yeast cells stationary while allowing rapid switching of extracellular media to monitor Nab3 dynamics before, during, and after glucose starvation. Cells that displayed granules kept their granules for the duration of glucose deprivation. Following the re-addition of glucose, Nab3 granule intensity shifted back to a pannuclear baseline distribution within minutes, showing the rapidity of the response to the reintroduction of glucose. Nab3 mutant lacking its PrLD did not form stable granules (particle size and count by microscopy) under the investigated conditions. (PMID:30557374)</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
sensitivity to 1,6-hexanediol (PMID:30557374); reversibility of formation and dissolution (PMID:30557374)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID:30557374)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Nikoletta Murvai</annotator>
<functional_class type="str">
sensor</functional_class>
<date type="str">
2019-09-11</date>
</P38996>
<Q94ET8 type="dict">
<id type="str">
123</id>
<phase_id type="str">
92</phase_id>
<common_name type="str">
EPYC1</common_name>
<name type="str">
LCI5</name>
<accession type="str">
Q94ET8</accession>
<organism type="str">
Chlamydomonas reinhardtii</organism>
<sequence type="str">
MATISSMRVGAASRVVVSGRVKTVKVAARGSWRESSTATVQASRASSATNRVSPTRSVLPANWRQELESLRNGNGSSSAASSAPAPARSSSASWRDAAPASSAPARSSSASKKAVTPSRSALPSNWKQELESLRSSSPAPASSAPAPARSSSASWRDAAPASSAPARSSSSKKAVTPSRSALPSNWKQELESLRSSSPAPASSAPAPARSSSASWRDAAPASSAPARSSSASKKAVTPSRSALPSNWKQELESLRSNSPAPARRPLPRPAPRRPAGVTPPPRAPARAPTRPAPTPGLASPSPRSSAPPCPLTGARACKQLA</sequence>
<gene type="str">
LCI5</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Four almost identical ~60 amino-acid tandem repeats in EPYC1</segment>
<boundaries type="str">
52-291</boundaries>
<region_ref type="str">
27166422</region_ref>
<partners type="str">
1) Rubisco (promotes LLPS)</partners>
<determinants type="str">
1) protein concentration of EPYC1 in the presence of crowding agents; 2) stochiometry of the components; 3) salt concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
pyrenoid</organelles>
<pmids type="str">
27166422 (research article), 28938114 (research article), 30498228 (research article), 30675061 (research article), 31001862 (review)</pmids>
<description type="str">
The pyrenoid is a carbon-fixing organelle in algae that undergoes LLPS owing to multivalent interactions between Rubisco and Essential Pyrenoid Component 1 (EPYC1). Rubisco and the linker protein EPYC1, are both necessary and sufficient to phase separate and form liquid droplets. The phase-separated Rubisco is functional. Droplet composition is dynamic and components rapidly exchange with the bulk solution. Rubisco has eight binding sites for EPYC1, while EPYC1 has four binding sites for Rubisco. Modeling suggests that such systems will exhibit a magic number effect where certain numbers of particles form an unusually stable state. The magic number effect manifests when the valency of one partner is an integral multiple of the valency of the second and the binding sites of the two partners can be saturated. This magic number effect could impact the phase diagram in many biological contexts and is predicted to give rise to unexpectedly sharp phase transition (PMID:30951647) If each repeat of EPYC1 binds Rubisco, then EPYC1 could link multiple Rubisco holoenzymes together to form the pyrenoid matrix. Multiple Rubisco binding sites on EPYC1 could arrange Rubisco into the hexagonal closely packed or cubic closely packed arrangement observed in recent cryoelectron tomography studies of the Chlamydomonas pyrenoid. EPYC1 and Rubisco could interact in one of two fundamental ways: (i) EPYC1 and Rubisco could form a codependent network, or (ii) EPYC1 could form a scaffold onto which Rubisco binds. Importantly, the 60-aa repeat length of EPYC1 is sufficient to span the observed 2- to 4.5-nm gap between Rubisco holoenzymes in the pyrenoid, and a stretched-out repeat could potentially span the observed 15-nm Rubisco center-to-center distance (PMID:27166422).</description>
<experiment_llps type="str">
Mixing pure C. reinhardtii Rubisco and EPYC1 led to immediate formation of a turbid solution that cleared over time in vitro. The turbidity was caused by the formation of spherical droplets (morphology) from the bulk solution that could be labeled by including a fluorescent EPYC1-GFP fusion protein in the reaction. The observed clearance of the solution was caused by fusion of the droplets into a large homogeneous droplet (coalescence), supporting their liquid nature. Demixed droplets could be harvested by centrifugation, and SDS-polyacrylamide gel electrophoresis analysis confirmed that both EPYC1 and Rubisco had entered the droplets (co-localization) (PMID:30498228). To confirm the pyrenoid localization of EPYC1, the authors coexpressed fluorescently tagged EPYC1 and RBCS. Venus-tagged EPYC1 showed clear colocalization with mCherry-tagged RBCS in the pyrenoid in vivo (PMID:27166422). Cryo-ET (imaging assay evidence) measurements revealed that the pyrenoid matrix is not crystalline, but exhibits liquid-like local order (morphology) and FRAP experiments revealed that the pyrenoid matrix mixes internally. The Chlamydomonas pyrenoid matrix also appears to undergo such a phase transition during division: a portion of the RBCS1-Venus and EPYC1-Venus signals rapidly dispersed from the pyrenoid matrix into the stroma investigated by fluorescent microscopy (PMID:28938114).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:28938114); dynamic exchange of molecules with surrounding solvent (PMID:30498228); morphological traits (PMID:30498228)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:28938114); electrostatic (cation-anion) interaction (PMID:30498228)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Nikoletta Murvai</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q94ET8>
<Q9JIR4 type="dict">
<id type="str">
108</id>
<phase_id type="str">
93</phase_id>
<common_name type="str">
RIM1</common_name>
<name type="str">
Regulating synaptic membrane exocytosis protein 1</name>
<accession type="str">
Q9JIR4</accession>
<organism type="str">
Rattus norvegicus</organism>
<sequence type="str">
MSSAVGPRGPRPPTVPPPMQELPDLSHLTEEERNIIMAVMDRQKEEEEKEEAMLKCVVRDMAKPAACKTPRNAESQPHQPPLNIFRCVCVPRKPSSEEGGPERDWRLHQQFESYKEQVRKIGEEARRYQGEHKDDAPTCGICHKTKFADGCGHLCSYCRTKFCARCGGRVSLRSNNEDKVVMWVCNLCRKQQEILTKSGAWFFGSGPQQPSQDGTLSDTATGAGSEVPREKKARLQERSRSQTPLSTAAVSSQDTATPGAPLHRNKGAEPSQQALGPEQKQASRSRSEPPRERKKAPGLSEQNGKGGQKSERKRVPKSVVQPGEGIADERERKERRETRRLEKGRSQDYSDRPEKRDNGRVAEDQKQRKEEEYQTRYRSDPNLARYPVKAPPEEQQMRMHARVSRARHERRHSDVALPHTEAAAAAPAEATAGKRAPATARVSPPESPRARAAAAQPPTEHGPPPPRPAPGPAEPPEPRVPEPLRKQGRLDPGSAVLLRKAKREKAESMLRNDSLSSDQSESVRPSPPKPHRPKRGGKRRQMSVSSSEEEGVSTPEYTSCEDVELESESVSEKGDLDYYWLDPATWHSRETSPISSHPVTWQPSKEGDRLIGRVILNKRTTMPKESGALLGLKVVGGKMTDLGRLGAFITKVKKGSLADVVGHLRAGDEVLEWNGKPLPGATNEEVYNIILESKSEPQVEIIVSRPIGDIPRIPESSHPPLESSSSSFESQKMERPSISVISPTSPGALKDAPQVLPGQLSVKLWYDKVGHQLIVNVLQATDLPPRVDGRPRNPYVKMYFLPDRSDKSKRRTKTVKKLLEPKWNQTFVYSHVHRRDFRERMLEITVWDQPRVQDEESEFLGEILIELETALLDDEPHWYKLQTHDESSLPLPQPSPFMPRRHIHGESSSKKLQRSQRISDSDISDYEVDDGIGVVPPVGYRASARESKATTLTVPEQQRTTHHRSRSVSPHRGDDQGRPRSRLPNVPLQRSLDEIHPTRRSRSPTRHHDASRSPADHRSRHVESQYSSEPDSELLMLPRAKRGRSAESLHMTSELQPSLDRARSASTNCLRPDTSLHSPERERHSRKSERCSIQKQSRKGTASDADRVLPPCLSRRGYATPRATDQPVVRGKYPTRSRSSEHSSVRTLCSMHHLAPGGSAPPSPLLLTRTHRQGSPTQSPPADTSFGSRRGRQLPQVPVRSGSIEQASLVVEERTRQMKVKVHRFKQTTGSGSSQELDHEQYSKYNIHKDQYRSCDNASAKSSDSDVSDVSAISRASSTSRLSSTSFMSEQSERPRGRISSFTPKMQGRRMGTSGRAIIKSTSVSGEIYTLERNDGSQSDTAVGTVGAGGKKRRSSLSAKVVAIVSRRSRSTSQLSQTESGHKKLKSTIQRSTETGMAAEMRKMVRQPSRESTDGSINSYSSEGNLIFPGVRVGPDSQFSDFLDGLGPAQLVGRQTLATPAMGDIQIGMEDKKGQLEVEVIRARSLTQKPGSKSTPAPYVKVYLLENGACIAKKKTRIARKTLDPLYQQSLVFDESPQGKVLQVIVWGDYGRMDHKCFMGVAQILLEELDLSSMVIGWYKLFPPSSLVDPTLAPLTRRASQSSLESSSGPPCIRS</sequence>
<gene type="str">
RIMS1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
IDR with P-rich motifs called PRM1, PRM2 and PRM</segment>
<boundaries type="str">
505-1206</boundaries>
<region_ref type="str">
30661983</region_ref>
<partners type="str">
1) RIM-BP (strictly required for LLPS); 2) N-type and P/Q-type Voltage-gated Ca²⁺ channels (promotes LLPS)</partners>
<determinants type="str">
1) protein concentration of Rimbp; 2) salt concentration (for RIM self-LLPS)</determinants>
<forms type="str">
protein-rich condensed liquid droplets</forms>
<organelles type="str">
cytoplasmic protein granule</organelles>
<pmids type="str">
30661983 (research article), 30849390 (review)</pmids>
<description type="str">
RIM1 and RIM-BP2 are two major scaffold proteins in synaptic transmissions located in the active zone. The two proteins together can undergo LLPS in vitro and the formed condensates cluster Ca²⁺ channels in solution and on membrane surface, this may be a key-finding to understand how presynaptic active zones form and function to regulate neurotransmitter release. Multivalent interactions between RIM1 and RIM-BP2 and their intrinsically disordered properties lead to the formation of self-organized, highly condensed and dynamic assemblies that are reminiscent of dense projection-like structures through liquid-liquid phase separation (LLPS) in vitro. In vitro study showed that RIM1 alone at high concentrations could undergo LLPS, and this LLPS is sensitive to the salt concentration in the assay buffer. RIM1 is the key determinant of the formation of RIM1/RIM-BP2 condensates. RIM1/RIM-BP2 LLPS is driven by the binding of the proline rich motifs (PRMs) within RIM1 sequence to the three SH3 domains of RIM-BP2. The formed condensed phase may act as a platform to recruit other scaffold proteins and signaling proteins, including ELKS, liprins, Munc13, and Rab3/27 in presynaptic termini. These condensates also cluster Ca²⁺ channels in solution and on membrane surface. N-type and P/Q-type Voltage-gated Ca²⁺ channels (VGCCs) directly bind to RIM1 and RIM-BP2 via their cytoplasmic tails, such binding significantly promotes LLPS of RIM1 and RIM-BP2 as well as enriches VGCCs to the condensed liquid phase. PRM or PBM of VGCCs are responsible for such behaviour as they drive multivalent interactions. Proteins concentration appeared to affect the clustering patterns of RIM, RIM- BP, and VGCC on supported lipid bilayer but does not affect their patterns in solution. As a conclusion, the presynaptic active zone is formed through LLPS where RIMs and RIM-BPs are considered as plausible organizers of active zones, and their condensates can cluster VGCCs into nano- or microdomains and position them with Ca²⁺ sensors on docked vesicles for efficient and precise synaptic transmissions (PMID:30661983).</description>
<experiment_llps type="str">
Purified RIM1α-PAS (PDZ-C2A-PRM) and the SH3 domains of RIM-BP2 (i.e., by deleting the three FN3 [fibronectin type III] domains due to their hitherto unknown functions) were used to study their physical interaction in vitro. Using sedimentation-based assay, it was found that mixing these two proteins at different molar ratios led to LLPS of both proteins. Fluorescent tagging of purified RIM1α- PAS and RBP2-(SH3)3 was done and when they were mixed, differential interference contrast (DIC) microscopy and fluorescence images have shown protein co-localization and enrichment in condensed droplets in vitro (protein localization). Droplet fusion events and fluorescence recovery after photobleaching (FRAP) confirmed the liquid state of the condensed droplets (morphology). Sedimentation-based assays showed that truncation of different PRM regions (PRM1: D502–510; PRM2: D873–876; PRM: D1,086–1,089) weakened or even abolished LLPS of RIM1α-PAS when mixed with RBP2-(SH3)3 (particle size and count), indicating that all three PRMs contribute to LLPS. An ITC-based assay showed that the RIM1α PRM2 and a stretch of disordered sequences following PRM2 could indeed bind to RBP2-(SH3)3. The model of RIM1α-PAS and RBP2-(SH3)3 LLPS was tested via the multivalent interaction between the two proteins: LLPS experiments were performed by titrating increasing amounts of RBP2-(SH3)3 to a fixed concentration of RIM1α-PAS (change in protein concentration). This titration experiment indicated that a high concentration of RBP2-(SH3)3 titrated away the large RIM1α/RBP2-(SH3)3 species and thus dispersed the formed RIM1α/RBP2-(SH3)3 droplets, an observation fitting the multivalent protein-protein-interaction-mediated LLPS model. ITC measurment showed that the segment encompassing the two proline-rich regions (aa 183–480 not found in RIMa-PAS), but not the zinc-finger domain, indeed binds to RBP2-(SH3)3, albeit with a relatively weak affinity. Sedimentation-based assay showed that when RIM1α-FL and RBP2-(SH3)3 were mixed at a 1:1 molar ratio, the mixture underwent LLPS at a concentration as low as 2.5 mM, indicating that the N-terminal proline-rich sequences indeed promote LLPS of RIM1α with RBP2-(SH3)3. DIC and fluorescence microscopy have shown RIM1α-FL and RBP2-(SH3)3 protein co-localization and enrichment in condensed droplets. FRAP experiment indicated the existence of a less mobile fraction of RIM1α-FL in the condensed droplet. Imaging-based assays and ITC experiments showed NCav-CT (cytoplasmic tail of the N-type VGCC alpha1 subunit) could be enriched (co-localization) and in return promote LLPS of RIM1α-FL and RBP2-(SH3)3.</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30661983); morphological traits (PMID:30661983)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:30661983)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rawan Abukhairan</annotator>
<functional_class type="str">
regulator of spatial patterns; activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9JIR4>
<Q9JIR1 type="dict">
<id type="str">
109</id>
<phase_id type="str">
93</phase_id>
<common_name type="str">
RIM-BP2</common_name>
<name type="str">
RIMS-binding protein 2</name>
<accession type="str">
Q9JIR1</accession>
<organism type="str">
Rattus norvegicus</organism>
<sequence type="str">
MREAAERRQQLELEHEQALAILNAKQQEIQLLQQSKVRELEEKCRVQSEQFNLLSRDLEKFRQHAGSIDLLGSNSVALLDVPLAPGKPFSQYMNGLATSIHKGHEGPTGHYSVIGDYIPLSGDKLESPCVKPSFLLRSSSPRCRFESEMDDDRSSNKSKHSSSGKVHLCVARYSYNPFDGPNENPEAELPLTAGKYLYVYGDMDEDGFYEGELLDGQRGLVPSNFVDFIQDNESRFAGTLGSEQDQNFLNHSGISLERDSILHLHSPTQVDSGITDNGGGTLDVNIDDIGEDIVPYPRKITLIKQLAKSVIVGWEPPAVPPGWGTVSSYNVLVDKETRMSLALGRRTKALIEKLNTAACTYRISVQCVTSRGNSDELQCTLLVGKDVVVAPSQLRVDNITQISAQLSWLPTNSNYSHIIFLNEEELDIVKAARYKYQFFNLRPNMAYKVKVLAQPHQMPWQLPLEQREKDEACVEFSTLPAGPPAPPQDVTVQAGATTASVQVSWKPPALTPTGLSNGANVTGYGVYAKGQRVAEVIAPTANGAAVELVRLRSLEAKAVSVRTLSAQGESMDSALAAIPPDLLVPPAPHPRTAPPPKPLTSDMDTKDLGPHVKVDESWEQSRPPGPAHGHMLEPPDMHSTGPGRRSPSPSRILPQPQGAPVSTTVAKAMAREAAQRVAETSKLEKRSLFLEQSSAGPYANSDEEDGYASPEVKRRGTSVDDFLKGSELGQQPHCCHGDEYHTESSRGSDLSDIMEEDEEELYSEMQLEDGGRRRPSGTSHNALKILGNSALMGRGDRMEHVSRRYSHSGGGPQRHRPMAPSIDEYTGRDHLSPDFYDESETDPGAEELPARIFVALFDYDPLTMSPNPDAAEEELPFKEGQIIKVYGDKDADGFYRGETCARLGLIPCNMVSEIHADDEEMMDQLLRQGFLPLNTPVEKIERSRRSGRGHSVPTRRMVALYDYDPRESSPNVDVEAELLFCTGDIITVFGEIDEDGFYYGELNGQKGLVPSNFLEEVPDDVEVHLSDAPPHYSHDPPMRTKAKRVSQPP</sequence>
<gene type="str">
RIMBP2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
SH3_1; SH3_2; SH3_3 domains</segment>
<boundaries type="str">
164-231; 848-916; 952-1019</boundaries>
<region_ref type="str">
30661983</region_ref>
<partners type="str">
1) RIM (strictly required for LLPS); 2) N-type and P/Q-type Voltage-gated Ca²⁺ channels (promotes LLPS)</partners>
<determinants type="str">
1) protein concentration of Rimbp; 2) salt concentration (for RIM self-LLPS)</determinants>
<forms type="str">
protein-rich condensed liquid droplets</forms>
<organelles type="str">
cytoplasmic protein granule</organelles>
<pmids type="str">
30661983 (research article), 30849390 (review)</pmids>
<description type="str">
RIM1 and RIM-BP2 are two major scaffold proteins in synaptic transmissions located in the active zone. The two proteins together can undergo LLPS in vitro and the formed condensates cluster Ca²⁺ channels in solution and on membrane surface, this may be a key-finding to understand how presynaptic active zones form and function to regulate neurotransmitter release. Multivalent interactions between RIM1 and RIM-BP2 and their intrinsically disordered properties lead to the formation of self-organized, highly condensed and dynamic assemblies that are reminiscent of dense projection-like structures through liquid-liquid phase separation (LLPS) in vitro. In vitro study showed that RIM1 alone at high concentrations could undergo LLPS, and this LLPS is sensitive to the salt concentration in the assay buffer. RIM1 is the key determinant of the formation of RIM1/RIM-BP2 condensates. RIM1/RIM-BP2 LLPS is driven by the binding of the proline rich motifs (PRMs) within RIM1 sequence to the three SH3 domains of RIM-BP2. The formed condensed phase may act as a platform to recruit other scaffold proteins and signaling proteins, including ELKS, liprins, Munc13, and Rab3/27 in presynaptic termini. These condensates also cluster Ca²⁺ channels in solution and on membrane surface. N-type and P/Q-type Voltage-gated Ca²⁺ channels (VGCCs) directly bind to RIM1 and RIM-BP2 via their cytoplasmic tails, such binding significantly promotes LLPS of RIM1 and RIM-BP2 as well as enriches VGCCs to the condensed liquid phase. PRM or PBM of VGCCs are responsible for such behaviour as they drive multivalent interactions. Proteins concentration appeared to affect the clustering patterns of RIM, RIM- BP, and VGCC on supported lipid bilayer but does not affect their patterns in solution. As a conclusion, the presynaptic active zone is formed through LLPS where RIMs and RIM-BPs are considered as plausible organizers of active zones, and their condensates can cluster VGCCs into nano- or microdomains and position them with Ca²⁺ sensors on docked vesicles for efficient and precise synaptic transmissions (PMID:30661983).</description>
<experiment_llps type="str">
Purified RIM1α-PAS (PDZ-C2A-PRM) and the SH3 domains of RIM-BP2 (i.e., by deleting the three FN3 [fibronectin type III] domains due to their hitherto unknown functions) were used to study their physical interaction in vitro. Using sedimentation-based assay, it was found that mixing these two proteins at different molar ratios led to LLPS of both proteins. Fluorescent tagging of purified RIM1α- PAS and RBP2-(SH3)3 was done and when they were mixed, differential interference contrast (DIC) microscopy and fluorescence images have shown protein co-localization and enrichment in condensed droplets in vitro (protein localization). Droplet fusion events and fluorescence recovery after photobleaching (FRAP) confirmed the liquid state of the condensed droplets (morphology). Sedimentation-based assays showed that truncation of different PRM regions (PRM1: D502–510; PRM2: D873–876; PRM: D1,086–1,089) weakened or even abolished LLPS of RIM1α-PAS when mixed with RBP2-(SH3)3 (particle size and count), indicating that all three PRMs contribute to LLPS. An ITC-based assay showed that the RIM1α PRM2 and a stretch of disordered sequences following PRM2 could indeed bind to RBP2-(SH3)3. The model of RIM1α-PAS and RBP2-(SH3)3 LLPS was tested via the multivalent interaction between the two proteins: LLPS experiments were performed by titrating increasing amounts of RBP2-(SH3)3 to a fixed concentration of RIM1α-PAS (change in protein concentration). This titration experiment indicated that a high concentration of RBP2-(SH3)3 titrated away the large RIM1α/RBP2-(SH3)3 species and thus dispersed the formed RIM1α/RBP2-(SH3)3 droplets, an observation fitting the multivalent protein-protein-interaction-mediated LLPS model. ITC measurment showed that the segment encompassing the two proline-rich regions (aa 183–480 not found in RIMa-PAS), but not the zinc-finger domain, indeed binds to RBP2-(SH3)3, albeit with a relatively weak affinity. Sedimentation-based assay showed that when RIM1α-FL and RBP2-(SH3)3 were mixed at a 1:1 molar ratio, the mixture underwent LLPS at a concentration as low as 2.5 mM, indicating that the N-terminal proline-rich sequences indeed promote LLPS of RIM1α with RBP2-(SH3)3. DIC and fluorescence microscopy have shown RIM1α-FL and RBP2-(SH3)3 protein co-localization and enrichment in condensed droplets. FRAP experiment indicated the existence of a less mobile fraction of RIM1α-FL in the condensed droplet. Imaging-based assays and ITC experiments showed NCav-CT (cytoplasmic tail of the N-type VGCC alpha1 subunit) could be enriched (co-localization) and in return promote LLPS of RIM1α-FL and RBP2-(SH3)3.</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30661983); morphological traits (PMID:30661983)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:30661983)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rawan Abukhairan</annotator>
<functional_class type="str">
regulator of spatial patterns; activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9JIR1>
<Q8L3W1 type="dict">
<id type="str">
110</id>
<phase_id type="str">
94</phase_id>
<common_name type="str">
VRN1</common_name>
<name type="str">
B3 domain-containing transcription factor VRN1</name>
<accession type="str">
Q8L3W1</accession>
<organism type="str">
Arabidopsis thaliana</organism>
<sequence type="str">
MPRPFFHKLIFSSTIQEKRLRVPDKFVSKFKDELSVAVALTVPDGHVWRVGLRKADNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYIFNLSHSEINYHSTGLMDSAHNHFKRARLFEDLEDEDAEVIFPSSVYPSPLPESTVPANKGYASSAIQTLFTGPVKAEEPTPTPKIPKKRGRKKKNADPEEINSSAPRDDDPENRSKFYESASARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAEKQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVNEYV</sequence>
<gene type="str">
VRN1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS: two B3 DNA-binding domains and an ID linker</segment>
<boundaries type="str">
1-341</boundaries>
<region_ref type="str">
30762296</region_ref>
<partners type="str">
1) DNA (strictly required for LLPS)</partners>
<determinants type="str">
1) DNA concentration; 2) ionic strength; 3) valency of Vrn1 (electrostatic pattern of the ID linker); 4) salt concentration</determinants>
<forms type="str">
liquid-like spherical droplet, puncta</forms>
<organelles type="str">
nuclear body</organelles>
<pmids type="str">
30762296 (research article)</pmids>
<description type="str">
VRN1 is a B3 domain-containing protein found in the model plant Arabidopsis thalia. VRN1 is a transcriptional repressor that binds DNA nonspecifically and accelerates flowering in response to vernalization, it has two B3 domains flanked by an intrinsicaly disordered ID linker. In vitro, VRN1 protein undergoes LLPS upon DNA binding forming liquid-like spherical droplets. LLPS is strictly driven by the multivaent interactions between the protein and DNA, thus their valencies are crucial for their intearction and droplet formation. Both of the basic B3 domains and the flexible ID linker are important for LLPS. The ID linker contains several Proline- Serine/Threonine (P-S/T) repeats, and oppositely charged residue patches are segregated. The charge distribution along the ID linker plays an important role in LLP. Based on mutation studies of the linker, the charge distribution importance for LLPS was confirmed. Multivalent interactions also drive puncta formation in plant cells. The fact that VRN1 plays an important role in silencing the flowering repressor gene Flowering Locus C (FLC) suggests that LLPS of the proetin with DNA might affect VRN1-mediated gene repression (PMID:30762296).</description>
<experiment_llps type="str">
Microscopy showed that titration of the purified VRN1 with dsDNA FLC55 (55 base pairs upstream of the FLC promoter) led to the formation of spherical liquid-like droplets in vitro, which underwent fusion in a few seconds (morphology). Change in DNA concentration confirmed the dependence of formed particle size and count on it. Fluorescent tagging of the protein and DNA was performed then, upon mixing in vitro, protein co-localization was observed with the DNA in droplets. FRAP confirmed the liquid state of the condensed droplets. Reduced phase seperation under microscopy was observed after increasing the ionic strength, confirming that electrostatic interactions are the major driving force of the VRN1/DNA phase separation. Deletion mutations of VRN1 were performed, their phase seperation was studied using DLS and showed that the two B3 DNA- binding domains in VRN1 are important in protein-DNA multivalent interactions and droplet formation. DNA Curtains, which is a high-throughput single-molecule technique that can monitor protein–DNA interactions directly by fluorescent imaging confirmed that multivalent interactions of VRN1 with DNA are required for phase separation. In vivo proteins expression (wild-type VRN1 and its deletion mutant) in N. benthamiana leaves was performed to study its phase seperation, and results showed that the multivalent DNA-binding of VRN1 facilitated puncta formation in plant cells (particle size and count), which may affect VRN1-mediated gene repression. Mutations on the flexible linker in between the two B3 domains of the protein were done, their phase seperation under microscopy was monitored (particle size and count), and it showed that both the acid and the basic residue patches are important for maintaining the right structure of VRN1 for LLPS formation. FRET analysis for phase seperation of wild type and mutants of the protein with DNA indicated that electrostatic interaction strength played important roles in regulating the condensation process. Strong electrostatic interactions promoted solid-like precipitates, and weak electrostatic interactions induced liquid droplet formation. (PMID:30762296).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30762296); morphological traits (PMID:30762296); sensitivity to 1,6-hexanediol (PMID:30762296); reversibility of formation and dissolution (PMID:30762296).</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-DNA interaction (PMID:30762296); electrostatic (cation-anion) interaction (PMID:30762296)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rawan Abukhairan</annotator>
<functional_class type="str">
protective storage/reservoir; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</Q8L3W1>
<Q07352 type="dict">
<id type="str">
111</id>
<phase_id type="str">
95</phase_id>
<common_name type="str">
TIS11B</common_name>
<name type="str">
mRNA decay activator protein ZFP36L1</name>
<accession type="str">
Q07352</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MTTTLVSATIFDLSEVLCKGNKMLNYSAPSAGGCLLDRKAVGTPAGGGFPRRHSVTLPSSKFHQNQLLSSLKGEPAPALSSRDSRFRDRSFSEGGERLLPTQKQPGGGQVNSSRYKTELCRPFEENGACKYGDKCQFAHGIHELRSLTRHPKYKTELCRTFHTIGFCPYGPRCHFIHNAEERRALAGARDLSADRPRLQHSFSFAGFPSAAATAAATGLLDSPTSITPPPILSADDLLGSPTLPDGTNNPFAFSSQELASLFAPSMGLPGGGSPTTFLFRPMSESPHMFDSPPSPQDSLSDQEGYLSSSSSSHSGSDSPTLDNSRRLPIFSRLSISDD</sequence>
<gene type="str">
ZFP36L1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS (charge pattern required)</segment>
<boundaries type="str">
1-338</boundaries>
<region_ref type="str">
30449617</region_ref>
<partners type="str">
1) ER membrane (TIS granules intertwined with it); 2) mRNA; 3) membrane proteins</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
TIS granules, gel-like TIS11B assemblies</forms>
<organelles type="str">
cytoplasmic ribonucleoprotein granule; TIS granule</organelles>
<pmids type="str">
30449617 (research article)</pmids>
<description type="str">
TIS11B is an RNA-binding protein encoded by the ZFP36L1 gene, which is widely expressed across human tissues and cell types. TIS11B was found to form TIS granules through physiological assembly. TIS11B generates reticular assemblies that are intertwined with the peri-nuclear ER and that enrichs specific mRNAs and proteins. The association between TIS granules and the ER creates a subcellular compartment—the TIGER domain (TIS granule-ER)—with a biophysically and biochemically distinct environment from the cytoplasm. TIS granules enable translation of mRNAs with AU-rich elements at an ER subdomain. Specific protein-protein interactions can only be formed in the TIS granule region. mRNAs that combine the presence of multiple AREs in their 3&apos;UTRs and the presence of at least one region that encodes a transmembrane domain, are enriched in TIS granules, whereas in the absence of both features mRNAs are excluded from TIS granules. TIS11B assemblies are called TIS granules as they enrich LU mRNA, because they have the characteristics of RNA granules. TIGER compartment promotes 3&apos;UTR-mediated interaction of SET with membrane proteins, thus allowing increased surface expression and functional diversity of proteins, including CD47 and PD-L1. It has been shown that TIS11B assembly is not caused by the presence of the IDR, but instead is charge pattern driven. Importantly, regulation of mRNA stability can be accomplished by soluble TIS11B, but TIS11B assembly is required for the collective properties of the protein that endow it with the ability to regulate protein functions through mediating 3&apos;UTR-dependent protein-protein interactions. TIS11B assembly is conserved among vertebrate species. However, no in vitro investigation of the protein were performed. As a conclusion, the association of TIS granules with the ER creates a subcellular compartment with special properties that is necessary and sufficient for SET transfer from mRNAs to proteins, and thus, for the 3&apos;UTR-dependent interaction of SET, and likely other proteins, with membrane proteins (PMID:30449617) </description>
<experiment_llps type="str">
In vivo fluorescent confocal microscopy of endogenous TIS11B protein in HeLa cells showed that the protein forms peri-nuclear assemblies that cover a substantial portion of the ER (protein localization). Live cell imaging using confocal microscopy and time lapse microscopy showed, in addition to soluble TIS11B in the cytoplasm, that TIS11B assemblies form a meshwork that is intertwined with the ER (morphology). 3D-reconstruction of confocal images showed that TIS11B assemblies have tubule-like structures that look similar to the ER, but are more bulky (morphology). FRAP assay suggested a gel-like state of the TIS11B assemblies (morphology). Using fluorescently tagged different costructs, RNA-fluorescence in situ hybridization (FISH) showed that membrane protein-encoding mRNAs that contain multiple AU-rich elements (AREs) in their 3&apos;UTRs co-localize with and are enriched in TIS granules. Confocal live cell imaging confirmed that TIS granules enrich specific proteins (protein localization). In vivo small hairpin RNA (shRNA)-mediated depletion of TIS11B (RNAi) and co-immunoprecipitation (coIP) showed that TIS11B is required for the 3&apos;UTR-mediated binding of SET to the membrane protein CD47. By introducing point and deletion mutations in TIS11B, as well as knockout of endogenous TIS11B it was shown by confocal live cell imaging microscopy and FACS analysis that TIS11B is the scaffold of TIS granules and its assembly is charge pattern-driven. Confocal live cell image microscopy showed that TIS11B is widely expressed and TIS granule formation is conserved among vertebrates. FRAP and retention assays showed that the biophysical and biochemical properties of the interior of TIS granules (morphology) are different from those of the cytoplasm. (PMID:30449617)</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30449617); morphological traits (PMID:30449617)</experiment_state>
<rna_req type="str">
mRNAs of membrane proteins with multiple AREs in their 3&apos;UTRs</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
linear oligomerization/self-association (PMID:30449617); electrostatic (cation-anion) interaction (PMID:30449617)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rawan Abukhairan</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; biomolecular filter/selectivity barrier</functional_class>
<date type="str">
2019-09-11</date>
</Q07352>
<P23771 type="dict">
<id type="str">
83</id>
<phase_id type="str">
99</phase_id>
<common_name type="str">
GATA3</common_name>
<name type="str">
Trans-acting T-cell-specific transcription factor GATA-3</name>
<accession type="str">
P23771</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEVTADQPRWVSHHHPAVLNGQHPDTHHPGLSHSYMDAAQYPLPEEVDVLFNIDGQGNHVPPYYGNSVRATVQRYPPTHHGSQVCRPPLLHGSLPWLDGGKALGSHHTASPWNLSPFSKTSIHHGSPGPLSVYPPASSSSLSGGHASPHLFTFPPTPPKDVSPDPSLSTPGSAGSARQDEKECLKYQVPLPDSMKLESSHSRGSMTALGGASSSTHHPITTYPPYVPEYSSGLFPPSSLLGGSPTGFGCKSRPKARSSTGRECVNCGATSTPLWRRDGTGHYLCNACGLYHKMNGQNRPLIKPKRRLSAARRAGTSCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINRPLTMKKEGIQTRNRKMSSKSKKCKKVHDSLEDFPKNSSFNPAALSRHMSSLSHISPFSHSSHMLTTPTPMHPPSSLSFGPHHPSSMVTAMG</sequence>
<gene type="str">
GATA3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
H/S/P/G-rich IDR</segment>
<boundaries type="str">
105-260</boundaries>
<region_ref type="str">
30833784</region_ref>
<partners type="str">
1) TFF1e eRNA (not required but promotes LLPS)</partners>
<determinants type="str">
1) crowding agent concentration</determinants>
<forms type="str">
liquid condensates, micron-sized droplets</forms>
<organelles type="str">
enhanceosome; nuclear body; robustly E2-activated enhancers (MegaTrans) enhancers</organelles>
<pmids type="str">
30833784 (research article)</pmids>
<description type="str">
A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. Estrogen signaling activates 7,000–8,000 enhancers genome-wide, out of which 1,248 are exceptionally active, on the basis of eRNA transcription and regulatory potential. These exceptionally active enhancers are characterized by E2-dependent recruitment of high levels of ERα, RNA Pol-II, MegaTrans components (for example, GATA3, FOXA1 and AP2γ), MED1 and P300 and by higher induced chromatin openness when compared to weak ERα-bound enhancers. These robustly E2-activated enhancers are referred to as MegaTrans enhancers. The initial, signal-dependent nucleation of enhanceosome complexes on potent, acutely activated enhancers, but not on basally active enhancers, represents an assembly process that is sensitive to 1,6-HD and is thus probably driven by phase separation. Chronic stimulation with E2 causes a fluid to hydrogel-like transition at enhancers and prevents ligand-induced enhancer proximity. Acutely active e2-responsive MegaTrans enhancers concentrate a protein complex that can undergo phase transition. GATA3 and ERα, two key components recruited to the MegaTrans enhancers, are capable of phase separating in vitro and in vivo, forming functional condensates with distinct fluid dynamics at MegaTrans enhancer loci (PMID:30833784).</description>
<experiment_llps type="str">
GATA3 was precipitated by b-isox in vitro that is indicative of LLPS. Condensates of purified GATA3 fused to MBP (with 5% PEG) exhibited typical characteristics of phase-separated liquid droplets (morphology), while MBP alone did not. Additionally, when GATA3-MBP and ERα-MBP (fusion protein) were mixed together in vitro, two-color confocal microscopy analysis revealed that they are enriched and coexist in a single, phase-separated condensate (protein co-localization). The IDR of GATA3 fused to mCherry-Cry2 (fusion protein) demonstrated efficient clustering and droplet formation on blue light stimulation and exhibited liquid droplet fusion behavior (morphology) in HEK293 cells in vivo. In MCF7 cells where endogenous GATA3 had been depleted by RNA interference, loss of E2-mediated activation of MegaTrans enhancers and their target genes was effectively rescued (other change in phenotype/functional readout) by expression of wild type GATA3 (genetic transformation), but not by the mutant protein lacking the IDR (res. 2-250). When in vitro transcribed, fluorescently labeled TFF1e eRNA was mixed with purified ERα-MBP or GATA3-MBP fusion proteins, in the presence of 5% PEG and 200 mM NaCl, it shortened the recovery time (t1/2) of GATA3-MBP and ERα-MBP fusion protein droplets by roughly 50% (change in RNA concentration). Also, in vivo depletion of TFF1e eRNA abolished recruitment of MegaTrans components GATA3, RARα and AP2γ to TFF1 enhancer region (localization) in response to E2, with no impact on the primary transcription factor, ERα. This supports a role for eRNAs in recruiting MegaTrans components (PMID:30833784).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30833784); morphological traits (PMID:30833784); sensitivity to 1,6-hexanediol (PMID:30833784)</experiment_state>
<rna_req type="str">
other specific RNA: TFF1e eRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P23771>
<P03372 type="dict">
<id type="str">
84</id>
<phase_id type="str">
100</phase_id>
<common_name type="str">
ERα</common_name>
<name type="str">
Estrogen receptor</name>
<accession type="str">
P03372</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLENEPSGYTVREAGPPAFYRPNSDNRRQGGRERLASTNDKGSMAMESAKETRYCAVCNDYASGYHYGVWSCEGCKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRGGRMLKHKRQRDDGEGRGEVGSAGDMRAANLWPSPLMIKRSKKNSLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLHAPTSRGGASVEETDQSHLATAGSTSSHSLQKYYITGEAEGFPATV</sequence>
<gene type="str">
ESR1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
H/S/P/G-rich IDR</segment>
<boundaries type="str">
79-174</boundaries>
<region_ref type="str">
30833784</region_ref>
<partners type="str">
1) TFF1e eRNA (not required but promotes LLPS)</partners>
<determinants type="str">
1) crowding agent concentration</determinants>
<forms type="str">
liquid condensates, micron-sized droplets</forms>
<organelles type="str">
enhanceosome; nuclear body; robustly E2-activated enhancers (MegaTrans) enhancers</organelles>
<pmids type="str">
30833784 (research article)</pmids>
<description type="str">
A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. Estrogen signaling activates 7,000–8,000 enhancers genome-wide, out of which 1,248 are exceptionally active, on the basis of eRNA transcription and regulatory potential. These exceptionally active enhancers are characterized by E2-dependent recruitment of high levels of ERα, RNA Pol-II, MegaTrans components (for example, GATA3, FOXA1 and AP2γ), MED1 and P300 and by higher induced chromatin openness when compared to weak ERα-bound enhancers. These robustly E2-activated enhancers are referred to as MegaTrans enhancers. The initial, signal-dependent nucleation of enhanceosome complexes on potent, acutely activated enhancers, but not on basally active enhancers, represents an assembly process that is sensitive to 1,6-HD and is thus probably driven by phase separation. Chronic stimulation with E2 causes a fluid to hydrogel-like transition at enhancers and prevents ligand-induced enhancer proximity. Acutely active e2-responsive MegaTrans enhancers concentrate a protein complex that can undergo phase transition. GATA3 and ERα, two key components recruited to the MegaTrans enhancers, are capable of phase separating in vitro and in vivo, forming functional condensates with distinct fluid dynamics at MegaTrans enhancer loci (PMID:30833784).</description>
<experiment_llps type="str">
Condensates of purified ERα fused to MBP (with 5% PEG) exhibited typical characteristics of phase-separated liquid droplets (morphology), while MBP alone did not. Additionally, when GATA3-MBP and ERα-MBP (fusion protein) were mixed together in vitro, two-color confocal microscopy analysis revealed that they are enriched and coexist in a single, phase-separated condensate (protein co-localization). The IDR of ERα fused to mCherry-Cry2 (fusion protein) demonstrated efficient clustering and droplet formation on blue light stimulation and exhibited liquid droplet fusion behavior (morphology) in transgenic HEK293 cells in vivo. Live-cell microscopy imaging revealed acute assembly of nuclear (fluorescently labeled) ERα foci within 1 min after E2 treatment in ~80% of the cells, with an average of 121 ± 25 distinct foci per nucleus (particle size and count), whereas no ERα foci were observed before E2 treatment. RNA fluorescence in situ hybridization (FISH) experiments showed that at least a subset of ERα foci develops in proximity to MegaTrans enhancers (protein co-localization). When in vitro transcribed, fluorescently labeled TFF1e eRNA was mixed with purified ERα-MBP or GATA3-MBP fusion proteins, in the presence of 5% PEG and 200 mM NaCl, it shortened the recovery time (t1/2) of GATA3-MBP and ERα-MBP fusion protein droplets by roughly 50% (change in RNA concentration). Also, depletion of TFF1e eRNA abolished recruitment of MegaTrans components GATA3, RARα and AP2γ to TFF1 enhancer region (localization) in response to E2, with no impact on the primary transcription factor, ERα. This supports a role for eRNAs in recruiting MegaTrans components. (PMID:30833784).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:30833784); morphological traits (PMID:30833784); sensitivity to 1,6-hexanediol (PMID:30833784)</experiment_state>
<rna_req type="str">
other specific RNA: TFF1e eRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P03372>
<O43781 type="dict">
<id type="str">
86</id>
<phase_id type="str">
103</phase_id>
<common_name type="str">
DYRK3</common_name>
<name type="str">
Dual specificity tyrosine-phosphorylation-regulated kinase 3</name>
<accession type="str">
O43781</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MGGTARGPGRKDAGPPGAGLPPQQRRLGDGVYDTFMMIDETKCPPCSNVLCNPSEPPPPRRLNMTTEQFTGDHTQHFLDGGEMKVEQLFQEFGNRKSNTIQSDGISDSEKCSPTVSQGKSSDCLNTVKSNSSSKAPKVVPLTPEQALKQYKHHLTAYEKLEIINYPEIYFVGPNAKKRHGVIGGPNNGGYDDADGAYIHVPRDHLAYRYEVLKIIGKGSFGQVARVYDHKLRQYVALKMVRNEKRFHRQAAEEIRILEHLKKQDKTGSMNVIHMLESFTFRNHVCMAFELLSIDLYELIKKNKFQGFSVQLVRKFAQSILQSLDALHKNKIIHCDLKPENILLKHHGRSSTKVIDFGSSCFEYQKLYTYIQSRFYRAPEIILGSRYSTPIDIWSFGCILAELLTGQPLFPGEDEGDQLACMMELLGMPPPKLLEQSKRAKYFINSKGIPRYCSVTTQADGRVVLVGGRSRRGKKRGPPGSKDWGTALKGCDDYLFIEFLKRCLHWDPSARLTPAQALRHPWISKSVPRPLTTIDKVSGKRVVNPASAFQGLGSKLPPVVGIANKLKANLMSETNGSIPLCSVLPKLIS</sequence>
<gene type="str">
DYRK3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Intrinsically disordered P-rich region</segment>
<boundaries type="str">
1-188</boundaries>
<region_ref type="str">
23415227</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of DYRK3; 2) phosphorylation state</determinants>
<forms type="str">
liquid-like DYRK3 speckles</forms>
<organelles type="str">
cytoplasmic stress granule; liquid-like DYRK3 speckles</organelles>
<pmids type="str">
23415227 (research article), 29973724 (research article)</pmids>
<description type="str">
Dual-specificity protein kinase that promotes disassembly of several types of membraneless organelles during mitosis, such as stress granules, nuclear speckles and pericentriolar material (PMID:29973724). Acts as a central dissolvase of membraneless organelles during the G2-to-M transition, after the nuclear-envelope breakdown: acts by mediating phosphorylation of multiple serine and threonine residues in unstructured domains of proteins, such as SRRM1 and PCM1 (PMID:29973724). Regulates mTORC1 by mediating the dissolution of stress granules: during stressful conditions, DYRK3 partitions from the cytosol to the stress granule, together with mTORC1 components, which prevents mTORC1 signaling (PMID:23415227). When stress signals are gone, the kinase activity of DYRK3 is required for the dissolution of stress granule and mTORC1 relocation to the cytosol: acts by mediating the phosphorylation of the mTORC1 inhibitor AKT1S1, allowing full reactivation of mTORC1 signaling (PMID:23415227). DYRK3 has the potential to condense granules in the cytosol of human cells to which the mRNA-binding protein GW182 can be recruited, and DYRK3 localizes to SGs during oxidative and osmotic stress. Following GFP-DYRK3 speckles by time-lapse microscopy revealed that the speckles move and merge in a liquid droplet-like manner. Overexpression of DYRK3 without the N-terminal domain (DYRK3-ΔNT) did not induce cytoplasmic granules and did not partitionin SGs induced by oxidative stress. Inhibition of DYRK3 affects SG dissolution through a specific state of DYRK3 when its kinase activity is compromised. This state depends on the N-terminal domain of DYRK3, which, when expressed alone or as part of kinase-deficient DYRK3, is able to induce the appearance of SGs in the absence of stress. DYRK3 regulates its own partitioning between SGs and the cytosol in a cyclic manner through its kinase activity. Also, DYRK3 directly phosphorylates PRAS40 at Thr246,a phosphorylation site responsible for regulation of PRAS40, resulting in decreased binding of PRAS40 to mTORC1, allowing activation of mTORC1 signaling in unstressed cells and reactivation of mTORC1 during stress recovery. DYRK inhibitors reduce mTORC1 signaling by blocking SG dissolution (PMID:23415227). In all, when SGs condense, for instance during stress, DYRK3 will partition in SGs via its N-terminal domain. Here, it contributes to preventing SG dissolution, leading to partitioning of the mTORC1 complex in SGs and thus blocking it from signaling to downstream effectors. To dissolve SGs, the kinase activity of DYRK3 is required, leading to partitioning of the mTORC1 complex in the cytosol, where DYRK3 phosphorylates PRAS40, which allows reactivation of mTORC1. Thus, DYRK3 represents a type of regulator that dynamically couples phase transition-mediated compartmentalization to signal transduction via its kinase activity (PMID:23415227).</description>
<experiment_llps type="str">
By transiently expressing GFP-fused DYRK3 in (transgenic) HeLa cells in vivo, GFP-DYRK3 localized predominantly on distinct speckles distributed throughout the cytoplasm of cells. At low levels of expression (change in protein concentration), however, GFP-DYRK3 displayed a homogeneous distribution throughout the cytoplasm (protein localization) and did not condense in speckles. GFP-DYRK3 condensation occured when a certain threshold of expression level was reached. Furthermore, following GFP-DYRK3 speckles by time-lapse microscopy revealed that the speckles move and merge in a liquid droplet-like manner (morphology, particle size and count). To test whether DYRK3 condenses RNA granule components, myc-DYRK3 was coexpressed with GFP-GW182, a scaffold protein of mRNA processing bodies (P bodies) in C. elegans. When co-expressed (change in protein concentration), myc-DYRK3 and GFP-GW182 condense in granules (co-localization) that were larger than formed by GFP-DYRK3 expression alone (morphology). Importantly, it was observed that during oxidative and osmotic stress, endogenous DYRK3, as well as GFP-DYRK3, localizes to SGs. Furthermore, DEAD box p54 protein 6(DDX6)-positive P-bodies, often in close proximity to SGs, were found docked on GFP-DYRK3-positive granules (co-localization). Moreover, endogenous DYRK3 remained localized to SGs after 240 min of stress recovery in the presence of DYRK inhibitors. RNAi-mediated depletion of DYRK3 did not disturb the condensation of SGs during oxidative stress or dissolution of SGs after oxidative stress (particle size and count by microscopy); instead DYRK3 depletion reduced the block in SG dissolution caused by GSK-626616 treatment, wich suggests that inhibited DYRK3 is in a state that specifically prevents the dissolution of SGs. In support of this, it was observed that expression of the kinase-deficient point mutant DYRK3-K218M is sufficient to cause the appearance of large cytoplasmic structures positive for mRNA granule markers (morphology, protein localization, particle size and count by microscopy), on which GFP-DYRK3-K218M accumulated, even in the absence of stress. To test whether a specific domain of DYRK3 mediates partitioning to RNA granules, series of DYRK3 truncations were generated. Expression of DYRK3-NT, which consists of the N-terminal residues 1–188 and contains a predicted low-complexity sequence but which excludes the kinase domain and C-terminal end, induced the appearance of large granules (particle size and count) at high expression levels (change in protein concentration). Similar to SGs, these large granules had P bodies in close proximity and stained positive for PABP1. Conversely, overexpression of DYRK3 without the N-terminal domain (DYRK3-DNT; truncation) did not induce cytoplasmic granules and did not partition in SGs induced by oxidative stress (protein localization, particle size and count by microscopy) (PMID:23415227).; </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:23415227); morphological traits (PMID:23415227)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Márton Kovács</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</O43781>
<Q92777 type="dict">
<id type="str">
87</id>
<phase_id type="str">
105</phase_id>
<common_name type="str">
SYN2</common_name>
<name type="str">
Synapsin-2</name>
<accession type="str">
Q92777</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MMNFLRRRLSDSSFIANLPNGYMTDLQRPEPQQPPPPPPPGPGAASASAAPPTASPGPERRPPPASAPAPQPAPTPSVGSSFFSSLSQAVKQTAASAGLVDAPAPAPAAARKAKVLLVVDEPHADWAKCFRGKKVLGDYDIKVEQAEFSELNLVAHADGTYAVDMQVLRNGTKVVRSFRPDFVLIRQHAFGMAENEDFRHLIIGMQYAGLPSINSLESIYNFCDKPWVFAQLVAIYKTLGGEKFPLIEQTYYPNHKEMLTLPTFPVVVKIGHAHSGMGKVKVENHYDFQDIASVVALTQTYATAEPFIDSKYDIRVQKIGNNYKAYMRTSISGNWKTNTGSAMLEQIAMSDRYKLWVDTCSEMFGGLDICAVKAVHGKDGKDYIFEVMDCSMPLIGEHQVEDRQLITELVISKMNQLLSRTPALSPQRPLTTQQPQSGTLKDPDSSKTPPQRPPPQGGPGQPQGMQPPGKVLPPRRLPPGPSLPPSSSSSSSSSSSAPQRPGGPTTHGDAPSSSSSLAEAQPPLAAPPQKPQPHPQLNKSQSLTNAFSFSESSFFRSSANEDEAKAETIRSLRKSFASLFSD</sequence>
<gene type="str">
SYN2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
P/Q-rich C-terminal IDR with S-tracts</segment>
<boundaries type="str">
421-582</boundaries>
<region_ref type="str">
29976799</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
presynaptic cytosol; a matrix holding together clusters of synaptic vesicles (SVs)</organelles>
<pmids type="str">
29976799 (research article)</pmids>
<description type="str">
Neurotransmitter-containing synaptic vesicles (SVs) form tight clusters at synapses. These clusters act as a reservoir from which SVs are drawn for exocytosis during sustained activity. Several components associated with SVs that are likely to help form such clusters have been reported, including synapsin. Synapsin can form a distinct liquid phase in an aqueous environment. Synaptins (there are 3 variants present in humans and mice) seem to be functionally redundant, as strong phenotipical changes in the clustering of synaptic vesicules could only be observed in mice wherein all three SYN variants were knocked out. Synapsin 2 most probably performs a similar role to Synapsin 1 (PMID:29976799). </description>
<experiment_llps type="str">
mCherry-fused Synapsin 2 formed droplets in vitro (particle size and count) as assessed by confocal microscopy. Synapsin 1 and synapsin 2 coassembled in the same droplets (co-localization) in vitro. In vivo, knock-out mice wherein all three synapsin genes were deleted showed a decrease in the number and packing of synaptic vesicles away from active zones (morphology) by electron microscopy (PMID:29976799).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:29976799)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:29976799)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</Q92777>
<Q60598 type="dict">
<id type="str">
115</id>
<phase_id type="str">
106</phase_id>
<common_name type="str">
Cortactin</common_name>
<name type="str">
Src substrate cortactin</name>
<accession type="str">
Q60598</accession>
<organism type="str">
Mus musculus</organism>
<sequence type="str">
MWKASAGHAVSITQDDGGADDWETDPDFVNDVSEKEQRWGAKTVQGSGHQEHINIHKLRENVFQEHQTLKEKELETGPKASHGYGGKFGVEQDRMDRSAVGHEYQSKLSKHCSQVDSVRGFGGKFGVQMDRVDQSAVGFEYQGKTEKHASQKDYSSGFGGKYGVQADRVDKSAVGFDYQGKTEKHESQKDYSKGFGGKYGIDKDKVDKSAVGFEYQGKTEKHESQKDYVKGFGGKFGVQTDRQDKCALGWDHQEKLQLHESQKDYKTGFGGKFGVQSERQDSSAVGFDYKERLAKHESQQDYAKGFGGKYGVQKDRMDKNASTFEEVVQVPSAYQKTVPIEAVTSKTSNIRANFENLAKEREQEDRRKAEAERAQRMAKERQEQEEARRKLEEQARAKKQTPPASPSPQPIEDRPPSSPIYEDAAPFKAEPSYRGSEPEPEYSIEAAGIPEAGSQQGLTYTSEPVYETTEAPGHYQAEDDTYDGYESDLGITAIALYDYQAAGDDEISFDPDDIITNIEMIDDGWWRGVCKGRYGLFPANYVELRQ</sequence>
<gene type="str">
CTTN</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Cortactin repeats</segment>
<boundaries type="str">
84-330</boundaries>
<region_ref type="str">
30531905</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration of cortactin; 2) modification state</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
intracellular non-membrane-bounded organelle</organelles>
<pmids type="str">
30531905 (research article)</pmids>
<description type="str">
Cortactin was observed to undergo LLPS in vitro, but the functional relevance of this is know yet elucidated. Acetylation of lysines of the cortacting repeat region impairs LLPS (less turbidity, fewer droplets) amon physiologically relevan conditions (PMID:30531905).</description>
<experiment_llps type="str">
The cortactin repeat region sample became turbid among physiologically relevant conditions (NaCl 125 mM, PEG 10%) in vitro and liqid droplets were observed by DIC microscopy (particle size and count). The acetylation mimic mutant (K→Q) showed weakened LLPS, less turbidity, less droplets (particle size and count by microscopy) (PMID:30531905).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:30531905)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
84-330|K|hyperacetylation|weakens|PMID:30531905|CBP/p300|Notes:</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:30531905)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q60598>
<O74718 type="dict">
<id type="str">
120</id>
<phase_id type="str">
107</phase_id>
<common_name type="str">
Sup35</common_name>
<name type="str">
Eukaryotic peptide chain release factor GTP-binding subunit</name>
<accession type="str">
O74718</accession>
<organism type="str">
Schizosaccharomyces pombe</organism>
<sequence type="str">
MASNQPNNGEQDEQLAKQTSKLSMSAKAPTFTPKAAPFIPSFQRPGFVPVNNIAGGYPYAQYTGQGQNSNSPHPTKSYQQYYQKPTGNTVDEDKSRVPDFSKKKSFVPPKPAIPKGKVLSLGGNTSAPKSTKPISISLGGTKAPTTTKPAAPAAQSKTETPAPKVTSESTKKETAAPPPQETPTKSADAELAKTPSAPAAALKKAAEAAEPATVTEDATDLQNEVDQELLKDMYGKEHVNIVFIGHVDAGKSTLGGNILFLTGMVDKRTMEKIEREAKEAGKESWYLSWALDSTSEEREKGKTVEVGRAYFETEHRRFSLLDAPGHKGYVTNMINGASQADIGVLVISARRGEFEAGFERGGQTREHAVLARTQGINHLVVVINKMDEPSVQWSEERYKECVDKLSMFLRRVAGYNSKTDVKYMPVSAYTGQNVKDRVDSSVCPWYQGPSLLEYLDSMTHLERKVNAPFIMPIASKYKDLGTILEGKIEAGSIKKNSNVLVMPINQTLEVTAIYDEADEEISSSICGDQVRLRVRGDDSDVQTGYVLTSTKNPVHATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNRKSKKPPMFATKGMKIIAELETQTPVCMERFEDYQYMGRFTLRDQGTTVAVGKVVKILD</sequence>
<gene type="str">
SUP35</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal prion domain (N) and a charged middle domain (M); </segment>
<boundaries type="str">
1-235</boundaries>
<region_ref type="str">
29301985</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) pH; 2) salt concentration; 3) protein concentration of Sup35</determinants>
<forms type="str">
gel-like condensates, a porous polymer meshwork</forms>
<organelles type="str">
cytoplasmic protein granule; Sup35 condensate</organelles>
<pmids type="str">
29301985 (research article), 30963611 (review)</pmids>
<description type="str">
Sup35 from Schizosaccharomyces pombe exhibited similar behavior compared with that of Saccharomyces cerevisiae (entry: P05453); in vivo, it formed stress-dependent intracellular condensates and in vitro, it formed reversible liquid droplets at low pH that cross-link into a meshwork that was indistinguishable from the one of Sup35 from S. cerevisiae. Importantly, and in contrast to S. cerevisiae, Sc. pombe is unable to induce and propagate the prion state of Sup35. Thus, condensate formation, but not prion formation, is conserved among distantly related yeast that diverged more than 400 million years ago and suggests that condensate formation may be the ancestral function of the prion domain of Sup35 (PMID:29301985).</description>
<experiment_llps type="str">
In vivo, S. pombe Sup35 formed stress-dependent intracellular condensates (particle size and count by microscopy). In vitro it formed reversible liquid droplets at low pH that cross-link into a meshwork (morphology) that was indistinguishable from the one of Sup35 from S. cerevisiae (PMID:29301985).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
reversibility of formation and dissolution (PMID:29301985); morphological traits (PMID:29301985); </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID:29301985)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</O74718>
<P29590-12 type="dict">
<id type="str">
126</id>
<phase_id type="str">
23</phase_id>
<common_name type="str">
PML</common_name>
<name type="str">
Isoform PML-12 of Protein PML</name>
<accession type="str">
P29590-12</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MEPAPARSPRPQQDPARPQEPTMPPPETPSEGRQPSPSPSPTERAPASEEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPLGADTPALDNVFFESLQRRLSVYRQIVDAQAVCTRCKESADFWCFECEQLLCAKCFEAHQWFLKHEARPLAELRNQSVREFLDGTRKTNNIFCSNPNHRTPTLTSIYCRGCSKPLCCSCALLDSSHSELKCDISAEIQQRQEELDAMTQALQEQDSAFGAVHAQMHAAVGQLGRARAETEELIRERVRQVVAHVRAQERELLEAVDARYQRDYEEMASRLGRLDAVLQRIRTGSALVQRMKCYASDQEVLDMHGFLRQALCRLRQEEPQSLQAAVRTDGFDEFKVRLQDLSSCITQGKDAAVSKKASPEAASTPRDPIDVDLDVSNTTTAQKRKCSQTQCPRKVIKMESEEGKEARLARSSPEQPRPSTSKAVSPPHLDGPPSPRSPVIGSEVFLPNSNHVASGAGEAEERVVVISSSEDSDAENSSSRELDDSSSESSDLQLEGPSTLRVLDENLADPQAEDRPLVFFDLKIDNESGFSWGYPHPFLI</sequence>
<gene type="str">
PML</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-585</boundaries>
<region_ref type="str">
17081985</region_ref>
<partners type="str">
1) SUMO-1 (most probably needed for LLPS)</partners>
<determinants type="str">
1) protein concentration of SUMO-1; 2) modification state (SUMOylation); 3) arsenic concentration</determinants>
<forms type="str">
PML nuclear bodies (PML-NB)</forms>
<organelles type="str">
PML body</organelles>
<pmids type="str">
17081985 (research article), 10806494 (research article), 29599493 (research article), 17928811 (review), 29723661 (review), 27211601 (research article), 25355412 (research article), 24637324 (research article), 30099028 (review)</pmids>
<description type="str">
PML nuclear bodies (NBs) are nuclear structures that have been implicated in processes such as transcriptional regulation, genome stability, response to viral infection, apoptosis, and tumor suppression. Unlike other, more specialized subnuclear structures such as Cajal and Polycomb group bodies, PML-NBs are functionally promiscuous and have been implicated in the regulation of diverse cellular functions. PML-NBs are dynamic structures that favour the sequestration and release of proteins, mediate their post-translational modifications and promote specific nuclear events in response to various cellular stresses. Post-translational modification (especially SUMOylation) of both the PML scaffold and clients can regulate client recruitment to PML NBs. Phosphorylation of the Daxx SUMO interacting motif increases its affinity for SUMO-1 and, presumably, SUMOylated PML. Several results illustrate how SUMOylation of PML and SUMOylation or phosphorylation of clients can regulate the composition of PML NBs through modulating scaffold–client interactions. PML is the only protein that has been found to be essential for the formation of the NBs; and these structures do not form in PML null cells, although PML add back fully rescues their formation (PMID:17081985, PMID:17928811, PMID:30099028).</description>
<experiment_llps type="str">
In in vivo experiments, human PML and human GFP-tagged SUMO-1 was knocked-in to PML deficient mouse embryonic fibroblasts and confocal immunofluorescence analysis was performed following protein localization and co-localization with SUMO-1. These cells contained 10–20 PML NBs per cell nucleus of heterogeneous sizes (particle size and count), and PML was found to completely colocalize with GFP-SUMO-1, as evidenced by immunofluorescence microscopy. PML with the induced mutation of the SUMO binding motif still formed NBs, however with aberrant morphologies, and with reduced particle size and count compared to those formed by wild type PML in the nucleus; yet mutant PML still colocalized with GFP-SUMO-1 in agreement with the notion that it can still be SUMOylated. These results show that the PML SUMO binding motif and an intact RING domain (physsical interaction between the two) are required for PML-NB formation (PMID:17081985).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID:17081985); </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
160|K|SUMOylation|enables|PMID:9756909||Notes:SUMOylation is probably mediated by sentrin family of ubiquitin-like proteins. Mutation in SUMOylation sites can be partially compensated for by non-covalent binding of SUMO-1 through the SUMO interacting motif.; 442|K|SUMOylation|enables|PMID:9756909||Notes:SUMOylation is probably mediated by sentrin family of ubiquitin-like proteins. Mutation in SUMOylation sites can be partially compensated for by non-covalent binding of SUMO-1 through the SUMO interacting motif.; </ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Isoform P29590-1|not affected|PMID:28851805; Isoform P29590-2|not affected|PMID:28851805; Isoform P29590-4|affected|PMID:28851805; Isoform P29590-8|affected|PMID:28851805</splice>
<interaction type="str">
coiled-coil formation (PMID:24637324); discrete oligomerization (PMID:25355412)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; protective storage/reservoir</functional_class>
<date type="str">
2019-09-11</date>
</P29590-12>
<P78352-3 type="dict">
<id type="str">
127</id>
<phase_id type="str">
48</phase_id>
<common_name type="str">
PSD-95</common_name>
<name type="str">
Isoform 3 of Disks large homolog 4</name>
<accession type="str">
P78352-3</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MDCLCIVTTKKYRYQDEDTPPLEHSPAHLPNQANSPPVIVNTDTLEAPGYVNGTEGEMEYEEITLERGNSGLGFSIAGGTDNPHIGDDPSIFITKIIPGGAAAQDGRLRVNDSILFVNEVDVREVTHSAAVEALKEAGSIVRLYVMRRKPPAEKVMEIKLIKGPKGLGFSIAGGVGNQHIPGDNSIYVTKIIEGGAAHKDGRLQIGDKILAVNSVGLEDVMHEDAVAALKNTYDVVYLKVAKPSNAYLSDSYAPPDITTSYSQHLDNEISHSSYLGTDYPTAMTPTSPRRYSPVAKDLLGEEDIPREPRRIVIHRGSTGLGFNIVGGEDGEGIFISFILAGGPADLSGELRKGDQILSVNGVDLRNASHEQAAIALKNAGQTVTIIAQYKPEEYSRFEAKIHDLREQLMNSSLGSGTASLRSNPKRGFYIRALFDYDKTKDCGFLSQALSFRFGDVLHVIDASDEEWWQARRVHSDSETDDIGFIPSKRRVERREWSRLKAKDWGSSSGSQGREDSVLSYETVTQMEVHYARPIIILGPTKDRANDDLLSEFPDKFGSCVPHTTRPKREYEIDGRDYHFVSSREKMEKDIQAHKFIEAGQYNSHLYGTSVQSVREVAEQGKHCILDVSANAVRRLQAAHLHPIAIFIRPRSLENVLEINKRITEEQARKAFDRATKLEQEFTECFSAIVEGDSFEEIYHKVKRVIEDLSGPYIWVPARERL</sequence>
<gene type="str">
DLG4_HUMAN</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal &quot;PSG&quot; region (composd of a PDZ domain, an SH3 domain, and a guanylatekinase domain)</segment>
<boundaries type="str">
306-721</boundaries>
<region_ref type="str">
27565345</region_ref>
<partners type="str">
1) SynGAP coiled-coil/PDZ binding motif fragment (strictly required)</partners>
<determinants type="str">
1) protein concentration; 2) temperature</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
postsynaptic density</organelles>
<pmids type="str">
28524815 (research article), 27565345 (research article)</pmids>
<description type="str">
SynGAP forms a stable trimer in solution. Trimeric SynGAP CC-PBM (coiled-coil domain and the following PDZ binding motif) recruits two PSD-95 PSG (3 PDZ+SH3+GK domains) to form a 3:2 complex. The SynGAP/PSD-95 3:2 complex undergoes LLPS and evolves into a postsynaptic density (PSD). PSDs are assemblies responsible for receiving, interpreting and storage of signals transmitted by presynaptic axonal termini. They are disc-shaped, electron-dense thickenings that contact with postsynaptic membranes on its one face and with cytoplasm on the other face, forming semi-open mesoscale cellular compartments. Mutations altering the SynGAP/PSD-95 interaction can contribute to various brain disorders, including autism and IDs (intellectual disordes) (PMID:27565345).</description>
<experiment_llps type="str">
Physical interaction between SynGAP and PSD-95 was verified in vitro using purified proteins. Isothermal titration calorimetry (ITC)-based titration assay showed that N-terminal thioredoxin-tagged last 30 residues of SynGAP binds to each of the three PDZ domains of PSD-95 with comparable and weak affinities, and this interaction is enhanced by the alpha helix following the third PDZ domain. Similar in vitro analysis using fast protein liquid chromatog-raphy (FPLC) coupled with a static light-scattering assay and circular dichroism revealed that SynGAP forms a paraller coiled-coil trimer. In vitro structural studies also showed that trimeric SynGAP CC-PBM (residues 1147-1308) recruits two PSD-95 PSG (306-721) to form a 3:2 stochiometric complex (physical interaction). In vitro mixing of purified SynGAP CC-PBM andPSD-95 PSG above certain concentrations caused the sample solutions to become opalescent immediately owing to the formation of small spherical (morphology) droplets spanning various diameters (particle size and count), as followed using light microscopy. Neither SynGAP CC-PBM nor PSD-95PSG alone could form condensed liquid phase. Liquid-to-liquid phase separation and condensed liquid phase droplets fusion of the SynGAP/PSD-95 complex (particle size and count) was followed using Alexa488-labeled SynGAP CC-PBM and Cy3-labeled PSD-95 PSG (fluorescent tagging) by fluorescence microscopy. Fluorescence recovery after photobleaching (FRAP) analysis of Cy3-labled PSD-95 droplets demonstrated that PSD-95 molecules constantly exchange between droplets and the surrounding aqueous solution (PMID:27565345). When GFP-SynGAP CC-PBM and RFP-PSD-95 PSG were co-expressed in HeLa cells in vivo, many bright puncta were observed containing both GFP and RFP signals. Both GFP and RFP signal intensities were much brighter within the puncta than the surrounding cytoplasm, indicating enrichment with SynGAP and PSD-95. No puncta were observed in cells when only PSD-95 PSG or SynGAP CC-PBM was expressed (PMID:27565345).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:27565345); dynamic exchange of molecules with surrounding solvent (PMID:27565345); morphological traits (PMID:27565345); temperature-dependence (PMID:27565345)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif (PMID:27565345); </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; sensor</functional_class>
<date type="str">
2019-09-11</date>
</P78352-3>
<Q9UKV8 type="dict">
<id type="str">
128</id>
<phase_id type="str">
47</phase_id>
<common_name type="str">
AGO2</common_name>
<name type="str">
Protein argonaute-2</name>
<accession type="str">
Q9UKV8</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA</sequence>
<gene type="str">
AGO2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
PIWI domain</segment>
<boundaries type="str">
517-818</boundaries>
<region_ref type="str">
29576456</region_ref>
<partners type="str">
1) TNRC6B (strictly required for LLPS)</partners>
<determinants type="str">
1) protein concentration of Ago2; 2) salt concentration; 3) crowding agent concentration; 4) valency of Ago2</determinants>
<forms type="str">
liquid-like droplets</forms>
<organelles type="str">
RISC complex; P-body; micro-ribonucleoprotein complex; miRISC; GW-body</organelles>
<pmids type="str">
29576456 (research article)</pmids>
<description type="str">
miRISC is a multi-protein assembly that uses microRNAs (miRNAs) to identify mRNAs targeted for repression. Two core protein components of human miRISC, Argonaute2 (Ago2) and TNRC6B, condense into phase-separated droplets in vitro and in live cells. Phase separation is promoted by multivalent interactions between the glycine/tryptophan (GW)-rich domain of TNRC6B and three evenly spaced tryptophan-binding pockets in the Ago2 PIWI domain. When exposed to mammalian cell lysate, miRISC droplets also recruit components of the CCR4-NOT complex as well as deadenylase activity, which can be accelerated by more than two orders of magnitude upon phase separation. These observations suggest a model in which miRISC uses molecular condensation to sequester miRNA targets and concentrate them with factors that mediate mRNA decay. The use of phase separating systems to control RNA localization and stability may be a feature common to many aspects of RNA metabolism (PMID:29576456).</description>
<experiment_llps type="str">
The combined results of in vitro protein-protein interaction detection assays and X-ray crystallography with multiple Ago2 and TNRC6B mutants indicate that all three pockets in the trp-binding region of Ago2 contribute to physical interaction with TNRC6B. Specific Trp residues in TNRC6B Ago-binding domain (ABD) have pocket preferences, suggesting that the three trp-binding pockets are not perfectly redundant with each other, however, each pocket is able to interact with multiple different trp residues in TNRC6B, thus the interaction is multivalent and the structures formed may be heterogeneous and complex. Under physiological salt concentrations, in vitro, solutions containing both Ago2 and the TNRC6B-ABD quickly became opaque (change in optical properties), indicative of the formation of massive particles. Concentrated solutions of the ABD alone (but not that of Ago2) also became turbid at temperatures below 15°C. The fluorescently labeled TNRC6B ABD and Ago2 formed liquid droplets (morphology) in a protein concentration-dependent and salt concentration-dependent manner (particle size and count) as assessed by confocal microscopy. Ago valency (finetuned with mutations of the Trp-binding pockets) had a strong effect on droplet formation (particle size and count by microscopy). In a 293 HEK cell line stably overexpressing GFP-fused TNRC6B (genetic transformation) GFP-labeled, dynamic foci formed in vivo with 0.2 to 1mm in size (particle size and count by microscopy). Transfecting cells with a plasmid encoding mCherry-fused Ago2 revealed that Ago2 co-localized with TNRC6B foci in vivo. Ago2-TNRC6B droplets selectively sequester miRNA targets from the bulk solution: when mixed with droplets containing Ago2-let7 (Ago2 loaded with the miRNA let-7) in vitro, a target RNA with eight seed-matched let-7 binding sites (8xlet7) appeared almost exclusively in the pellet fraction (co-localization). In contrast, the 8xlet7 target RNA remained in the supernatant when added to droplets formed with Ago2-miR122. Ago2 kept its endonucleolytic cleavage (termed‘‘slicing’’) activity towards target RNAs within the condensates in the presence of a small RNA guide and the required ions in vitro (enzymatic activity assay). Ago2 and TNRC6B were mixed in the presence of soluble lysate from HEK293 cells, and the resulting droplets were isolated by centrifugation. Analysis by proteomics techniques (western blot) revealed that subunits of the CCR4-NOT deadenylase complex (a known miRISC component) co-pelleted with TNRC6B, while actin, which is not a component of miRISC, did not. (PMID:29576456).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:29576456); dynamic exchange of molecules with surrounding solvent (PMID:29576456); morphological traits (PMID:29576456)</experiment_state>
<rna_req type="str">
other type of RNA: miRNAs</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:29576456)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9UKV8>
<P00873 type="dict">
<id type="str">
130</id>
<phase_id type="str">
92</phase_id>
<common_name type="str">
Rubisco</common_name>
<name type="str">
Ribulose bisphosphate carboxylase small chain 1, chloroplastic</name>
<accession type="str">
P00873</accession>
<organism type="str">
Chlamydomonas reinhardtii</organism>
<sequence type="str">
MAAVIAKSSVSAAVARPARSSVRPMAALKPAVKAAPVAAPAQANQMMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRFGSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKTARDFQPANKRSV</sequence>
<gene type="str">
RBCS-1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
surface-exposed alpha helice 1 of the small subunit; surface-exposed alpha helice 2 of the small subunit</segment>
<boundaries type="str">
68-80; 131-144</boundaries>
<region_ref type="str">
27166422</region_ref>
<partners type="str">
1) EPYC1 </partners>
<determinants type="str">
1) protein concentration of Rubisco; 2) stochiometry of the components; 3) salt concentration</determinants>
<forms type="str">
liquid droplets</forms>
<organelles type="str">
pyrenoid</organelles>
<pmids type="str">
27166422 (research article), 28938114 (research article), 30498228 (research article), 30675061 (research article), 31001862 (review)</pmids>
<description type="str">
The pyrenoid is a carbon-fixing organelle in algae that undergoes LLPS owing to multivalent interactions between Rubisco and Essential Pyrenoid Component 1 (EPYC1). Rubisco and the linker protein EPYC1, are both necessary and sufficient to phase separate and form liquid droplets. The phase-separated Rubisco is functional. Droplet composition is dynamic and components rapidly exchange with the bulk solution. Rubisco has eight binding sites for EPYC1, while EPYC1 has four binding sites for Rubisco. Modeling suggests that such systems will exhibit a magic number effect where certain numbers of particles form an unusually stable state. The magic number effect manifests when the valency of one partner is an integral multiple of the valency of the second and the binding sites of the two partners can be saturated. This magic number effect could impact the phase diagram in many biological contexts and is predicted to give rise to unexpectedly sharp phase transition (PMID:30951647) If each repeat of EPYC1 binds Rubisco, then EPYC1 could link multiple Rubisco holoenzymes together to form the pyrenoid matrix. Multiple Rubisco binding sites on EPYC1 could arrange Rubisco into the hexagonal closely packed or cubic closely packed arrangement observed in recent cryoelectron tomography studies of the Chlamydomonas pyrenoid. EPYC1 and Rubisco could interact in one of two fundamental ways: (i) EPYC1 and Rubisco could form a codependent network, or (ii) EPYC1 could form a scaffold onto which Rubisco binds. Importantly, the 60-aa repeat length of EPYC1 is sufficient to span the observed 2- to 4.5-nm gap between Rubisco holoenzymes in the pyrenoid, and a stretched-out repeat could potentially span the observed 15-nm Rubisco center-to-center distance (PMID:27166422).</description>
<experiment_llps type="str">
Mixing pure C. reinhardtii Rubisco and EPYC1 led to immediate formation of a turbid solution that cleared over time in vitro. The turbidity was caused by the formation of spherical droplets (morphology) from the bulk solution that could be labeled by including a fluorescent EPYC1-GFP fusion protein in the reaction. The observed clearance of the solution was caused by fusion of the droplets into a large homogeneous droplet (coalescence), supporting their liquid nature. Demixed droplets could be harvested by centrifugation, and SDS-polyacrylamide gel electrophoresis analysis confirmed that both EPYC1 and Rubisco had entered the droplets (co-localization) (PMID:30498228). To confirm the pyrenoid localization of EPYC1, the authors coexpressed fluorescently tagged EPYC1 and RBCS. Venus-tagged EPYC1 showed clear colocalization with mCherry-tagged RBCS in the pyrenoid in vivo (PMID:27166422). Cryo-ET (imaging assay evidence) measurements revealed that the pyrenoid matrix is not crystalline, but exhibits liquid-like local order (morphology) and FRAP experiments revealed that the pyrenoid matrix mixes internally. The Chlamydomonas pyrenoid matrix also appears to undergo such a phase transition during division: a portion of the RBCS1-Venus and EPYC1-Venus signals rapidly dispersed from the pyrenoid matrix into the stroma investigated by fluorescent microscopy (PMID:28938114).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID:28938114); dynamic exchange of molecules with surrounding solvent (PMID:30498228); morphological traits (PMID:30498228)</experiment_state>
<rna_req type="str">
RNA not required</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID:28938114); electrostatic (cation-anion) interaction (PMID:30498228)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Nikoletta Murvai</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P00873>
<P78953 type="dict">
<id type="str">
129</id>
<phase_id type="str">
108</phase_id>
<common_name type="str">
Mid1p</common_name>
<name type="str">
Division mal foutue 1 protein</name>
<accession type="str">
P78953</accession>
<organism type="str">
Schizosaccharomyces pombe</organism>
<sequence type="str">
MKEQEFSYREAKDVSLDSKGLENSFLSSPNREKTPLFFEGNSNETSGYDQTKNFTHGDGDMSLGNLSELNVATDLLESLDLRSMYMHGYGHLDSSFSSQHSPDNRKRMSSTSVFKRINSEEEGRIPSLTYSAGTMNSTSSSTASLKGADIVADYETFNPDQNLAELSFDRSKSSRKRAVEVAEFSRAKTMSPLEYTVQHPYQSHNELSTNPARARAGSVPNLARIPSDVKPVPPAHLSASSTVGPRILPSLPKDTTEDNPALERVETTASLDMDYKPLEPLAPIQEAPVEDTSEPFSSVPEATLDDSDISTESLRKKVLAKMEAKRISSGSSYASTLRKVYDFSELSLPTNGKDYDELYLQSSRNSEPEISTIINDSLQQENMDEDISATSIPKSQAAYGHGSVTYHEVPRYNLTSASVGYSISSQRGRIKSSSTIDNLSAILSSEDLRHPSMQPVPGTKRTYSNYCENEPNKSSQSLVSSESHNVEGWNYSETGTVGFYDPSAEISASIDELRQSTPVARDSELLSRAHSFDLNRLDLPSQDKSTSYEVPNGTENQSPRPVTSLGFVNETFFEEKPKAPLPLGRFYIHLNSILNISISEVHSPIKIIVNTPTQNMQLPWQAVNGNNRLDHDFAFHVDDNFKVSFMFLDIPIEDKSNGSKGVSATKDVSNGKPAETKSKARKFFDKLFNRRKKRKLNKAAAVENSKAKKSVVIKKVSGTATLNLGNVKDSCFGKAFNVEIPIISRGFLEAIPVKINSIGKRTLGNLTLTCLYIPELSVPEQELPFTLEQATMDLRHVRSNYLYNEGYLYRLEDSSIRRRFVVLRSKQLNFYAEKGGQYLDTFQLSKTVVSIPMVNFSEAVSNLGLVAGILATSVDRRHVQLFADSKKVCQKWLQVMNSRSFALDRGTEKLWLQEYVNFMA</sequence>
<gene type="str">
MID1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Disordered N-terminal region (expressed in insect cells, so it is hyperphosphorylated)</segment>
<boundaries type="str">
1-452</boundaries>
<region_ref type="str">
31243991</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration</determinants>
<forms type="str">
droplets</forms>
<organelles type="str">
contractile ring</organelles>
<pmids type="str">
31243991 (research article)</pmids>
<description type="str">
Anillin Mid1p is not essential for the viability of fission yeast, but cytokinesis fails in one-third of cells with the mid1Δ deletion mutation. The cleavage furrow is misplaced or oblique in many of the surviving cells. Purified Mid1p-N452 monomers have a strong tendency to aggregate in vitro when concentrated. Some of the protein precipitates, but much of it forms droplets that grow in size and decrease in number over time, which is characteristic for phase separation of proteins. At a concentration of ∼20 μM, most of the protein partitioned into large droplets after 3 h. During mitosis, these N-terminal constructs concentrated in nodes around the equator that acquired Myo2 and other contractile ring proteins. These cells formed contractile rings from strands of actin filaments and Myo2 slower than wild type cells but placed the septum closer to its normal position and orientation than the Δmid1 strain. In vivo the core of cytokinetic nodes consists of ∼10 copies of Mid1p, 10 dimers of F-BAR protein Cdc15p and IQGAP Rng2p, and 2 dimers of formin Cdc12p. High-resolution fluorescence microscopy of live cells has provided data about the organization of the proteins in cytokinetic nodes. More than 2 mDa of protein is crowded together in nodes near the membrane, their local concentrations are ∼500 μM, far above the concentrations that favor phase separation by Mid1p-N452. Formation of a separate phase by Mid1p may facilitate the assembly of nodes.  (PMID: 31243991).</description>
<experiment_llps type="str">
Mid1p-N452 purified from insect cells with phosphatase inhibitors aggregates over time in vitro. Differential interference contrast microscopy at room temperature (DIC) revealed that Mid1p-N452 at concentrations from 3.8 to 23 μM formed droplets, which increased in size over time. These concentrations are far below of those in nodes. Droplets formed earlier and grew faster at higher concentrations. As time passed, numerous small droplets with diameters of ∼0.5 μm were replaced by fewer droplets with diameters of ∼10 μm. A cysteine at the C-terminus of Mid1p-N452 was labeled with Alexa Fluor 488 C5 maleimide. Labeling strengthened the tendency of the protein to aggregate. In vitro fluorescence microscopy was used to study the droplet formation. The labeled protein (10 μM) formed fluorescent droplets, confirming that they are composed of Mid1p-N452 (PMID: 31243991). High-resolution fluorescence microscopy of live cells in vivo has provided data about the organization of the proteins in cytokinetic nodes. More than 2 mDa of protein is crowded together in nodes near the membrane, wherein its local concentration is ∼500 μM, far above the concentrations that favor phase separation by Mid1p-N452.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31243991)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
1-452|SYT|hyperphosphorylation|affect|PMID:31243991|Sid2p,Cdk1,Plo1|Notes: protein fragment with less phosphorylations tends to self aggregate</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Beáta Szabó</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P78953>
<Q9W4W2 type="dict">
<id type="str">
131</id>
<phase_id type="str">
109</phase_id>
<common_name type="str">
Female sterile (1) Yb</common_name>
<name type="str">
Female sterile (1) Yb</name>
<accession type="str">
Q9W4W2</accession>
<organism type="str">
Drosophila melanogaster</organism>
<sequence type="str">
MEPIGDLQVPSFKVVSGGTTFTYASPKSGAASLDFLAHTLRKREANTEKTILICQQNFEAERLKFELAERDVNTILLPPHGAMVGQVLLLWSKGYINQALILCDGMLEHLGVVEANLVIHTTLPELNKFEERLKWLSISARNAEMLVITPCDEENEKEGKGETEPEIVQQRMPLKVDALNSMQLYEIKENTPPTSSEDYKAEADVLLSAATPATIPNDNKEQEINLSVEDATVKLLASFELGSTDSAAVDESSPAAAKFNAPVYSPFVTENPTKSLDAEFQELVKSFKVQNVFKNMNLPPPPSVSIEEPVSSASASDYRHQIDTTSLDSIRTVKDSPASLAVVPFSAGGITYNNYGVLGWSRHAVVPCYGLTEAPDISTIIRRAMQQMGVARSRARAVQRFAWPHVSLGKSVLVVGNLQIGKTWSYLPTVCQRSHEDLQRRPDVGRGPTCIFVCPNQGQGKQIERWMSTLLCLLGSASGFEDVVTHWDKTQLVDIVRRLKKPVGILLTSVDLLLQLLNHNPVGSIFDAQAVKCIALDNLNDMVRVLPNDTMKLLQRLPEMFQLTQNKCQLLVSGRIWHTDLMVQHILPLMPDVLVLFDDALEASVYGGVQLDVRVVADEPEKIEHLKALIAERRNFANEPAVMVCSNSTEVLLLRRSLQAIGVNAHICVSEACYSNVAEWLRQSPSGLLLVTDDVVPRLKCGKIPLLIHYSFASMWARFKNRFSLFYANLKSPTTRPVGQSVVFAKPTDLENIWKLCDFYMKHKLPRPGHLLGILSQRRLEEQPTSRSLCHQMAAFGDCLRHKCMYRHVMWRDEVLPPDHYPKNGLIRFLVLVCYSPAALAVRLSDQFPTAIRFLNFPMSDLGERVQRHYELEANRHMHPNPVPGEMAVVKNINRYERVHIVSVESNVMVLVQLLDTSTECFSYKTSQLYSCDKIFKDSPREAMDLRILGLQPESLDRIWPDDARNLVRKDFFRRTHNKRNRQFHAVVQSAIHRTIFVRNIYDDEGNDLLSFVINRFRSHQDECCQLKLDAMVMSSKDCPYM</sequence>
<gene type="str">
FS(1)YB</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Full protein sequence contributes to LLPS (HelC domain, RNA helicase domain, eTud domain)</segment>
<boundaries type="str">
1-1042</boundaries>
<region_ref type="str">
31267711</region_ref>
<partners type="str">
1) Armitage (Armi); 2) Sister of Yb (SoYb); 3) Vreteno (Vret); 4) piRNAs</partners>
<determinants type="str">
1) Yb self-association; 2) Presence of flamenco RNA transcripts</determinants>
<forms type="str">
Yb bodies</forms>
<organelles type="str">
Yb body</organelles>
<pmids type="str">
31267711 (research article)</pmids>
<description type="str">
Yb bodies are gonadal soma-specific membraneless organelles to which PIWI-interacting RNA (piRNA) biogenesis factors, female sterile (1) Yb (Yb), Armitage (Armi), Sister of Yb (SoYb), Vreteno (Vret), and Shutdown (Shu) are localized. Loss of these factors abrogates piRNA biogenesis; thus, Yb bodies are considered to be the site of piRNA production. Yb body formation is required for producing transposon-repressing piRNAs but unnecessary for producing non-transposon-repressing genic piRNAs. Female sterile (1) Yb (Yb) is a primary component of Yb bodies that are liquid-like multivalent condensates whose assembly depends on Yb–Yb homotypic interaction and Yb binding particularly with flamenco RNA transcripts, the source of transposon-repressing piRNAs. All three domains of Yb are necessary for Yb body assembly and transposon silencing. Hel-C domain is both necessary and sufficient for Yb–Yb interaction. eTud serves as the Armi-interacting domain, and the SoYb–Vret heterodimer also binds Yb in an Armi-dependent manner. The eTud domain is required for and provides the specificity of Yb–RNA association and Yb body assembly in a coordinated manner with the RNA helicase domain. The hierarchical manner of Yb body assembly is as follows: Yb triggers Yb body formation in a manner independent of Armi,  SoYb, and Vret. Armi then joins the foci via a physical interaction with Yb. At this step, Armi may or may not be accompanied by SoYb and Vret. Finally, the SoYb–Vret heterodimer localizes to Yb bodies by interacting with Armi (PMID: 31267711).</description>
<experiment_llps type="str">
Yb bodies disappeared upon treatment with 1,6-hexanediol in vivo. In vivo, live-cell imaging of GFP-fused Yb was performed in Drosophila ovarian somatic cells (OSCs), fusion- and fission-type phenomena (morphology), which are common in liquid-like condensates, were also observed. The deltaHel-C mutant lacks the N-terminal 150 amino acids (1–150) that include the Hel-C domain (33–133), while the delta-eTud mutant lacks the 218 most C-terminal amino acids (825–1,042) involving the eTud domain (825–1,014). In normal OSCs in which endogenous Yb was present, delta-eTud showed greatly reduced binding of Armi. However, the mutant did associate with endogenous Yb. In contrast, the deltaHel-C mutant behaved in the completely opposite manner: deltaHel-C associated with Armi but not with endogenous Yb. Both Yb mutants failed to assemble punctate structures and instead scattered evenly in the cytosol. In both cases, endogenous Armi remained dispersed in the cytosol (localization). Therefore, both the Hel-C and the eTud domains are necessary for Yb body formation, as is the RNA helicase domain (PMID: 31267711).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31267711); sensitivity to 1,6-hexanediol (PMID: 31267711); </experiment_state>
<rna_req type="str">
piRNA</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Ágnes Tantos</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q9W4W2>
<P43243 type="dict">
<id type="str">
132</id>
<phase_id type="str">
110</phase_id>
<common_name type="str">
Matrin-3</common_name>
<name type="str">
Matrin-3</name>
<accession type="str">
P43243</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSKSFQQSSLSRDSQGHGRDLSAAGIGLLAAATQSLSMPASLGRMNQGTARLASLMNLGMSSSLNQQGAHSALSSASTSSHNLQSIFNIGSRGPLPLSSQHRGDADQASNILASFGLSARDLDELSRYPEDKITPENLPQILLQLKRRRTEEGPTLSYGRDGRSATREPPYRVPRDDWEEKRHFRRDSFDDRGPSLNPVLDYDHGSRSQESGYYDRMDYEDDRLRDGERCRDDSFFGETSHNYHKFDSEYERMGRGPGPLQERSLFEKKRGAPPSSNIEDFHGLLPKGYPHLCSICDLPVHSNKEWSQHINGASHSRRCQLLLEIYPEWNPDNDTGHTMGDPFMLQQSTNPAPGILGPPPPSFHLGGPAVGPRGNLGAGNGNLQGPRHMQKGRVETSRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVLRIPNRGIDLLKKDKSRKRSYSPDGKESPSDKKSKTDGSQKTESSTEGKEQEEKSGEDGEKDTKDDQTEQEPNMLLESEDELLVDEEEAAALLESGSSVGDETDLANLGDVASDGKKEPSDKAVKKDGSASAAAKKKLKKVDKIEELDQENEAALENGIKNEENTEPGAESSENADDPNKDTSENADGQSDENKDDYTIPDEYRIGPYQPNVPVGIDYVIPKTGFYCKLCSLFYTNEEVAKNTHCSSLPHYQKLKKFLNKLAEERRQKKET</sequence>
<gene type="str">
MATR3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
N-terminal disordered region</segment>
<boundaries type="str">
1-397</boundaries>
<region_ref type="str">
31019288</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) presence of RRM2</determinants>
<forms type="str">
spherical structures that resemble droplets, droplet-like structures</forms>
<organelles type="str">
nuclear protein granule; </organelles>
<pmids type="str">
29511296 (research article), 30015619 (research article), 31019288 (research article)</pmids>
<description type="str">
In live cells, MATR3 lacking RRM2 (ΔRRM2) formed intranuclear spherical structures that fused over time into large structures (PMID: 29511296). Elimination of its RNA recognition motifs had no effect on survival, instead facilitating its self-assembly into liquid-like droplets. (PMID: 30015619). The N-terminal 397 amino acids of MATR3 (tagged with a nuclear localization signal and expressed as a fusionprotein with YFP) formed droplet-like structures within nuclei. Introduction of the myopathic S85C mutation into NLS-N397 MATR3:YFP, but not ALS mutations F115C or P154S, inhibited droplet formation (PMID: 31019288).</description>
<experiment_llps type="str">
Similar to what was observed in other cell types, in vivo WT and mutant MATR3 were primarily localized to the nucleus of C2C12 myoblasts. In a small subset of cells (estimated to be &lt;5%) that were exceptionally fluorescent, a portion of the expressed MATR3:YFP was localized in puncta scattered within the cytosol; however, in the vast majority of the cells the fluorescence was exclusively nuclear. MATR3:YFP constructs lacking RRM1 produced a globular distribution of the protein within nuclei, whereas deletion of RRM2 produced a protein that was organized into spherical structures that resemble droplets. In cells expressing NLS-N397-MATR3:YFP, all of the fluorescent protein was nuclear and organized into spherical droplet-like structures that were dispersed throughout the nucleus. Introduction of the S85C mutation, which is associated with myopathy, into the NLS-N397-MATR3:YFP construct largely inhibited droplet formation compared to WT-N397-MATR3:YFP. By contrast, the F115C and P154S mutations appeared to have little impact on droplet formation. In cells coexpressing the two constructs, a portion of NLS-C263-TDP43:mCher resided within the droplets formed by NLS-N397-MATR3WT:YFP. However, when expressed alone, the NLS-C263-TDP43:mCher construct did not generate droplet-like structures (PMID: 31019288). No in vitro results available.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 29511296)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
S85C|dbSNP:rs121434591|Amyotrophic lateral sclerosis 21 (ALS21)|OMIM:606070|weakens|PMID:31019288|Notes:the mutation is reported to be associated to myopathy, not ALS, in the given publication.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
Not known</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</P43243>
<Q54VP4 type="dict">
<id type="str">
133</id>
<phase_id type="str">
111</phase_id>
<common_name type="str">
HSP48</common_name>
<name type="str">
Heat shock protein DDB_G0280215</name>
<accession type="str">
Q54VP4</accession>
<organism type="str">
Dictyostelium discoideum</organism>
<sequence type="str">
MSINWLTHPFEELSNLKHSLDETLKNWTEPAPTAATSMDWGWKPRMDVCENKDYYKIILELPSFNKDEIEVQVNGRFLSIKGQKIEHTTDEWKYHRRERYSGGEFHRAVALPEGIDGSSIQAKFQSGVLLLLIPKTGGKTSQHISLFGREEHGNKRNVIDLEEKERKRRMEESDPMLGRRWGTGRSLFSGSKLNNQNDTMYRKPSASDLRLVKQMETKERERRIRDTKGETEKKKNALKVSRYIKSLGMNPRSTLRRGGREMEKIIHLEERERQARIRDKGRMRQQQALAKKVSNLIKHSGGAARLRHTGFNYSTITKGYNTNKTKFDRFGKENDSFGGFNINKSFTNQFKGFGKNSGGKSINITTGGFKAPSQFNKFTHNLEEKERQRRLNDKKGQNDAKRLAAEISHMIGNAHF</sequence>
<gene type="str">
DDB_G0280215</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal disordered region</segment>
<boundaries type="str">
146-416</boundaries>
<region_ref type="str">
31217303</region_ref>
<partners type="str">
1) polyphosphate (possible role in phase separation)</partners>
<determinants type="str">
N/A</determinants>
<forms type="str">
biomolecular condensates</forms>
<organelles type="str">
intracellular non-membrane-bounded organelle</organelles>
<pmids type="str">
31217303 (research article)</pmids>
<description type="str">
A crystallin domain-containing protein, heat shock protein 48 (HSP48), is upregulated during D. discoideum development. HSP48 forms a biomolecular condensate via its highly positively charged intrinsically disordered C-terminus. In addition to HSP48, the highly negatively charged primordial chaperone polyphosphate is also upregulated during D. discoideum development, and probably functions to stabilize HSP48. Upon germination, levels of both HSP48 and polyphosphate dramatically decrease, consistent with a role in development (PMID: 31217303).</description>
<experiment_llps type="str">
GFP-HSP48 was present inthe cytosol; however, rather than being diffuse, it formed puncta in cells in vivo. Consistent with a region next to HSP48’s C terminus driving phase separation, GFP-HSP48ΔC-term did not form a biomolecular condensate but instead was diffuse, while both wild-type GFP-HSP48 and the GFP-HSP48ΔN-term retained their ability to form puncta in cells. To determine if polyphosphate was necessary for HSP48 phase separation, GFP-HSP48 was expressed in D. discoideum cells lacking polyphosphate kinase 1(PPK1), the major enzyme responsible for polyphosphate production in D. discoideum. In ΔPPK1 cells, the size and number of the GFP-HSP48 biomolecular condensates formed were dramatically decreased. GFP-HSP48 levels were also decreased in ΔPPK1 cells, suggesting a potential role for polyphosphate in regulating HSP48 protein levels. Because transcription and translation were unaffected, this suggested that polyphosphate may be functioning to stabilize HSP48 by preventing its degradation. Consistent with polyphosphate and HSP48 transcript levels being downregulated upon germination, nearly no HSP48 transcripts were detected in germinated cells (PMID: 31217303). No in vitro results available.</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
dynamic movement/reorganization of molecules within the droplet (PMID: 31217303); morphological traits (PMID: 31217303)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
electrostatic (cation-anion) interaction (PMID: 31217303)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Not known.</ptm_dep>
<domain_dep type="str">
Not known.</domain_dep>
<discrete_oligo type="str">
Not known.</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q54VP4>
<P26368 type="dict">
<id type="str">
134</id>
<phase_id type="str">
112</phase_id>
<common_name type="str">
U2AF65</common_name>
<name type="str">
Splicing factor U2AF 65 kDa subunit</name>
<accession type="str">
P26368</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSDFDEFERQLNENKQERDKENRHRKRSHSRSRSRDRKRRSRSRDRRNRDQRSASRDRRRRSKPLTRGAKEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVSPPSTINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW</sequence>
<gene type="str">
U2AF2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
RS domain; RRMs; UHM domain</segment>
<boundaries type="str">
27-62; 149-337; 385-466</boundaries>
<region_ref type="str">
31271494</region_ref>
<partners type="str">
1) SF3b155c (promotes LLPS through its ULM motifs binding to the UHM domain of U2AF65); 2) SPY-rich RNAs (promote LLPS through binding to the RRMs of U2AF65)</partners>
<determinants type="str">
1) protein concentration of U2AF65; 2) salt concentration; 3) crowding agent concentration</determinants>
<forms type="str">
U2AF65 assemblies</forms>
<organelles type="str">
nuclear speckle</organelles>
<pmids type="str">
31271494 (research article)</pmids>
<description type="str">
In cells, knockdown of either U2AF65 or CAPERa improves the inclusion of cassette exons that are preceded by repeated pyrimidine-rich motifs. In the second step of spliceosome assembly, SF1 that was bound to the branchpoint sequence is replaced by the U2 snRNA-containing ribonucleoprotein (U2 snRNP) with the help of U2AF65. The N-terminal arginine- and serine-rich (RS) domain of U2AF65 contacts the branchpoint sequence (BPS) and favors the formation of a U2 snRNA-BPS duplex. The U2AF65 UHM domain engages interactions with ULM motifs of the U2 snRNP subunit SF3b155. The results support a model in which liquid-like assemblies  of  U2AF65 and  CAPERa on  repetitive  pyrimidine-rich  RNA sequences  are  driven  by  their  RS  domains, and  facilitate the recruitment of the multi-ULM domain of SF3b155. RNA increases RS-dependent sedimentation most probably by favoring local concentration of U2AF65 on repeated binding sites for its RRMs. The U2AF65 RS domain mediates multivalent interactions in vitro and localization to compartments thought to originate from LLPS in vivo. At the light of the in vitro and in cells results, a mechanistic model is proposed in which the recruitment of U2 snRNP at the 3&apos; intronic sequences is regulated by liquid-like assemblies of U2AF65 and CAPERa generated by self-attracting RS domains, multiple UHM–ULM interactions with SF3B155, and bindings of RRMs to repeated pyrimidine-rich sequences. In all, U2AF65 assemblies contribute to sequence-specific splice site recognition (PMID: 31271494).</description>
<experiment_llps type="str">
Phase-contrast microscopy revealed the presence of droplets of U2AF65 which were sensitive to salt, SDS, concentration, and PEG-induced crowding as expected for a LLPS mechanism. This LLPS mechanism was also supported by the dynamics of these objects as evidenced by time-lapse microscopy. To ascertain the role of the low complexity RS domain in LLPS of U2AF65, the RS domain fused to GST was purified. The results indicate that liquid droplets are formed with the RS domain alone. In addition, deletion of the RS domain resulted in reduced sedimentation of U2AF65, indicating that this domain is mostly responsible for the formation of U2AF65 assemblies. SPY-rich RNAs had a concentration-dependent positive effect on the formation of U2AF65 assemblies. The formation of U2AF65 assemblies upon DNM2 RNA addition was exacerbated by the presence of the SF3b155 multi-ULM domain but not by a mutated domain lacking the essential tryptophan residues of the seven ULM motifs (tryptophan residues replaced by alanine). While SF3b155c was mainly soluble even at high concentration, it was efficiently recruited to U2AF65 assemblies in the presence of SPY-rich but not SPY-poor RNA. This effect of SF3b155c on U2AF65 assemblies was not observed for SF1c which presents a single ULM. Similar to repeated SPY sequences on RNA, the multi-ULM domain of SF3b155 probably increases the local concentration of U2AF65, thereby favoring liquid-like U2AF65 assemblies. In vivo overexpressed myc-tagged U2AF65 presented a distribution (protein localization) similar to the endogenous protein, but deletion of the RS domain dramatically reduced its sedimentation as confirmed by immunofluorescence microscopy. U2AF65 showed a co-localization with SF3b155 (PMID: 31271494).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31271494)</experiment_state>
<rna_req type="str">
SPY-rich RNAs (intronic RNA with repeated pyrimidine tracts)</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID: 31271494); protein-RNA interaction (PMID: 31271494); </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</P26368>
<Q14149 type="dict">
<id type="str">
135</id>
<phase_id type="str">
113</phase_id>
<common_name type="str">
MORC3</common_name>
<name type="str">
MORC family CW-type zinc finger protein 3</name>
<accession type="str">
Q14149</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MAAQPPRGIRLSALCPKFLHTNSTSHTWPFSAVAELIDNAYDPDVNAKQIWIDKTVINDHICLTFTDNGNGMTSDKLHKMLSFGFSDKVTMNGHVPVGLYGNGFKSGSMRLGKDAIVFTKNGESMSVGLLSQTYLEVIKAEHVVVPIVAFNKHRQMINLAESKASLAAILEHSLFSTEQKLLAELDAIIGKKGTRIIIWNLRSYKNATEFDFEKDKYDIRIPEDLDEITGKKGYKKQERMDQIAPESDYSLRAYCSILYLKPRMQIILRGQKVKTQLVSKSLAYIERDVYRPKFLSKTVRITFGFNCRNKDHYGIMMYHRNRLIKAYEKVGCQLRANNMGVGVVGIIECNFLKPTHNKQDFDYTNEYRLTITALGEKLNDYWNEMKVKKNTEYPLNLPVEDIQKRPDQTWVQCDACLKWRKLPDGMDQLPEKWYCSNNPDPQFRNCEVPEEPEDEDLVHPTYEKTYKKTNKEKFRIRQPEMIPRINAELLFRPTALSTPSFSSPKESVPRRHLSEGTNSYATRLLNNHQVPPQSEPESNSLKRRLSTRSSILNAKNRRLSSQFENSVYKGDDDDEDVIILEENSTPKPAVDHDIDMKSEQSHVEQGGVQVEFVGDSEPCGQTGSTSTSSSRCDQGNTAATQTEVPSLVVKKEETVEDEIDVRNDAVILPSCVEAEAKIHETQETTDKSADDAGCQLQELRNQLLLVTEEKENYKRQCHMFTDQIKVLQQRILEMNDKYVKKETCHQSTETDAVFLLESINGKSESPDHMVSQYQQALEEIERLKKQCSALQHVKAECSQCSNNESKSEMDEMAVQLDDVFRQLDKCSIERDQYKSEVELLEMEKSQIRSQCEELKTEVEQLKSTNQQTATDVSTSSNIEESVNHMDGESLKLRSLRVNVGQLLAMIVPDLDLQQVNYDVDVVDEILGQVVEQMSEISST</sequence>
<gene type="str">
MORC3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
ATPase domain</segment>
<boundaries type="str">
1-400</boundaries>
<region_ref type="str">
31284181</region_ref>
<partners type="str">
1) DNA (strictly required for LLPS); 2) ATP; 3) histone H3K4me3 peptide (strictly required for LLPS)</partners>
<determinants type="str">
1) valency (length) of DNA; 2) cell cycle phase; 3) H3 histone methylation state</determinants>
<forms type="str">
MORC3-NBs</forms>
<organelles type="str">
MORC3-NBs</organelles>
<pmids type="str">
31284181 (research article)</pmids>
<description type="str">
Microrchidia 3 (MORC3) ATPase is associated with a number of human diseases, including autoimmune disorders, Down syndrome, cancer, and viral infection. It contains an N-terminal ATPase-CW cassette followed by a long and largely disordered C-terminal region, harboring at least one coiled-coil and several SUMOylation sites. MORC3 exists in autoinhibited and active states: if the CW domain binds to the adjacent catalytic ATPase domain that impedes the ATPase domain’s association with DNA necessary for the catalytic activity of MORC3 (autoinhibition). Partners that bind the CW domain in a competitive manner (like histone H3 and influenza virus A protein NS1) free the ATPase domain and thus induce the active state (PMID: 30850548). In cells, both endogenous and overexpressed MORC3 forms nuclear bodies (NBs) in promyelocytic leukemia protein (PML)-dependent and PML-independent manner. MORC3 forms phase-separated liquid condensates in the cell nucleus that are heterogenous and undergo dynamic morphological changes during the cell cycle. Phase separation of the ATPase domain is promoted by ATP and the presence of DNA. However, the ATPase-CW cassette did not show phase separation. Only addition of both DNA and H3K4me3 led to the formation of ATPase-CW liquid droplets, indicating that the autoinhibited state needs to be resolved and the ATPase activity restored for LLPS to occur (PMID: 31284181). </description>
<experiment_llps type="str">
In vivo time-lapse live cell confocal microscopy experiments using live HeLa cells expressing mCherry-MORC3 and H2B-GFP showed that a representative cell undergoing a complete cycle of cell division underwent drastic changes in the number and volume of MORC3-NBs between interphase and metaphase (protein localization), which suggested that MORC3-NBs functioning is cell cycle dependent. In vivo, the number of MORC3-NBs decreases concomitantly with chromatin compaction, as indicated by H2B volume, and increases after nuclear division coinciding with chromatin decondensation. A clear solution of the in vitro recombinantly purified ATPase domain of MORC3 became visibly cloudy upon addition of 37-bp double-stranded DNA (change in optical properties). Visualizing the solution under a microscope revealed liquid-liquid separated droplets (particle size and count). We note that this process is ATPase concentration dependent and that phase separation can be detected with naked eye when the ATPase concentration is above 13.3 μM. Addition of ATP to the ATPase domain greatly stimulated the formation of condensates. It was particularly evident when 147-bp 601 DNA and 37-bp DNA were used in the reactions, in which we observed an 8- to 9-fold increase in droplet counts. Considerably fewer droplets were formed upon addition of 15-bp DNA with or without ATP, consistent with previous findings that the dimeric MORC3 ATPase domain cooperatively binds to 37-bp DNA but is incapable of the cooperative binding to the short 15-bp DNA. DNA was concentrated in the MORC3 condensates. To determine if the phase separation capability of MORC3 is also suppressed by CW, the ATPase-CW cassette was tested in in vitro condensate formation assays. DNA or H3K4me3 peptide that was added individually to the ATPase-CW cassette failed to promote phase separation; however, addition of both DNA and H3K4me3 led to the formation of ATPase-CW liquid droplets. The mixture of unmodified H3 peptide and DNA also promoted ATPase-CW droplet formation, although to a lesser degree, which is in agreement with a 5-to-10-fold decrease in binding activity of CW toward non-methylated H3 (H3K4me0) (PMID: 31284181). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31284181); dynamic movement/reorganization of molecules within the droplet (PMID: 31284181); dynamic exchange of molecules with surrounding solvent (PMID: 31284181); sensitivity to 1,6-hexanediol (PMID: 31284181)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-DNA interaction (PMID:31284181)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q14149>
<O65934 type="dict">
<id type="str">
136</id>
<phase_id type="str">
114</phase_id>
<common_name type="str">
Rv1747</common_name>
<name type="str">
ABC transporter ATP-binding/permease protein Rv1747</name>
<accession type="str">
O65934</accession>
<organism type="str">
Mycobacterium tuberculosis</organism>
<sequence type="str">
MPMSQPAAPPVLTVRYEGSERTFAAGHDVVVGRDLRADVRVAHPLISRAHLLLRFDQGRWVAIDNGSLNGLYLNNRRVPVVDIYDAQRVHIGNPDGPALDFEVGRHRGSAGRPPQTTSIRLPNLSAGAWPTDGPPQTGTLGSGQLQQLPPATTRIPAAPPSGPQPRYPTGGQQLWPPSGPQRAPQIYRPPTAAPPPAGARGGTEAGNLATSMMKILRPGRLTGELPPGAVRIGRANDNDIVIPEVLASRHHATLVPTPGGTEIRDNRSINGTFVNGARVDAALLHDGDVVTIGNIDLVFADGTLARREENLLETRVGGLDVRGVTWTIDGDKTLLDGISLTARPGMLTAVIGPSGAGKSTLARLVAGYTHPTDGTVTFEGHNVHAEYASLRSRIGMVPQDDVVHGQLTVKHALMYAAELRLPPDTTKDDRTQVVARVLEELEMSKHIDTRVDKLSGGQRKRASVALELLTGPSLLILDEPTSGLDPALDRQVMTMLRQLADAGRVVLVVTHSLTYLDVCDQVLLLAPGGKTAFCGPPTQIGPVMGTTNWADIFSTVADDPDAAKARYLARTGPTPPPPPVEQPAELGDPAHTSLFRQFSTIARRQLRLIVSDRGYFVFLALLPFIMGALSMSVPGDVGFGFPNPMGDAPNEPGQILVLLNVGAVFMGTALTIRDLIGERAIFRREQAVGLSTTAYLIAKVCVYTVLAVVQSAIVTVIVLVGKGGPTQGAVALSKPDLELFVDVAVTCVASAMLGLALSAIAKSNEQIMPLLVVAVMSQLVFSGGMIPVTGRVPLDQMSWVTPARWGFAASAATVDLIKLVPGPLTPKDSHWHHTASAWWFDMAMLVALSVIYVGFVRWKIRLKAC</sequence>
<gene type="str">
RV1747</gene>
<taxon type="str">
Bacteria</taxon>
<segment type="str">
ABC transporter cytoplasmic regulatory module: FHA domains and ID linker</segment>
<boundaries type="str">
1-310</boundaries>
<region_ref type="str">
31366629</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration; 2) phosphorylation state</determinants>
<forms type="str">
condensates</forms>
<organelles type="str">
intracellular non-membrane-bounded organelle</organelles>
<pmids type="str">
31366629 (research article)</pmids>
<description type="str">
The ABC transporter Rv1747 is a virulence factor that has been implicated in transporting intermediates of the cell wall biosynthesis pathway across the Mtb membrane. The Rv1747 regulatory module undergoes reversible phase separation that is enhanced on phosphorylation by multiple Mtb STPKs. The isolated FHA-1 and FHA-2 domains each bind with micromolar affinity to phosphopeptides corresponding to the mapped PknF phospho-acceptor sites T152 and T210 within the ID linker. Rv1747 phase separation is regulated by it cognate kinase PknF (encoded on the same operon as Rv1747), other Mtb STPKs and the sole phosphatase PstP. Rv1747 1–310 also phase-separated when tethered to lipid bilayers, suggesting that phase separation of the regulatory module could drive the clustering of wild-type Rv1747 in its native context. Rv1747 regulatory module also phase-separated both on model membranes and in live cells (PMID: 31366629).</description>
<experiment_llps type="str">
Unmodified and phosphorylated Rv1747 1 –310 phase-separated at different threshold concentrations. Solutions of the construct Rv1747 1–310 (50 μM), spanning the full regulatory module, became visibly turbid on phosphorylation (change in optical properties), formation of spheroidal condensates with well-defined boundaries were observed when phosphorylated by PknF. Phase separation was impaired, but not fully abrogated, by alanine substitutions of the mapped phospho-acceptors T152/T210. Nonphosphorylated Rv1747 1–310 also phase-separated, albeit at a significantly higher saturation concentration (∼250 μM) than the PknF-treated protein. Also, PstP, the sole serine/threonine phosphatase present in Mtb, dissolved PknF-induced Rv1747 1–310 droplets. Both AF647-labeled PknF and PstP were enriched in phosphorylated OG-Rv1747 1–310 droplets. However, unlike uniformly-distributed PknF, fluorescently labeled PstP appeared as foci on the surface of the droplets. This points to the presence of coexisting phases that are differentially penetrated and enriched in components of this Mtb signaling system.; Neither the isolated FHA domains nor the ID linker formed condensates at concentrations as high as 350 μM. This suggests that nonspecific electrostatic interactions between the linker (theoretical pI 11.9) and the FHA domains (pI 6.4 and 5.0, respectively) may play an important role in phase separation (in the unphosphorylated form). Consistent with this hypothesis, the saturation concentration of nonphosphorylated Rv1747 1–310 increased with ionic strength.; In vivo, yeast cells expressing msfGFP-Rv1747 1–310 had dense foci. These foci displayed properties consistent with phase separation. Also, live cell imaging of M. smegmatis expressing the regulatory module tagged with the fluorescent protein mEos2 showed that whereas mEos2 signals were mainly uniformly distributed, mEos2-Rv1747 1–310 formed multiple discrete foci along the length of the bacterium. When expressing mEso2-tagged Rv1747 in M. smegmatis, similar to the regulatory module, the full-length protein also formed foci, however, these foci were more dynamic, as they assembled and disassembled during the time scale of imaging. Therefore the presence of the transmembrane and nucleotide binding domains may modulate the dynamics of the foci formed by full-length Rv1747 (PMID: 31366629).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31366629); dynamic movement/reorganization of molecules within the droplet (PMID: 31366629); dynamic exchange of molecules with surrounding solvent (PMID: 31366629); </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
152|T|phosphorylation|promotes|PMID:31366629|PknF, other Mtb STPKs|Notes: besides the two mapped sites, the regulatory region may gets phosphorylated at other residues as well.; 210|T|phosphorylation|promotes|PMID:31366629|PknF, other Mtb STPKs|Notes: besides the two mapped sites, the regulatory region may gets phosphorylated at other residues as well.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-PTM interactions (PMID: 31366629); electrostatic (cation-anion) interaction (PMID: 31366629); </interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</O65934>
<A0QSY1 type="dict">
<id type="str">
137</id>
<phase_id type="str">
115</phase_id>
<common_name type="str">
MSMEG_1642</common_name>
<name type="str">
ABC transporter, ATP-binding protein</name>
<accession type="str">
A0QSY1</accession>
<organism type="str">
Mycobacterium smegmatis</organism>
<sequence type="str">
MSRPSPPALTVRYEGSTRTFAPGSDVVIGRDLRADVRIAHPLISRAHLVLRFDQGRWVAIDNGSLNGMYVNGRRVSSVDLQDGQVLNIGNPDGPQLSFEVGRHQGSAGRTPTAAVPVAGHTGTSWPTQAPTGGGWQQPYTQPPRTQYPQTTGTQQRYPSAPQHGYPNGPQTGYPSGPQRGYPSGPQTGYPTNGPAGAPQSYQSQPVRTPPPAPANSSQAPTTMGPAAAPRGGAEPASNLATSMLKILRPGRSAPAPAGAVKIGRATDNDIVIPDVLASRHHATLIPLPGGTEIRDERSINGTFVNGTRVDSAVLHDGDVVTIGNVDLVFSGGTLARRSETEADTRTGGLEVRGLTWTIEGNKTLLDNISIDARPGTLTAVIGPSGAGKSTFARQVAGYTHPTSGTIKFEGHDVHAEYASLRSRIGMVPQDDVVHGQLTVRQALMYAAELRLPPDTTKEDREQVVMQVLEELEMTKHLDTRVDKLSGGQRKRASVALELLTGPSLLILDEPTSGLDPALDRQVMTMLRQLADAGRVVLVVTHSLTYLDVCDQVLLLAPGGKTAFFGPPSQIGPELGTTNWADIFSTVADDPAEANRRYLARTPEAPPASASSEAPADLGAPAKTSLRRQFSTIGRRQLRLIISDRGYFIFLALLPFIMGTLSLSVPGTVGFGVPNPMGDAPNEPGQILVLLNVGAIFMGTALTIRDLIGERAIFRREQAVGLSTTAYLLAKVCVYSVFAVVQSAIVTVITISGKGWGEGAVERGVVIPNRSLELFLSMAATTVTAAMVGLALSALAKTSEQIMPLLVVAIMSQLVFSGGMIPVTGRIGLDQLSWITPARWGFAASASTVDLIRLVPGPLTPKDSHWEHTSGTWLFDMAMLGVLSVFYVTFVRWKIRLKAG</sequence>
<gene type="str">
MSMEG_1642</gene>
<taxon type="str">
Bacteria</taxon>
<segment type="str">
ABC transporter cytoplasmic regulatory module: FHA domains and ID linker</segment>
<boundaries type="str">
1-340</boundaries>
<region_ref type="str">
31366629</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) protein concentration; 2) phosphorylation state</determinants>
<forms type="str">
condensates</forms>
<organelles type="str">
intracellular non-membrane-bounded organelle</organelles>
<pmids type="str">
31366629 (research article)</pmids>
<description type="str">
MSMEG_1642 is the M. smegmatis homolog of Rv1747. Phase separation and phosphorylation dependence have also been demonstrated for MSMEG_1642 to show that the mechanism observed for Rv1747 is conserved in evolution (PMID: 31366629).</description>
<experiment_llps type="str">
A construct spanning the regulatory module, MSMEG_1642 1–340, phase separated in vitro. Phosphorylation by PknF also reduced the threshold concentration for MSMEG_1642 1–340 to form condensates (PMID: 31366629).</experiment_llps>
<in_vivo type="str">
False</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31366629)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-PTM interactions (PMID: 31366629); electrostatic (cation-anion) interaction (PMID: 31366629); </interaction>
<membrane_clust type="str">
Y</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</A0QSY1>
<P35972 type="dict">
<id type="str">
138</id>
<phase_id type="str">
116</phase_id>
<common_name type="str">
Nucleoprotein</common_name>
<name type="str">
Nucleoprotein</name>
<accession type="str">
P35972</accession>
<organism type="str">
Measles virus</organism>
<sequence type="str">
MATLLRSLALFKRNKDKPPITSGSGGAIRGIKHIIIVPIPGDSSITTRSRLLDRLVRLIGNPDVSGPKLTGALIGILSLFVESPGQLIQRITDDPDVSIRLLEVVQSDQSQSGLTFASRGTNMEDEADKYFSHDDPISSDQSRFGWFENKEISDIEVQDPEGFNMILGTILAQIWVLLAKAVTAPDTAADSELRRWIKYTQQRRVVGEFRLERKWLDVVRNRIAEDLSLRRFMVALILDIKRTPGNKPRIAEMICDIDTYIVEAGLASFILTIKFGIETMYPALGLHEFAGELSTLESLMNLYQQMGETAPYMVNLENSIQNKFSAGSYPLLWSYAMGVGVELENSMGGLNFGRSYFDPAYFRLGQEMVRRSAGKVSSTLASELGITAEDARLVSEIAMHTTEDKISRAVGPRQAQVSFLHGDQSENELPRLGGKEDRRVKQSRGEARESYRETGPSRASDARAAHLPTGTPLDIDTASESSQDPQDSRRSADALLRLQAMAGISEEQGSDTDTPIVYNDRNLLD</sequence>
<gene type="str">
N</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
C-terminal motif-containing unstructured region</segment>
<boundaries type="str">
392-525</boundaries>
<region_ref type="str">
31375591</region_ref>
<partners type="str">
1) Phosphoprotein</partners>
<determinants type="str">
1) phosphorylation state of P; 2) activity of host dynein</determinants>
<forms type="str">
IBs, spherical puncta</forms>
<organelles type="str">
inclusion body</organelles>
<pmids type="str">
31375591 (research article)</pmids>
<description type="str">
Measles viruses (MeV) are assumed to replicate in cytoplasmic inclusion bodies (IBs). These cytoplasmic viral factories are not membrane-bound and serve to concentrate the viral RNA replication machinery. The formation of IBs is dependent on the P (Phosphoprotein) and N (Nucleoprotein) proteins. Multivalent domain-motif interactions between the C-terminal XD domain of P and the motif-containing C-terminal region of N drive LLPS. Phosphorylations of P outside the XD domain by CK2 affect the size distribution of IBs. Inhibiting CK2 phosphorylations or the activity of host dyneins eliminated the formation of large IBs but small IBs where still formed in both conditions (PMID: 31375591).</description>
<experiment_llps type="str">
In vivo the nascent MeV IBs exist initially as small spheres that subsequently increase in size and adopt different shapes (protein localization, particle size and count). MeV N expressed alone in vivo in transfected cells mislocalized and was enriched in the nucleoli of 95% of the cells (protein localization). Expression of MeV P in the absence of N in transfected cells exhibited diffuse cytoplasmic staining in most (65%) of the cells (protein localization). P expression alone also formed perinuclear puncta in 35% of the transfected cells, however these puncta were rarely spherical and often displayed unusually large size (particle size and count). By contrast, the characteristic spherical puncta seen in infected cells were prevalent in transfected cells (95%) co-expressing both N and P. The formation of spherical puncta in transfected cells co-expressing N and P did not depend on the ability of N to bind RNA since co-expression of the N(KRR/AAA) mutant and P resulted in puncta of comparable size and morphology as co-expression of WT N with P.  Deletion of the XD domain of P prevented the formation of IB in 80% of transfected cells as revealed by the comparison of truncated mutant P (1 -458) to WT P. Compared to either deletion of XD or alanine substitution mutations within the XD domain of P protein, the deletion of the C-terminal MoRE-containing unstructured region from N (aa 392-525) produced the most dramatic phenotype. In nearly all transfected cells (97%), only a few small irregular-shaped puncta could be observed. Treating MeV-infected cells with DMAT, a cell-permeable inhibitor of CK2, decreased the IB size without significantly affecting N protein expression. Being expressed at a similar level as wild-type P protein, the S86A/S151A mutant compared to WT P protein did not trigger the production of large IBs when co-expressed with N. When cells that displayed comparable levels of N and P between the control and experimental groups were analyzed, the volume of the largest punctum within each cell was significantly reduced for the phospho site S86A/S151A mutant of P, further indicating a role for S86 and S151 phosphorylation in modulating the size of IBs formed by N and P co-expression. Host dynein promotes viral replication by facilitating the formation of large IBs (PMID: 31375591).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31375591); dynamic exchange of molecules with surrounding solvent (PMID: 31375591); </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID: 31375591)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P35972>
<Q9Y5A9 type="dict">
<id type="str">
139</id>
<phase_id type="str">
117</phase_id>
<common_name type="str">
YTHDF2, DF2</common_name>
<name type="str">
YTH domain-containing family protein 2</name>
<accession type="str">
Q9Y5A9</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSASSLLEQRPKGQGNKVQNGSVHQKDGLNDDDFEPYLSPQARPNNAYTAMSDSYLPSYYSPSIGFSYSLGEAAWSTGGDTAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGSTPFLGQHGFNFFPSGIDFSAWGNNSSQGQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNTIDQGMAALKLGSTEVASNVPKVVGSAVGSGSITSNIVASNSLPPATIAPPKPASWADIASKPAKQQPKLKTKNGIAGSSLPPPPIKHNMDIGTWDNKGPVAKAPSQALVQNIGQPTQGSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTRWVAPRNRGSGFGHNGVDGNGVGQSQAGSGSTPSEPHPVLEKLRSINNYNPKDFDWNLKHGRVFIIKSYSEDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQDKWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSHYEKRQEEEESVKKERQGRGK</sequence>
<gene type="str">
YTHDF2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Low complexity region with Pro-Xn-Gly motifs; YTH domain</segment>
<boundaries type="str">
1-409; 410-544</boundaries>
<region_ref type="str">
31292544</region_ref>
<partners type="str">
1) polymethylated (m6A) mRNAs (promote LLPS)</partners>
<determinants type="str">
1) temperature; 2) protein concentration; 3) salt concentration; 4) m6A modification level of mRNA</determinants>
<forms type="str">
droplets</forms>
<organelles type="str">
P-body; cytoplasmic stress granule; neuronal ribonucleoprotein granule</organelles>
<pmids type="str">
31292544 (research article), 31388144 (research article)</pmids>
<description type="str">
The cytosolic m6A-binding proteins—YTHDF1, YTHDF2 and YTHDF3—undergo LLPS in vitro and in cells. This LLPS is markedly enhanced by mRNAs that contain multiple, but not single, m6A residues. Polymethylated mRNAs act as a multivalent scaffold for the binding of YTHDF proteins, juxtaposing their low-complexity domains and thereby leading to phase separation. The resulting mRNA–YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules or neuronal RNA granules. Although mRNAs are targeted to diverse intracellular condensates through diverse RNA–RNA and RNA–protein interactions, the presence of m6A further enhances the partitioning into these structures. Furthermore, singly methylated and polymethylated mRNAs have different fates, which probably reflect their different abilities to promote LLPS. Importantly, monomethylated and polymethylated mRNAs are linked to distinct cellular processes. LLPS may therefore influence specific cellular processes by selectively affecting the translation of mRNAs on the basis of their polymethylation status (PMID: 31292544).</description>
<experiment_llps type="str">
Solutions of DF2 were clear at 4 °C, became turbid upon warming to 37 °C, and then became clear again after cooling to 4 °C (PMID: 31292544).; The LCDs of all three YTHDF proteins underwent concentration-dependent phase separation in the absence of RNA. Full-length YTHDF1/2/3 proteins also underwent phase separation under physiological conditions in the absence of RNA, although their capacity for phase separation was decreased in comparison with their LCDs. Under stringent conditions such as high salt, the quadruple m6A RNA oligo, but not the quadruple unmodified RNA oligo, promoted phase separation of YTHDF2. The enhancement is m6A valency-dependent, as the quadruple m6A RNA motif enhance phase separation of YTHDF2 much more than single m6A motif. The enhancement is also YTH domain-dependent, as the quadruple m6A RNA oligo failed to enhance phase separation of the LCD of YTHDF2 (PMID:31388144).; To address whether DF2 exhibits liquid-like properties in vivo, CRISPR–Cas9 was used to insert NeonGreen into the genomic YTHDF2 locus of HEK293 cells, resulting in the endogenous expression of NeonGreen-labelled DF2 (NeonGreen–DF2). Photobleaching of sodium arsenite-induced stress granules resulted in a rapid recovery of NeonGreen–DF2 fluorescence, which is consistent with the liquid-like behaviour of DF2 in vitro. m6A-containing mRNAs are enriched in distinct DF-containing RNA granules, such as P-bodies, stress granles and neuronal granules. DF2 is guided to P-bodies and stress granules by forming complexes with m6A-mRNA, thus m6A enhances the ability of DF proteins to partition into intracellular phase-separated compartments (PMID: 31292544).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
reversibility of formation and dissolution (PMID: 31292544); morphological traits (PMID: 31292544, PMID: 31388144); dynamic movement/reorganization of molecules within the droplet (PMID: 31292544); </experiment_state>
<rna_req type="str">
Polymethylated mRNAs (m6A)</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID: 31292544); protein-RNA interaction (PMID: 31292544)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q9Y5A9>
<Q9BYJ9 type="dict">
<id type="str">
140</id>
<phase_id type="str">
118</phase_id>
<common_name type="str">
YTHDF1, DF1</common_name>
<name type="str">
YTH domain-containing family protein 1</name>
<accession type="str">
Q9BYJ9</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSATSVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYLSSYYPPSIGFPYSLNEAPWSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNNIYQHRFNFFPENPAFSAWGTSGSQGQQTQSSAYGSSYTYPPSSLGGTVVDGQPGFHSDTLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVALTGVLSGNGGTNVNMPVSKPTSWAAIASKPAKPQPKMKTKSGPVMGGGLPPPPIKHNMDIGTWDNKGPVPKAPVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPRNRNAAFGQSGGAGSDSNSPGNVQPNSAPSVESHPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKERQSRNKQ</sequence>
<gene type="str">
YTHDF1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Low complexity region with Pro-Xn-Gly motifs; YTH domain</segment>
<boundaries type="str">
1-388; 389-523</boundaries>
<region_ref type="str">
31388144</region_ref>
<partners type="str">
1) polymethylated (m6A) mRNAs (promote LLPS)</partners>
<determinants type="str">
1) protein concentration; 2) m6A modification level of mRNA</determinants>
<forms type="str">
droplets</forms>
<organelles type="str">
P-body; cytoplasmic stress granule; neuronal ribonucleoprotein granule</organelles>
<pmids type="str">
31292544 (research article), 31388144 (research article)</pmids>
<description type="str">
The cytosolic m6A-binding proteins—YTHDF1, YTHDF2 and YTHDF3—undergo LLPS in vitro and in cells. This LLPS is markedly enhanced by mRNAs that contain multiple, but not single, m6A residues. Polymethylated mRNAs act as a multivalent scaffold for the binding of YTHDF proteins, juxtaposing their low-complexity domains and thereby leading to phase separation. The resulting mRNA–YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules or neuronal RNA granules. Although mRNAs are targeted to diverse intracellular condensates through diverse RNA–RNA and RNA–protein interactions, the presence of m6A further enhances the partitioning into these structures. Furthermore, singly methylated and polymethylated mRNAs have different fates, which probably reflect their different abilities to promote LLPS. Importantly, monomethylated and polymethylated mRNAs are linked to distinct cellular processes. LLPS may therefore influence specific cellular processes by selectively affecting the translation of mRNAs on the basis of their polymethylation status (PMID: 31292544).</description>
<experiment_llps type="str">
DF1 and DF3 undergo phase separation in vitro as assessed by the formation of protein droplets. Mixing the three recombinant proteins DF1, DF2 and DF3 shows that these proteins can phase-separate together to form protein droplets that contain all three proteins. In vivo, diverse stimuli—including heat shock, sodium arsenite and endoplasmic reticulum stress—caused all three DF proteins to relocalize from throughout the cytosol to stress granules in a range of cell types (PMID: 31292544). The isolated LC domain are capabe of LLPS in a concentration-dependent manner. Polymethylated mRNAs (m6A) promote the LLPS of the full-lengh proteins but not that of the isolated LC domain (PMID: 31388144), pointing out the role of the YTH domain in binding of polymethylated mRNAs that certainly plays a crcial role in the in vivo LLPS of these proteins. </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31292544)</experiment_state>
<rna_req type="str">
Polymethylated mRNAs (m6A)</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID: 31292544); protein-RNA interaction (PMID: 31292544)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q9BYJ9>
<Q7Z739 type="dict">
<id type="str">
141</id>
<phase_id type="str">
119</phase_id>
<common_name type="str">
YTHDF3, DF3</common_name>
<name type="str">
YTH domain-containing family protein 3</name>
<accession type="str">
Q7Z739</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MSATSVDQRPKGQGNKVSVQNGSIHQKDAVNDDDFEPYLSSQTNQSNSYPPMSDPYMPSYYAPSIGFPYSLGEAAWSTAGDQPMPYLTTYGQMSNGEHHYIPDGVFSQPGALGNTPPFLGQHGFNFFPGNADFSTWGTSGSQGQSTQSSAYSSSYGYPPSSLGRAITDGQAGFGNDTLSKVPGISSIEQGMTGLKIGGDLTAAVTKTVGTALSSSGMTSIATNSVPPVSSAAPKPTSWAAIARKPAKPQPKLKPKGNVGIGGSAVPPPPIKHNMNIGTWDEKGSVVKAPPTQPVLPPQTIIQQPQPLIQPPPLVQSQLPQQQPQPPQPQQQQGPQPQAQPHQVQPQQQQLQNRWVAPRNRGAGFNQNNGAGSENFGLGVVPVSASPSSVEVHPVLEKLKAINNYNPKDFDWNLKNGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDAAYRSLNGKGPLYLLFSVNGSGHFCGVAEMKSVVDYNAYAGVWSQDKWKGKFEVKWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIIATFKHTTSIFDDFAHYEKRQEEEEAMRRERNRNKQ</sequence>
<gene type="str">
YTHDF3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Low complexity region with Pro-Xn-Gly motifs; YTH domain</segment>
<boundaries type="str">
1-415; 416-550</boundaries>
<region_ref type="str">
31388144</region_ref>
<partners type="str">
1) polymethylated (m6A) mRNAs (promote LLPS)</partners>
<determinants type="str">
1) protein concentration; 2) m6A modification level of mRNA</determinants>
<forms type="str">
droplets</forms>
<organelles type="str">
P-body; cytoplasmic stress granule; neuronal ribonucleoprotein granule</organelles>
<pmids type="str">
31292544 (research article), 31388144 (research article)</pmids>
<description type="str">
The cytosolic m6A-binding proteins—YTHDF1, YTHDF2 and YTHDF3—undergo LLPS in vitro and in cells. This LLPS is markedly enhanced by mRNAs that contain multiple, but not single, m6A residues. Polymethylated mRNAs act as a multivalent scaffold for the binding of YTHDF proteins, juxtaposing their low-complexity domains and thereby leading to phase separation. The resulting mRNA–YTHDF complexes then partition into different endogenous phase-separated compartments, such as P-bodies, stress granules or neuronal RNA granules. Although mRNAs are targeted to diverse intracellular condensates through diverse RNA–RNA and RNA–protein interactions, the presence of m6A further enhances the partitioning into these structures. Furthermore, singly methylated and polymethylated mRNAs have different fates, which probably reflect their different abilities to promote LLPS. Importantly, monomethylated and polymethylated mRNAs are linked to distinct cellular processes. LLPS may therefore influence specific cellular processes by selectively affecting the translation of mRNAs on the basis of their polymethylation status (PMID: 31292544).</description>
<experiment_llps type="str">
DF1 and DF3 undergo phase separation in vitro as assessed by the formation of protein droplets. Mixing the three recombinant proteins DF1, DF2 and DF3 shows that these proteins can phase-separate together to form protein droplets that contain all three proteins. In vivo, diverse stimuli—including heat shock, sodium arsenite and endoplasmic reticulum stress—caused all three DF proteins to relocalize from throughout the cytosol to stress granules in a range of cell types (PMID: 31292544). The isolated LC domain are capabe of LLPS in a concentration-dependent manner. Polymethylated mRNAs (m6A) promote the LLPS of the full-lengh proteins but not that of the isolated LC domain (PMID: 31388144), pointing out the role of the YTH domain in binding of polymethylated mRNAs that certainly plays a crcial role in the in vivo LLPS of these proteins. </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31292544, PMID: 31388144); dynamic exchange of molecules with surrounding solvent (PMID: 31388144)</experiment_state>
<rna_req type="str">
Polymethylated mRNAs (m6A)</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
prion-like aggregation (PMID: 31292544); protein-RNA interaction (PMID: 31292544)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q7Z739>
<Q9U2F5 type="dict">
<id type="str">
142</id>
<phase_id type="str">
120</phase_id>
<common_name type="str">
TIAR-2</common_name>
<name type="str">
TIA-1/TIAL RNA binding protein homolog</name>
<accession type="str">
Q9U2F5</accession>
<organism type="str">
Caenorhabditis elegans</organism>
<sequence type="str">
MATSFYTGGGEDGDGFNPRVHARIAEREGFQLASGSEDPRTLFVANLDPAITDEFLATLFNQIGAVMKAKIIFEGLNDPYAFVEFSDHNQATLALQSHNGRELLEKEMHVTWAFEPREPGENRSKPETSRHFHVFVGDLCSEIDSTKLREAFVKFGEVSEAKIIRDNNTNKGKGYGFVSYPRREDAERAIDEMNGAWLGRRTIRTNWATRKPDEDGERGGDRGDRRGGGGGGRDRYHNQSEKTYDEIFNQAAADNTSVYVGNIANLGEDEIRRAFDRFGPINEVRTFKIQGYAFVKFETKESAARAIVQMNNADIGGQIVRCSWGKSGDSGKPSERGSGGGGGSGNYGYGYGNSGGGGGSGGPGNSQFSNFNQRPPPSGNGGSGGGSGGQNNQYWQYYSQYYNNPHLMQQWNNYWQKDGPPPPPAAAASSTGGN</sequence>
<gene type="str">
TIAR-2</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal prion-like domain</segment>
<boundaries type="str">
328-434</boundaries>
<region_ref type="str">
31378567</region_ref>
<partners type="str">
N/A</partners>
<determinants type="str">
1) phosphorylation state of TIAR-2</determinants>
<forms type="str">
droplets, TIAR-2 granules</forms>
<organelles type="str">
axonal TIAR-2 granules</organelles>
<pmids type="str">
31378567 (research article)</pmids>
<description type="str">
TIAR-2 undergoes liquid-liquid phase separation in vitro and forms granules with liquid-like properties in vivo. Axon injury induces a transient increase in TIAR-2 granule number. The PrLD is necessary and sufficient for granule formation and inhibiting regeneration. Tyrosine residues within the PrLD are important for granule formation and inhibition of regeneration. TIAR-2 is also serine phosphorylated in vivo. Non-phosphorylatable TIAR-2 variants do not form granules and are unable to inhibit axon regeneration (PMID:31378567).</description>
<experiment_llps type="str">
In vivo, in mechanosensory neurons, GFP-TIAR-2 expressed from transgenes was present throughout the cell body and axons, appearing as either diffuse or in granules (protein localization). Both GFP-TIAR-2 and TIAR-2 formed phase separated droplets in vitro. Within 5 min of axon injury, TIAR-2 granule number increased, remaining elevated for 60 min and returning to baseline levels by 180 min post-injury. Immediately after injury, granules became less motile, underwent fewer fusion events, and were less circular than prior to injury, suggesting that axon injury can modulate the properties of TIAR-2 granules. TIAR-2 lacking all three RRM domains formed granules and restored tiar-2(0) mutants to control levels of regeneration, comparable to full-length TIAR-2. Conversely, TIAR-2 lacking the entire PrLD or with a truncated PrLD did not form granules and did not affect axon regrowth. Thus, the PrLD of TIAR-2 is necessary and sufficient for granule formation and to repress axon regrowth. Substitution of tyrosine residues in the PrLD completely abolished activity independent of the number of tyrosine altered, while the substitution of glycine residues to tyrosines did not further enhance TIAR-2 activity beyond that of wild-type. Manipulation of tyrosine residues within the PrLD affected GFP-TIAR-2’s ability to form granules and respond to injury. Serine phosphorylations within the PrLD are required for LLPS because non-phosphorylable mutants could not phase separate, but phosphomimetic mutants could (PMID:31378567). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31378567); dynamic exchange of molecules with surrounding solvent (PMID: 31378567)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
328-434|S|hyperphosphorylation|enable|PMID:31378567||Notes: there are ten serines within the PrLD, non-phosphorylable mutants could not phase separate, but phosphomimetic mutants could. S338 and S369 seem to be the most prominent sites, because if these two sites are mutated to alanines, the granule-forming propensity already dramatically drops.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
cation-π (cation-pi) interactions (PMID:31378567); π-π (pi-pi) interactions (PMID:31378567); electrostatic (cation-anion) interaction (PMID:31378567)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
not known/not clear</functional_class>
<date type="str">
2019-09-11</date>
</Q9U2F5>
<Q8NE35 type="dict">
<id type="str">
143</id>
<phase_id type="str">
121</phase_id>
<common_name type="str">
CPEB3</common_name>
<name type="str">
Cytoplasmic polyadenylation element-binding protein 3</name>
<accession type="str">
Q8NE35</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MQDDLLMDKSKTQPQPQQQQRQQQQPQPESSVSEAPSTPLSSETPKPEENSAVPALSPAAAPPAPNGPDKMQMESPLLPGLSFHQPPQQPPPPQEPAAPGASLSPSFGSTWSTGTTNAVEDSFFQGITPVNGTMLFQNFPHHVNPVFGGTFSPQIGLAQTQHHQQPPPPAPAPQPAQPAQPPQAQPPQQRRSPASPSQAPYAQRSAAAAYGHQPIMTSKPSSSSAVAAAAAAAAASSASSSWNTHQSVNAAWSAPSNPWGGLQAGRDPRRAVGVGVGVGVGVPSPLNPISPLKKPFSSNVIAPPKFPRAAPLTSKSWMEDNAFRTDNGNNLLPFQDRSRPYDTFNLHSLENSLMDMIRTDHEPLKGKHYPPSGPPMSFADIMWRNHFAGRMGINFHHPGTDNIMALNNAFLDDSHGDQALSSGLSSPTRCQNGERVERYSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDGSQPLDPRKTIFVGGVPRPLRAVELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFSNQQSYIAAISARFVQLQHNDIDKRVEVKPYVLDDQMCDECQGTRCGGKFAPFFCANVTCLQYYCEYCWASIHSRAGREFHKPLVKEGGDRPRHVPFRWS</sequence>
<gene type="str">
CPEB3</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
Only full-length protein studied</segment>
<boundaries type="str">
1-698</boundaries>
<region_ref type="str">
31416913</region_ref>
<partners type="str">
1) specific partner mRNAs of CPEB3</partners>
<determinants type="str">
1) SUMOylation state of CPEB3; 2) crowding agent concentration</determinants>
<forms type="str">
droplets</forms>
<organelles type="str">
P-body</organelles>
<pmids type="str">
31416913 (research article)</pmids>
<description type="str">
The RNA-binding protein CPEB3 mediates the translation of several identified mRNA targets. CPEB3 leaves the nucleus by virtue of its nuclear export signal, and localizes to P bodies through its RNA recognition motif 1 in the cytoplasm, where it interacts with granular proteins Ago2 and GW182 and where mRNAs are known to be inhibited from translation. CPEB3 acts as a translational inhibitor in P-bodies. Furthermore, SUMOylation of CPEB3 is critical for P-body localization and biophysical phase separation. When an appropriate stimulus (like synaptic stimulation in neurons) is registered, the CPEB3 leaves the P body and moves to the polysome, presumably to mediate the translation of its targets. In all, when inhibitory, CPEB3 is in the P body, it is soluble, monomeric, and SUMOylated. However, after neuronal stimulation leading to de-SUMOylation CPEB3 leaves the P body to move into polysomes switched in a promotional form that is insoluble and oligomeric, which is necessary for long-term memory maintenance (PMID:31416913).</description>
<experiment_llps type="str">
CPEB3 undergoes phase separation in vitro when SUMOylated with SUMO1, SUMO2, and SUMO3, and when exposed to a specific mRNA target in an environment with molecular crowding agents. Temperature, salt, and metal did not have an obvious influence on phase separation of CPEB3, nor did general HeLa mRNA. Incubation of CPEB3 with SUMO2 3 ′ UTR induced phase separation, which caused a significant turbidity of the solution. However, a mutated SUMO2 3 ′ UTR, which prevents the binding of CPEB3, did not induce phase separation. In vivo, CPEB3 was observed to localize to P-bodies based on co-lacalization with typical P-body marker proteins. When SUMOylation is inhibited, transfected CPEB3-GFP colocalizes less with the P-body marker Dcp1 (PMID:31416913). </experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:31416913)</experiment_state>
<rna_req type="str">
specific CPEB3 target mRNAs</rna_req>
<ptm_affect type="str">
1-698|K|SUMOylation|enable|PMID:31416913||Notes: it is not known which lysine residue of CPEB3 gets SUMOylated, however SUMOylation is required for in vitro phase separation and in vivo P-body localization.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
protein-RNA interaction (PMID: 31416913)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
Y</rna_dep>
<ptm_dep type="str">
Y</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa </annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q8NE35>
<P35974 type="dict">
<id type="str">
145</id>
<phase_id type="str">
116</phase_id>
<common_name type="str">
Phosphoprotein</common_name>
<name type="str">
Phosphoprotein</name>
<accession type="str">
P35974</accession>
<organism type="str">
Measles virus</organism>
<sequence type="str">
MAEEQARHVKNGLECIRALKAEPIGSLAIEEAMAAWSEISDNPGQERATCREEKAGSSGLSKPCLSAIGSTEGGAPRIRGQGPGESDDDAETLGIPPRNLQASSTGLQCYYVYDHSGEAVKGIQDADSIMVQSGLDGDSTLSGGDNESENSDVDIGEPDTEGYAITDRGSAPISMGFRASDVETAEGGEIHELLRLQSRGNNFPKLGKTLNVPPPPDPGRASTSGTPIKKGTERRLASFGTEIASLLTGGATQCARKSPSEPSGPGAPAGNVPEYVSNAALIQEWTPESGTTISPRSQNNEEGGDYYDDELFSDVQDIKTALAKIHEDNQKIISKLESLLLLKGEVESIKKQINRQNISISTLEGHLSSIMIAIPGLGKDPNDPTADVEINPDLKPIIGRDSGRALAEVLKKPVASRQLQGMTNGRTSSRGQLLKEFQPKPIGKKMSSAVGFVPDTGPASRSVIRSIIKSSRLEEDRKRYLMTLLDDIKGANDLAKFHQMLMKIIMK</sequence>
<gene type="str">
P/V</gene>
<taxon type="str">
Viruses</taxon>
<segment type="str">
XD domain</segment>
<boundaries type="str">
459-507</boundaries>
<region_ref type="str">
31375591</region_ref>
<partners type="str">
1) Nucleoprotein</partners>
<determinants type="str">
1) phosphorylation state of P; 2) activity of host dynein</determinants>
<forms type="str">
IBs, spherical puncta</forms>
<organelles type="str">
inclusion body</organelles>
<pmids type="str">
31375591 (research article)</pmids>
<description type="str">
Measles viruses (MeV) are assumed to replicate in cytoplasmic inclusion bodies (IBs). These cytoplasmic viral factories are not membrane-bound and serve to concentrate the viral RNA replication machinery. The formation of IBs is dependent on the P (Phosphoprotein) and N (Nucleoprotein) proteins. Multivalent domain-motif interactions between the C-terminal XD domain of P and the motif-containing C-terminal region of N drive LLPS. Phosphorylations of P outside the XD domain by CK2 affect the size distribution of IBs. Inhibiting CK2 phosphorylations or the activity of host dyneins eliminated the formation of large IBs but small IBs where still formed in both conditions (PMID: 31375591).</description>
<experiment_llps type="str">
In vivo the nascent MeV IBs exist initially as small spheres that subsequently increase in size and adopt different shapes (protein localization, particle size and count). MeV N expressed alone in vivo in transfected cells mislocalized and was enriched in the nucleoli of 95% of the cells (protein localization). Expression of MeV P in the absence of N in transfected cells exhibited diffuse cytoplasmic staining in most (65%) of the cells (protein localization). P expression alone also formed perinuclear puncta in 35% of the transfected cells, however these puncta were rarely spherical and often displayed unusually large size (particle size and count). By contrast, the characteristic spherical puncta seen in infected cells were prevalent in transfected cells (95%) co-expressing both N and P. The formation of spherical puncta in transfected cells co-expressing N and P did not depend on the ability of N to bind RNA since co-expression of the N(KRR/AAA) mutant and P resulted in puncta of comparable size and morphology as co-expression of WT N with P.  Deletion of the XD domain of P prevented the formation of IB in 80% of transfected cells as revealed by the comparison of truncated mutant P (1 -458) to WT P. Compared to either deletion of XD or alanine substitution mutations within the XD domain of P protein, the deletion of the C-terminal MoRE-containing unstructured region from N (aa 392-525) produced the most dramatic phenotype. In nearly all transfected cells (97%), only a few small irregular-shaped puncta could be observed. Treating MeV-infected cells with DMAT, a cell-permeable inhibitor of CK2, decreased the IB size without significantly affecting N protein expression. Being expressed at a similar level as wild-type P protein, the S86A/S151A mutant compared to WT P protein did not trigger the production of large IBs when co-expressed with N. When cells that displayed comparable levels of N and P between the control and experimental groups were analyzed, the volume of the largest punctum within each cell was significantly reduced for the phospho site S86A/S151A mutant of P, further indicating a role for S86 and S151 phosphorylation in modulating the size of IBs formed by N and P co-expression. Host dynein promotes viral replication by facilitating the formation of large IBs (PMID: 31375591).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
False</in_vitro>
<experiment_state type="str">
morphological traits (PMID: 31375591); dynamic exchange of molecules with surrounding solvent (PMID: 31375591); </experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
86|S|phosphorylation|affects|PMID:31375591|CK2|Notes: blocking of the two phosphorylations by CK2 alters the size distribution of IBs, so that the formation of larger IBs is inhibited; 151|S|phosphorylation|affects|PMID:31375591|CK2|Notes: blocking of the two phosphorylations by CK2 alters the size distribution of IBs, so that the formation of larger IBs is inhibited</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
multivalent domain-motif interactions (PMID: 31375591)</interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
Y</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
Y</domain_dep>
<discrete_oligo type="str">
N</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Rita Pancsa</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor; inactivation/separation/molecular shield</functional_class>
<date type="str">
2019-09-11</date>
</P35974>
<Q12888 type="dict">
<id type="str">
144</id>
<phase_id type="str">
122</phase_id>
<common_name type="str">
53BP1</common_name>
<name type="str">
TP53-binding protein 1</name>
<accession type="str">
Q12888</accession>
<organism type="str">
Homo sapiens</organism>
<sequence type="str">
MDPTGSQLDSDFSQQDTPCLIIEDSQPESQVLEDDSGSHFSMLSRHLPNLQTHKENPVLDVVSNPEQTAGEERGDGNSGFNEHLKENKVADPVDSSNLDTCGSISQVIEQLPQPNRTSSVLGMSVESAPAVEEEKGEELEQKEKEKEEDTSGNTTHSLGAEDTASSQLGFGVLELSQSQDVEENTVPYEVDKEQLQSVTTNSGYTRLSDVDANTAIKHEEQSNEDIPIAEQSSKDIPVTAQPSKDVHVVKEQNPPPARSEDMPFSPKASVAAMEAKEQLSAQELMESGLQIQKSPEPEVLSTQEDLFDQSNKTVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQRSLVQDSLSTNSSDLVAPSPDAFRSTPFIVPSSPTEQEGRQDKPMDTSVLSEEGGEPFQKKLQSGEPVELENPPLLPESTVSPQASTPISQSTPVFPPGSLPIPSQPQFSHDIFIPSPSLEEQSNDGKKDGDMHSSSLTVECSKTSEIEPKNSPEDLGLSLTGDSCKLMLSTSEYSQSPKMESLSSHRIDEDGENTQIEDTEPMSPVLNSKFVPAENDSILMNPAQDGEVQLSQNDDKTKGDDTDTRDDISILATGCKGREETVAEDVCIDLTCDSGSQAVPSPATRSEALSSVLDQEEAMEIKEHHPEEGSSGSEVEEIPETPCESQGEELKEENMESVPLHLSLTETQSQGLCLQKEMPKKECSEAMEVETSVISIDSPQKLAILDQELEHKEQEAWEEATSEDSSVVIVDVKEPSPRVDVSCEPLEGVEKCSDSQSWEDIAPEIEPCAENRLDTKEEKSVEYEGDLKSGTAETEPVEQDSSQPSLPLVRADDPLRLDQELQQPQTQEKTSNSLTEDSKMANAKQLSSDAEAQKLGKPSAHASQSFCESSSETPFHFTLPKEGDIIPPLTGATPPLIGHLKLEPKRHSTPIGISNYPESTIATSDVMSESMVETHDPILGSGKGDSGAAPDVDDKLCLRMKLVSPETEASEESLQFNLEKPATGERKNGSTAVAESVASPQKTMSVLSCICEARQENEARSEDPPTTPIRGNLLHFPSSQGEEEKEKLEGDHTIRQSQQPMKPISPVKDPVSPASQKMVIQGPSSPQGEAMVTDVLEDQKEGRSTNKENPSKALIERPSQNNIGIQTMECSLRVPETVSAATQTIKNVCEQGTSTVDQNFGKQDATVQTERGSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHRHMRTIREVRTLVTRVITDVYYVDGTEVERKVTEETEEPIVECQECETEVSPSQTGGSSGDLGDISSFSSKASSLHRTSSGTSLSAMHSSGSSGKGAGPLRGKTSGTEPADFALPSSRGGPGKLSPRKGVSQTGTPVCEEDGDAGLGIRQGGKAPVTPRGRGRRGRPPSRTTGTRETAVPGPLGIEDISPNLSPDDKSFSRVVPRVPDSTRRTDVGAGALRRSDSPEIPFQAAAGPSDGLDASSPGNSFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLGPYEAVTPLTKAADISLDNLVEGKRKRRSNVSSPATPTASSSSSTTPTRKITESPRASMGVLSGKRKLITSEEERSPAKRGRKSATVKPGAVGAGEFVSPCESGDNTGEPSALEEQRGPLPLNKTLFLGYAFLLTMATTSDKLASRSKLPDGPTGSSEEEEEFLEIPPFNKQYTESQLRAGAGYILEDFNEAQCNTAYQCLLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNYLLPAGYSLEEQRILDWQPRENPFQNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEALQLPVVSQEWVIQCLIVGERIGFKQHPKYKHDYVSH</sequence>
<gene type="str">
TP53BP1</gene>
<taxon type="str">
Eukaryota</taxon>
<segment type="str">
C-terminal half</segment>
<boundaries type="str">
1203-1972</boundaries>
<region_ref type="str">
31267591</region_ref>
<partners type="str">
1) DNA with double strand breaks (not strictly required); 2) p53 (not strictly required)</partners>
<determinants type="str">
1) osmotic stress/salt concentration; 2) temperature; 3) 1,6-hexanediol concentration; 4) pH; </determinants>
<forms type="str">
foci, nuclear bodies</forms>
<organelles type="str">
nuclear body</organelles>
<pmids type="str">
31267591 (research article)</pmids>
<description type="str">
The DNA damage response (DDR) generates transient repair compartments to concentrate repair proteins and activate signaling factors. Silent heterochromatin domains were shown to phase separate within the nucleus. Moreover, phase separation occurs at gene promoters and super-enhancers. To which extent other chromatin domains rely on phase separation for their spatio-temporal confinement and for their biological functions is a matter of intense investigation. 53BP1-marked repair compartments are dynamic, show droplet-like behavior, and undergo frequent fusion and fission events. The tumor suppressor protein p53 is enriched within 53BP1 droplets, and conditions that disrupt 53BP1 phase separation impair 53BP1-dependent induction of p53 and diminish p53 target gene expression. Thus, 53BP1 phase separation integrates localized DNA damage recognition and repair factor assembly with global p53-dependent gene activation and cell fate decisions.</description>
<experiment_llps type="str">
In vivo in time‐lapse microscopy experiments, DNA damage‐induced 53BP1 compartments showed droplet‐like behavior and underwent frequent fusion and occasional fission events (morphology, paricle size and count). Moreover, addition of the aliphatic alcohol 1,6‐hexanediol, resulted in disassembly of 53BP1 foci. After employing CRISPR/Cas9 to engineer the endogenous 53BP1 locus and integrate an in‐frame sequence encoding for the small monomeric red fluorescent protein mScarlet, the resulting fusion protein could be visualized by fluorescence microscopy. The fusion protein did not affect the cell cycle, localized to γH2AX‐positive sites of DNA damage (protein localization), showed the typical cell cycle‐regulated pattern of 53BP1 accumulation, and was sensitive to siRNA treatment targeted against 53BP1, confirming the role of 53BP1 in the formation of the observed compartments. Consistent with prior results, a short hyperosmotic challenge led to disassembly of 53BP1‐mScarlet compartments without affecting γH2AX accumulation. More importantly, however, live cell experiments with endogenously tagged 53BP1 expressed from its native promoter confirmed the dynamic, droplet‐like morphology of 53BP1 assemblies, their spherical shape, and their frequent fusions and fissions. 53BP1 nuclear bodies, occurring spontaneously and at enhanced frequency upon mild replication stress by low‐dose aphidicolin (APH) and ATR inhibitor (ATRi) treatment, showed droplet‐like behavior as well, and underwent frequent fusion events. In order to directly test whether 53BP1 possesses the capacity to phase separate, a system based on mCherry‐labeled Arabidopsis photoreceptor cryptochrome 2 (Cry2) fusion proteins was used to measure target protein optoDroplet formation in living cells. A Cry2‐53BP1 fusion resulted in rapid, light‐induced optoDroplet formation. Introducing a single amino acid mutation (W1495A) within the 53BP1 tandem tudor domain (TTD) to abrogate potentially confounding effects from TTD chromatin and protein interactions, and to assess the intrinsic capacity of 53BP1 to phase separate, further enhanced light‐induced optoDroplet formation. A series of deletion mutants used to identify the sequence elements driving 53BP1 phase separation revealed that the C‐terminus, comprising amino acids 1140–1972, was sufficient for optoDroplet formation, while the largely unstructured N‐terminus of 53BP1 was not, and that the oligomerization domain (OD) was critically involved. The 53BP1 C‐terminus is highly enriched for Arg and Tyr residues, implying that preferential optoDroplet formation of this region relies on cation-pi interactions (PMID:31267591).; In vitro, the purified 53BP1 C‐terminus showed condensation into μm‐sized droplets in presence of Ficoll (morphology, particle size and count), and 53BP1 condensates co‐assembled double strand break‐mimicking fluorescently labeled DNA (PMID:31267591).</experiment_llps>
<in_vivo type="str">
True</in_vivo>
<in_vitro type="str">
True</in_vitro>
<experiment_state type="str">
morphological traits (PMID:31267591); temperature-dependence (PMID:31267591); reversibility of formation and dissolution (PMID:31267591)</experiment_state>
<rna_req type="str">
RNA not required.</rna_req>
<ptm_affect type="str">
Not known.</ptm_affect>
<disease type="str">
Not known.</disease>
<splice type="str">
Not known.</splice>
<interaction type="str">
discrete oligomerization (PMID:31267591); cation-π (cation-pi) interactions (PMID:31267591); </interaction>
<membrane_clust type="str">
N</membrane_clust>
<partner_dep type="str">
N</partner_dep>
<rna_dep type="str">
N</rna_dep>
<ptm_dep type="str">
N</ptm_dep>
<domain_dep type="str">
N</domain_dep>
<discrete_oligo type="str">
Y</discrete_oligo>
<under_annot type="str">
True</under_annot>
<annotator type="str">
Bálint Mészáros</annotator>
<functional_class type="str">
activation/nucleation/signal amplification/bioreactor</functional_class>
<date type="str">
2019-09-11</date>
</Q12888>
</root>