Entry created on 1 July 2019 (Revision 1.0) Annotator: Rita Pancsa
Basic protein information
Accession P04050
Common name RPB1
Gene RPO21
Organism Saccharomyces cerevisiae
Uniprot name DNA-directed RNA polymerase II subunit RPB1
Basic LLPS information
Organelle RNA polymerase II, holoenzyme; POLII clusters
Type of experimental evidence
Protein region(s) mediating LLPS
1542
-
1733
C-terminal tail with 26 heptade repeats of YSPTSPS
Based on the experimental results of the following publication: 30127355
Molecular features viewer
PDB structures
View on PDBe
Extended LLPS information
Functional description
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).
Literature supporting the LLPS: 30127355
Functional class of membraneless organelle: activation/nucleation/signal amplification/bioreactor
Binding partners (at biological protein concentrations)
N/A
Type of RNA(s) required/used for the LLPS at biological protein concentrations
Not required.
Molecular interaction types contributing to LLPS
Not known
Determinants of phase separation and droplet properties
1) phosphorylation state 2) valency of CTD
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
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).
Experimental observations supporting the liquid material state of the condensate
dynamic movement/reorganization of molecules within the droplet (PMID:30127355) morphological traits (PMID:30127355) sensitivity to 1,6-hexanediol (PMID:30127355)