Entry created on 1 July 2019 (Revision 1.0) Annotator: Rita Pancsa; Ágnes Tantos
Basic protein information
Accession D0PV95
Common name LAF-1
Gene LAF-1
Organism Caenorhabditis elegans
Uniprot name ATP-dependent RNA helicase laf-1
Basic LLPS information
Organelle P granule
Type of experimental evidence
Protein region(s) mediating LLPS
1
-
168
N-terminal R/G-rich disordered region
Based on the experimental results of the following publication: 26015579
Molecular features viewer
PDB structures
Extended LLPS information
Functional description
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).
Literature supporting the LLPS: 26015579, 29064502, 30061688
Functional class of membraneless organelle: regulator of spatial patterns
Binding partners (at biological protein concentrations)
1) RNA (via N-terminal RGG region, not strictly required)
Type of RNA(s) required/used for the LLPS at biological protein concentrations
model RNA (polyU 50)
Molecular interaction types contributing to LLPS
protein-RNA interaction (PMID:30765518) electrostatic (cation-anion) interaction (PMID:30765518) π-π (pi-pi) interactions (PMID:30765518)
Determinants of phase separation and droplet properties
1) protein concentration of LAF-1 2) salt concentration 3) RNA concentration
Membrane cluster No
Partner-dependent No
RNA-dependent No
PTM required No
Domain-motif interactions No
Discrete oligomerization No
Regulation and disease
Post-translational modifications affecting LLPS
Position Residue PTM Effect Reference Modifying enzyme Notes
Isoforms known to affect LLPS
Isoform Effect Reference
All known isoforms containing sequence changes in the LLPS region(s)
Position type Isoform names from UniProt
Disease mutations affecting LLPS
Mutation dbSNP Disease OMIM Effect Reference Notes
Experimental information
Experimental techniques applied to prove/investigate LLPS
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).
Experimental observations supporting the liquid material state of the condensate
morphological traits (PMID:26015579) rheological traits (PMID:26015579) dynamic movement/reorganization of molecules within the droplet (PMID:26015579)