The table below lists all cases where the involvement in LLPS is indicated by some evidence, but where there isn’t enough available experimental information for inclusion into the core dataset of PhaSePro.
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Common name Gene Organism Uniprot Acc Name Reference(s) Short description Notes
Ataxin-2 ATXN2 Homo sapiens Q99700 Ataxin-2 22579281 Ataxin-2 showed bisox-mediated precipitation from cell lysates. This was confirmed by western blotting assay, which further established that it quantitatively precipitated in response to 100 μM of the b-isox compound and that the precipitation reaction was reversible. For Drosophila Ataxin-2 LLPS was confirmed both in vivo and in vitro, but for human Ataxin-2 there is not enough evidence yet. B-isox mediated precipitation is a good indication for LLPS, but we cannot accept the proteins for which other evidence was not available.
CIRBP CIRBP Homo sapiens Q14011 Cold-inducible RNA-binding protein 22579281 The LC domain is both necessary and sufficient for b-isox-mediated precipitation. The LC domain also adhered to the FUS and hnRNPA2 hydrogels without b-isox. B-isox mediated precipitation is a good indication for LLPS, but we cannot accept the proteins for which other evidence was not available.
RBM3 RBM3 Homo sapiens P98179 RNA-binding protein 3 22579281 The LC domain is both necessary and sufficient for b-isox-mediated precipitation. The LC domain also adhered to the FUS and hnRNPA2 hydrogels without b-isox. B-isox mediated precipitation is a good indication for LLPS, but we cannot accept the proteins for which other evidence was not available.
FXR1 FXR1 Homo sapiens P51114 Fragile X mental retardation syndrome-related protein 1 22579281 FXR1 showed bisox-mediated precipitation from cell lysates. This was confirmed by western blotting assay, which further established that it quantitatively precipitated in response to 100 μM of the b-isox compound and that the precipitation reaction was reversible. B-isox mediated precipitation is a good indication for LLPS, but we cannot accept the proteins for which other evidence was not available.
WDR46 WDR46 Homo sapiens O15213 WD repeat-containing protein 46 23848194 WDR46 is a major structural scaffold protein for the assembly of nucleoli and for organizing the 18S ribosomal RNA processing machinery. Both the N- and C-terminal IDRs are critical for its nucleolar localization and for the association with its binding partners. Proper recruitement of nucleolin and DDX21 to the granular component of nucleoli is ensured by WDR46. Liquid nature of WDR46 assemblies was not proven by the experiments, and there are no in vitro experiments available yet that could confirm that the protein acts as an LLPS driver itself.
Coilin COIL Homo sapiens P38432 Coilin 11102515, 11641277, 12361597, 12482916, 27715441, 25970135, 27661468, 29120326, 29886015 Cajal bodies (CBs) are nuclear liquid-like (PMID:27768897) suborganelles implicated in the post-transcriptional maturation of small nuclear and small nucleolar RNAs (PMID:12482916). The CB becomes phase separated from the surrounding nucleoplasm, enriching specific CB factors within the microenvironment. Recruitment of SMN and splicing snRNPs to Cajal bodies depends on the coilin C-terminal RG motif (PMID:11641277). Coilin contains symmetrical dimethylarginines that modulate its affinity for SMN, and, thus, localization of SMN complexes to CBs (PMID:12361597). Although Cajal bodies are known to have liquid properties, and coilin is known to play a major role in their assembly, it is not clear how coilin assembles Cajal bodies, what are the strictly required partners and if coilin in itself is capable of driving liquid phase separation. Due to presence or RGGs it is probably capable, but in vitro experiments are largely lacking.
G3BP1, G3BP G3BP1 Homo sapiens Q13283 Ras GTPase-activating protein-binding protein 1 12642610, 17210633, 29728455, 28972166, 27601476, 27920254, 27022092, 26101899, 23092511, 29463567 G3BP1 and G3BP2 are considered to be potent SG-nucleating proteins based on in vivo experiments. Only in vivo experiments prove the accumulation in RNA stress granules. G3BP1 and G3BP2 are considered to be a potent SG-nucleating proteins, however no in vitro experiments have been performed yet to prove their ability to drive phase separation.
G3BP2 G3BP2 Homo sapiens Q9UN86 Ras GTPase-activating protein-binding protein 2 12642610, 17210633 G3BP1 and G3BP2 are considered to be potent SG-nucleating proteins based on in vivo experiments. Only in vivo experiments prove the accumulation in RNA stress granules. G3BP1 and G3BP2 are considered to be a potent SG-nucleating proteins, however no in vitro experiments have been performed yet to prove their ability to drive phase separation.
Mip6, Mip6p MIP6 Saccharomyces cerevisiae P38760 RNA-binding protein MIP6 27320918 The dosage-sensitive protein Mip6p changes localization when overexpressed: at concentrations that impair growth, the protein re-localizes to cytoplasmic foci. Mip6p foci have liquid properties and associate with P-body components. Both foci formation and cellular toxicity are primarily driven by the RNA-binding domains of Mip6p. Requirement for RNA for foci formation is also supported by the fact that cycloheximide treatment dissolved foci formed upon Mip6p overexpression. Mip6p foci, by titrating proteins and mRNAs from the cytoplasm, impair the translation capacity of the cell and thus impair growth. There are no in vitro experiments available, no prove that the protein is capable of phase separation alone (and if not what partners are required) and no prove that the applied overexpression levels are physiologically relevant among any conditions.
PCM1 PCM1 Homo sapiens Q15154 Pericentriolar material 1 protein 12571289, 12403812, 26755742 S372 phosphorylation by Plk4 kinase plays a critical role in dimer/oligomer formation of PCM1 and interaction with other satellite components, which are prerequisites for its role in centriolar satellite integrity. In contrast to PCM1-S372A, PCM1-S372D (and PCM1-S372E) formed larger, less motile aggregates around the centrosome. We consider that the dephosphorylation of S372 renders PCM1 particles more motile. It is possible that dephosphorylation is required for destabilising the interaction between PCM1 and the dynein complex. Centriolar satellites are known to dissolve during mitosis and reassemble upon mitotic exit and the following G1 phase. It is therefore tempting to speculate that this cell cycle-dependent reorganisation of centriolar satellites might be coupled with oscillatory Plk4 activity through PCM1 phosphorylation. PMID:26755742 The liquid nature of PCM1 assemblies have not been shown yet. There isn`t enough evidence that the self assembly of the protein progresses through an LLPS-like mechanism.
RBFOX1 RBFOX1 Homo sapiens Q9NWB1 RNA binding protein fox-1 homolog 1 29358748, 28708999 Proteins of the Rbfox family act with a complex of proteins called the Large Assembly of Splicing Regulators (LASR). RBFOX1 interacts with LASR via its C-terminal domain (CTD) and this domain is essential for its splicing activity. In addition to LASR recruitment, a low-complexity (LC) sequence within the CTD contains repeated tyrosines that mediate higher-order assembly of RBFOX/LASR and are required for splicing activation by RBFOX. The CTD formed aggregates on its own in vitro and in vivo (PMID:28708999). RBFOX1 could be precipitated from humanfibroblast cell lysates with b-isox. It incorporates into larger protein assemblies in the nucleus and in the perinuclear area of the cytoplasm and many of these granules are mitochondria-associated (PMID:29358748). There is not enough evidence hat the granules are liquid-like, they have irregular shapes and bare typical amyloid properties according the the authors.
velo1, Xvelo VELO1 Xenopus laevis Q7T226 Velo1 27471966 In many vertebrate species, the cytoplasm of the early oocytes contains a highly specialized compartment called the Balbiani body. It is non-membrane bound and densely packed with mitochondria, RNA, ER, and Golgi. Germline specification is the only known function of the Balbiani body. Xvelo, a disordered protein with an N-terminal prion-like domain, is an abundant constituent of Xenopus Balbiani bodies. Disruption of the prion-like domain of Xvelo, or substitution with a PLD from an unrelated protein, interferes with its incorporation into Balbiani bodies in vivo. Recombinant Xvelo forms amyloid-like, micron-scale networks in vitro. Amyloid-like assemblies of Xvelo recruit both RNA and mithocondria in binding assays. Xenopus Balbiani bodies form by amyloid-like assembly of Xvelo, accompanied by co-recruitment of mithocondria and RNA. Balbiani body formation by amyloid-like assembly could be a conserved mechanism that helps oocytes function as long-lived germ cells. Xvelo displayed amyloid-like properties, not liquid like. Similarly to its homolog Buc, it might assemble liquid organelles together with a Tudor domain-containing partner, but this has not been demonstrated yet.
ParB SPO0J Bacillus subtilis P26497 Stage 0 sporulation protein J 24927534, 30907359 The ParABS system mediates chromosome segregation and plasmid partitioning in many bacteria. As part of the partitioning mechanism, ParB proteins form a nucleoprotein complex at parS sites. The biophysical basis underlying ParB-DNA complex formation and localization remains elusive. ParB binding to parS triggers a conformational switch in ParB that could overcome a nucleation barrier. Conceptually, the combination of spreading and bridging bonds in the model provides a surface tension ensuring the condensation of the ParB-DNA complex, with analogies to liquid-like compartments such as nucleoli in eukaryotes. The authors conclude that they suspect that ParB might form liquid condensates, but there are no experiments yet to support this premis.
Ki-67 MKI67 Homo sapiens P46013 Proliferation marker protein Ki-67 27362226, 29322240 Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly. Associates with the surface of the mitotic chromosome, forming the so called perichromosomal layer (PCL), and covers a substantial fraction of the chromosome surface. Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility. The chromosome separation function of human Ki-67 is not confined within a specific protein domain, but correlates with size and net charge of truncation mutants that apparently lack secondary structure. This suggests that Ki-67 forms a steric and electrostatic charge barrier, similar to surface-active agents (surfactants) that disperse particles or phaseseparated liquid droplets in solvents. (PMID:27362226). There are no experiments available which would confidently prove that the perichromosomal layer has liquid properties.
Dvl1, Dvl DVL1 Homo sapiens O14640 Segment polarity protein dishevelled homolog DVL-1 30782412 A major component of the Wnt signalosome. Multiple evidence point to the direction that the destruction complex formed during Wnt/Beta-Catenin Signaling behaves as liqid condensates, but there is not enogh evidence yet and the exact role of Dvl2 in driving the formation of liquid-like condensates is not clear.
LSM4 LSM4 Saccharomyces cerevisiae P40070 U6 snRNA-associated Sm-like protein LSm4 17984320, 26412307, 29425497 In vivo, P-bodies can form through bot Edc3 dependent and independent mechanisms. In the Edc3 dependent pathway, the Lsm and Yjef-N domains of Edc3 form complexes with Dcp2 to drive P-body assembly. In the Edc3 independent pathway, the Q/N-rich prion-like domain of Lsm4 is involved. LSM4 aggregates on its own and only phase separated when the PLD of LSM4 was fused to the Polpyrimidine tract binding protein PTB domain. Since the PTB domain was previosly shown to undergo LLPS with RNA, the role of the PLD of LSM4 is not clear, thus we cannot accept it into the database based on these preliminary experiments.
ZNFX-1 CELE_ZK1067.2 Caenorhabditis elegans E9P860 Uncharacterized protein 29769721 ZNFX-1 and WAGO-4 are inheritence factors that localize to Caenorhabditis elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1 and WAGO-4 separate from P granules to define an independent liquid-like condensate termed the Z granule. In adult germ cells, Z granules assemble into ordered tri-condensate assemblages with P granules and Mutator foci termed PZM granules. One possible biological function of ZNFX-1 and WAGO-4 is to interact with silencing RNAs in the C. elegans germline to direct transgenerational epigenetic inheritance. Thus the temporal and spatial ordering of liquid droplet organelles may help cells to organize and coordinate the complex RNA processing pathways that underlie gene regulatory systems, such as RNA-directed transgenerational epigenetic inheritance. (PMID:29769721) Only in vivo experiments prove that ZNFX-1 localizes to P-granules and it is not strictly required for P-granule formation. During germline development ZNFX-1 and WAGO-4 separate from P granules to define an independent liquid-like condensate termed Z granule, but this process is also only proved by in vivo experiments and thus the role of the two proteins is questionable.
WAGO-4 WAGO-4 Caenorhabditis elegans O62275 Piwi-like protein 29769721 ZNFX-1 and WAGO-4 are inheritence factors that localize to Caenorhabditis elegans germ granules (P granules) in early germline blastomeres. Later in germline development, ZNFX-1 and WAGO-4 separate from P granules to define an independent liquid-like condensate termed the Z granule. In adult germ cells, Z granules assemble into ordered tri-condensate assemblages with P granules and Mutator foci termed PZM granules. One possible biological function of ZNFX-1 and WAGO-4 is to interact with silencing RNAs in the C. elegans germline to direct transgenerational epigenetic inheritance. Thus the temporal and spatial ordering of liquid droplet organelles may help cells to organize and coordinate the complex RNA processing pathways that underlie gene regulatory systems, such as RNA-directed transgenerational epigenetic inheritance. (PMID: 29769721) Only in vivo experiments prove that ZNFX-1 localizes to P-granules and it is not strictly required for P-granule formation. During germline development ZNFX-1 and WAGO-4 separate from P granules to define an independent liquid-like condensate termed Z granule, but this process is also only proved by in vivo experiments and thus the role of the two proteins is questionable.
Pin2 PIN2 Saccharomyces cerevisiae Q12057 [PSI+] induction protein 2 24656818 S. cerevisiae exomer-dependent cargo protein Pin2 is involved in the regulation of protein transport and localization. Pin2 is a single transmembrane domain (TMD) protein with a large cytoplasmic region that contains a PLD. The PLD serves as a Pin2 retention signal in the trans-Golgi network (TGN). Pin2 is localized in a polarized fashion at the plasma membrane of the bud early in the cell cycle and the bud neck at cytokinesis. This polarized localization is dependent on both exo- and endocytosis. Upon environmental stress, Pin2 is rapidly endocytosed, and the PLD aggregates and causes sequestration of Pin2. The aggregation of Pin2 is reversible upon stress removal and Pin2 is rapidly re-exported to the plasma membrane. (PMID:24656818) The authors mention aggregation for Pin2, aggregates which did not dissolve in SDS only when also adding some detergents. The aggregates were reversible and dissolved when the stress condition was over, suggesting that they might have liquid-like properties. Still, based on the presented experiments we cannot yet acccept Pin2 into the database.
PGL-1 PGL-1 Caenorhabditis elegans Q9TZQ3 Guanyl-specific ribonuclease pgl-1 19460965, 21402787, 27594427, 30173914 Together with the P-granule component pgl-3, is involved in the formation of P-granules (PMID:21402787, PMID:24746798). Together with pgl-3, probably recruits other granule components such as pos-1, mex-3 and glh-1 to P-granules (PMID:21402787). 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. PGL proteins, but not GLH-1, have the ability to form granules autonomously in the absence of other germlinespecifi factors in C. elegans. PGL-1 is a close homolog of PGL-3, but in case of PGL-1 the role of different regions in phase separation was not addressed. However no phase separation of PGL-1 was seen in vitro in buffer containing physiological level of salt (PMID: 27594427). Not enough evidence that PGL-1 can undergo LLPS on it own, moreover it could not phase separate alone in virto when they have looked at it.
CAR-1 CAR-1 Caenorhabditis elegans Q9XW17 Cytokinesis, Apoptosis, RNA-associated 24176641 Distinct large RNP assemblies (here called grP-bodies or grPBs) form in arrested oocyte cytoplasm, where they recruit repressed mRNAs. GFP:CAR-1 droplets in live animals had aspect ratios that tended toward ∼1, consistent with a liquid-like state driven toward spherical shapes by surface tension. Thus grPBs are most probably formed by a liquid phase transition. GFP:CAR-1 inside grPBs has slow random mobility, and limited exchange with cytosol. Collective polymeric interactions among many CAR-1 and CCF-1 RNP complexes induce a semiliquid/semisolid, viscoelastic state. FRAP, fusion kinetics, and elastic behavior indicate that the Lsm protein CAR-1/RAP55 and the deadenylase CCF-1 are components of a dynamically polymerizing/depolymerizing matrix within these RNP assemblies. Interestingly, after loss of the RNA helicase CGH-1, GFP:CAR-1 accumulated into large solid sheet-like granules. Majority of GFP:CAR-1 (∼75%) in square sheets is immobile, whereas minor fraction rapidly exchanges with sheet surface. These results suggest that oocyte grPB RNPs may undergo regulated phase transitions from diffuse to different condensed states that can be either liquid-like or solid-like. Phase transitions of CAR-1 complexes are modulated in two ways upon transition from arrested oocyte to early embryo. First, CAR-1 dynamics within and from RNP assemblies are activated, leading to far more extensive droplet-cytosol exchange. Second, RNP modifications allow mixing of components that are segregated in oocyte grPBs (PMID:24176641). Not enough evidence that CAR-1 can undergo LLPS on it own, no in vitro results.
CELF1 CELF1 Homo sapiens Q92879 CUGBP Elav-like family member 1 29610944 When in the lampbrush configuration, chromosomes display thousands of visible DNA loops that are transcribed at exceptionally high rates by RNA polymerase II (pol II). A prominent feature of the physical and functional organization of the interchromatin space is the presence of a variety of nuclear bodies that are now thought to reflect the formation of liquid-liquid phase-separated compartments. In intact nuclei from lampbrush-stage Xenopus oocytes isolated under mineral oil, highly specific targeting of fluorescent fusions of the RNA-binding protein CELF1 to nascent transcripts allowed funtional transcription loops to be observed and their longevity assessed over time. CELF1 exchanges freely between the accumulated nascent ribonucleoprotein (RNP) and the surrounding nucleoplasm, and it exits RNP with similar kinetics to its entrance. It appears that on transcription loops, nascent transcripts contribute to a dynamic self-organizing structure that exemplifies a phase-separated nuclear compartment. Nascent RNP is therefore a key determinant of chromatin structure and dynamics rather than playing a passive role as simply the product of transcription. Not enough evidence that CELF1 can undergo LLPS on it own, no in vitro results available.