Genomes and Genes
Gene Symbol: RPB5
Description: DNA-directed RNA polymerase core subunit RPB5
Alias: DNA-directed RNA polymerase core subunit RPB5
Species: Saccharomyces cerevisiae S288c
- Flores A, Briand J, Gadal O, Andrau J, Rubbi L, Van Mullem V, et al. A protein-protein interaction map of yeast RNA polymerase III. Proc Natl Acad Sci U S A. 1999;96:7815-20 pubmed..Together with parallel interaction studies based on dosage-dependent suppression of conditional mutants, our data suggest a model of the pol III preinitiation complex. ..
- Gstaiger M, Luke B, Hess D, Oakeley E, Wirbelauer C, Blondel M, et al. Control of nutrient-sensitive transcription programs by the unconventional prefoldin URI. Science. 2003;302:1208-12 pubmed..large member of this family, termed URI, that forms complexes with other small-molecular weight PFDs and with RPB5, a shared subunit of all three RNA polymerases...
- Möckli N, Deplazes A, Hassa P, Zhang Z, Peter M, Hottiger M, et al. Yeast split-ubiquitin-based cytosolic screening system to detect interactions between transcriptionally active proteins. Biotechniques. 2007;42:725-30 pubmed..The cytoY2H system extends existing methods for the detection of protein interactions by providing a convenient solution for screening a wide range of transcriptionally active proteins. ..
- Briand J, Navarro F, Rematier P, Boschiero C, Labarre S, Werner M, et al. Partners of Rpb8p, a small subunit shared by yeast RNA polymerases I, II and III. Mol Cell Biol. 2001;21:6056-65 pubmed..A ygr089-Delta null mutant has no detectable growth defect but aggravates the conditional growth defect of rpb8 mutants, suggesting that the interaction with Rpb8p may be physiologically relevant. ..
- Cramer P, Bushnell D, Fu J, Gnatt A, Maier Davis B, Thompson N, et al. Architecture of RNA polymerase II and implications for the transcription mechanism. Science. 2000;288:640-9 pubmed..Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center...
- Kuhn C, Geiger S, Baumli S, Gartmann M, Gerber J, Jennebach S, et al. Functional architecture of RNA polymerase I. Cell. 2007;131:1260-72 pubmed..In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming. ..
- Luo J, Fishburn J, Hahn S, Ranish J. An integrated chemical cross-linking and mass spectrometry approach to study protein complex architecture and function. Mol Cell Proteomics. 2012;11:M111.008318 pubmed publisher..As such, it is an attractive approach to study the topology of protein complexes. ..
- Nouraini S, Archambault J, Friesen J. Rpo26p, a subunit common to yeast RNA polymerases, is essential for the assembly of RNA polymerases I and II and for the stability of the largest subunits of these enzymes. Mol Cell Biol. 1996;16:5985-96 pubmed..Furthermore, A190p and Rpo21p continued to accumulate at low levels under these conditions. We suggest that Rpo26p is essential for the assembly of RNAPI and RNAPII and for the stability of the largest subunits of these enzymes. ..
- Takagi Y, Calero G, Komori H, Brown J, Ehrensberger A, Hudmon A, et al. Head module control of mediator interactions. Mol Cell. 2006;23:355-64 pubmed..The head module evidently controls Mediator-RNA polymerase II and Mediator-promoter interactions. ..
- CieÅ›la M, MakaÅ‚a E, PÅ‚onka M, Bazan R, Gewartowski K, Dziembowski A, et al. Rbs1, a new protein implicated in RNA polymerase III biogenesis in yeast Saccharomyces cerevisiae. Mol Cell Biol. 2015;35:1169-81 pubmed publisher..Rbs1 physically interacts with a subset of Pol III subunits, AC19, AC40, and ABC27/Rpb5. Additionally, Rbs1 interacts with the Crm1 exportin and shuttles between the cytoplasm and nucleus...
- Martínez Fernández V, Garrido Godino A, Mirón García M, Begley V, Fernández Pévida A, de la Cruz J, et al. Rpb5 modulates the RNA polymerase II transition from initiation to elongation by influencing Spt5 association and backtracking. Biochim Biophys Acta Gene Regul Mech. 2018;1861:1-13 pubmed publisherb>Rpb5 is a subunit shared by the three eukaryotic RNA polymerases although its role in transcription remains unclear...
- Suh M, Meyer P, Gu M, Ye P, Zhang M, Kaplan C, et al. A dual interface determines the recognition of RNA polymerase II by RNA capping enzyme. J Biol Chem. 2010;285:34027-38 pubmed publisher..Our results indicate that the dual interface based on combining PCI1 and PCI2 is required for directing CE to Pol II elongation complexes. ..
- Babbarwal V, Fu J, Reese J. The Rpb4/7 module of RNA polymerase II is required for carbon catabolite repressor protein 4-negative on TATA (Ccr4-not) complex to promote elongation. J Biol Chem. 2014;289:33125-30 pubmed publisher..The interplay between Ccr4-Not and Rpb4/7 described here suggests a mechanism for how the cell coordinates mRNA synthesis and decay. ..
- Allepuz Fuster P, MartÃnez FernÃ¡ndez V, Garrido Godino A, Alonso Aguado S, Hanes S, Navarro F, et al. Rpb4/7 facilitates RNA polymerase II CTD dephosphorylation. Nucleic Acids Res. 2014;42:13674-88 pubmed..Based on these and other results, we suggest a model in which Rpb4/7 helps recruit and potentially stimulate the activity of CTD-modifying enzymes, a role that is central to RNAPII function. ..
- Tan Q, Prysak M, Woychik N. Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol Cell Biol. 2003;23:3329-38 pubmed..The association of Rpb4/Rpb7 with Rpb6 suggests that analogous subunits of each RNA polymerase impart class-specific functions through a conserved core subunit. ..
- Schaft D, Roguev A, Kotovic K, Shevchenko A, Sarov M, Shevchenko A, et al. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res. 2003;31:2475-82 pubmed..Since SET2 is also a histone methyltransferase, these results suggest a role for histone 3 lysine 36 methylation in transcriptional elongation. ..
- Mirón García M, Garrido Godino A, Martínez Fernández V, Fernández Pévida A, Cuevas Bermúdez A, Martín Expósito M, et al. The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription. Nucleic Acids Res. 2014;42:9666-76 pubmed publisher..It has recently been shown to mediate the assembly of the three RNA polymerases in an Rpb5-dependent manner. In this work, we present evidence of Bud27 modulating RNA pol II transcription elongation...
- Lehmann E, Brueckner F, Cramer P. Molecular basis of RNA-dependent RNA polymerase II activity. Nature. 2007;450:445-9 pubmed..The RdRP activity of Pol II provides a missing link in molecular evolution, because it suggests that Pol II evolved from an ancient replicase that duplicated RNA genomes. ..
- Lee Y, Min S, Gim B, Kim Y. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol Cell Biol. 1997;17:4622-32 pubmed..A database search revealed the existence of MED6-related genes in humans and Caenorhabditis elegans, suggesting that the role of mediator in transcriptional activation is conserved throughout the evolution. ..
- Myer V, Young R. RNA polymerase II holoenzymes and subcomplexes. J Biol Chem. 1998;273:27757-60 pubmed
- Otero G, Fellows J, Li Y, de Bizemont T, Dirac A, Gustafsson C, et al. Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell. 1999;3:109-18 pubmed..Our data indicate that the transition from transcriptional initiation to elongation involves an exchange of the multiprotein mediator complex for elongator in a reaction coupled to CTD hyperphosphorylation. ..
- Sayre M, Tschochner H, Kornberg R. Reconstitution of transcription with five purified initiation factors and RNA polymerase II from Saccharomyces cerevisiae. J Biol Chem. 1992;267:23376-82 pubmed..TFIIA failed to substitute for any purified factor or to stimulate transcription with the complete set of factors, indicating that its function in crude extracts is primarily as an anti-inhibitor. ..
- Kolodziej P, Woychik N, Liao S, Young R. RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol. 1990;10:1915-20 pubmed..These results more precisely define the subunit composition and phosphorylation of a eucaryotic RNA polymerase II enzyme. ..
- Duan R, Rhie B, Ryu H, Ahn S. The RNA polymerase II Rpb4/7 subcomplex regulates cellular lifespan through an mRNA decay process. Biochem Biophys Res Commun. 2013;441:266-70 pubmed
- Harris B, Bose T, Lee K, Wang F, Lu S, Ross R, et al. Cohesion promotes nucleolar structure and function. Mol Biol Cell. 2014;25:337-46 pubmed publisher..Our results strongly suggest that organization of the rDNA provided by cohesion is critical for formation and function of the nucleolus. ..
- Vannini A, Ringel R, Kusser A, Berninghausen O, Kassavetis G, Cramer P. Molecular basis of RNA polymerase III transcription repression by Maf1. Cell. 2010;143:59-70 pubmed publisher..These results explain how Maf1 specifically represses transcription initiation from Pol III promoters and indicate that Maf1 also prevents reinitiation by binding Pol III during transcription elongation. ..
- Van Mullem V, Landrieux E, Vandenhaute J, Thuriaux P. Rpa12p, a conserved RNA polymerase I subunit with two functional domains. Mol Microbiol. 2002;43:1105-13 pubmed..Thus, the N-terminal zinc domain of Rpa12p determines its anchoring to RNA polymerase I and is the only critical part of that subunit in vivo. ..
- Harel Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell. 2010;143:552-63 pubmed publisher..We propose that Rpb4/7, through its interactions at each step in the mRNA lifecycle, represents a class of factors, "mRNA coordinators," which integrate the various stages of gene expression into a system. ..
- Vasiljeva L, Buratowski S. Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts. Mol Cell. 2006;21:239-48 pubmed..Since Nrd1 is known to bind RNA polymerase II and be important for sn/snoRNA 3' end processing, Nrd1 may link transcription and RNA 3' end formation with surveillance by the exosome. ..
- Porrúa O, Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol. 2013;20:884-91 pubmed publisher..We also show that termination is inhibited by RNA-DNA hybrids. Our results elucidate the role of Sen1p in controlling pervasive transcription. ..
- Mosley A, Pattenden S, Carey M, Venkatesh S, Gilmore J, Florens L, et al. Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation. Mol Cell. 2009;34:168-78 pubmed publisher..Functional characterization of Rtr1 reveals its role as a CTD phosphatase essential for the S5-to-S2-P transition. ..
- Donaldson I, Friesen J. Zinc stoichiometry of yeast RNA polymerase II and characterization of mutations in the zinc-binding domain of the largest subunit. J Biol Chem. 2000;275:13780-8 pubmed..Core activity of the mutant enzyme was reduced 20-fold. We conclude that mutations in the zinc-binding domain can reduce core activity without altering the association of any of the subunits required for this activity. ..
- Daulny A, Geng F, Muratani M, Geisinger J, Salghetti S, Tansey W. Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc Natl Acad Sci U S A. 2008;105:19649-54 pubmed publisher..Our data demonstrate that ubiquitylation can directly alter the subunit composition of a core component of the transcriptional machinery and provide a paradigm for how ubiquitin can influence gene activity. ..
- Christie K, Awrey D, Edwards A, Kane C. Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37. J Biol Chem. 1994;269:936-43 pubmed
- Sung P, Guzder S, Prakash L, Prakash S. Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3 and Rad25, in the incision step of nucleotide excision repair. J Biol Chem. 1996;271:10821-6 pubmed..These studies reveal the differential requirement of Rad3 DNA helicase and CTD kinase activities in damage-specific incision versus RNA polymerase II transcription. ..
- Keener J, Josaitis C, Dodd J, Nomura M. Reconstitution of yeast RNA polymerase I transcription in vitro from purified components. TATA-binding protein is not required for basal transcription. J Biol Chem. 1998;273:33795-802 pubmed..The role of TBP in pol I transcription is fundamentally different from its role in pol II or pol III transcription. ..
- Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nat Commun. 2017;8:15741 pubmed publisher..We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ..
- Huet J, Riva M, Sentenac A, Fromageot P. Yeast RNA polymerase C and its subunits. Specific antibodies as structural and functional probes. J Biol Chem. 1985;260:15304-10 pubmed..These results are discussed in terms of the participation of these polypeptides to the active enzyme molecule, and of their possible role in DNA binding or transcription factor recognition. ..
- Fellows J, Erdjument Bromage H, Tempst P, Svejstrup J. The Elp2 subunit of elongator and elongating RNA polymerase II holoenzyme is a WD40 repeat protein. J Biol Chem. 2000;275:12896-9 pubmed..Generally, different combinations of double and triple ELP gene deletions cause the same phenotypes as single ELP1, ELP2, or ELP3 deletion, providing genetic evidence that the ELP gene products work together in a complex. ..
- Alonso B, Beraud C, Meguellati S, Chen S, Pellequer J, Armengaud J, et al. Eukaryotic GPN-loop GTPases paralogs use a dimeric assembly reminiscent of archeal GPN. Cell Cycle. 2013;12:463-72 pubmed publisher..These results suggest that all three GPN proteins act at the molecular level in sister chromatid cohesion mechanism as a GPN|GPN complex reminiscent of the homodimeric structure of PAB0955, an archaeal member of GPN-loop GTPase. ..
- Kurat C, Lambert J, van Dyk D, Tsui K, van Bakel H, Kaluarachchi S, et al. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. Genes Dev. 2011;25:2489-501 pubmed publisher..Our study identified the chromatin boundary protein Yta7 as a key regulator that links S-phase kinases with RNAPII function at cell cycle-regulated histone gene promoters. ..
- Leblanc B, Benham C, Clark D. An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proc Natl Acad Sci U S A. 2000;97:10745-50 pubmed..The role of transcription factors might be to mark the promoter and to regulate specific melting of promoter DNA. ..
- Kruk J, Dutta A, Fu J, Gilmour D, Reese J. The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev. 2011;25:581-93 pubmed publisher..Our comprehensive analysis shows that Ccr4-Not directly regulates transcription, and suggests it does so by promoting the resumption of elongation of arrested RNAPII when it encounters transcriptional blocks in vivo. ..
- Kettenberger H, Armache K, Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell. 2004;16:955-65 pubmed..Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling. ..
- Ferri M, Peyroche G, Siaut M, Lefebvre O, Carles C, Conesa C, et al. A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70. Mol Cell Biol. 2000;20:488-95 pubmed..The data indicate that C17 is a novel specific subunit of Pol III which participates together with C34 in the recruitment of Pol III by the preinitiation complex. ..
- Gibney P, Fries T, Bailer S, Morano K. Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins. Eukaryot Cell. 2008;7:938-48 pubmed publisher..The core RNAPII subunits RPB5, RPB7, and RPB9 were isolated as potent high-copy-number suppressors of the rtr1Delta temperature-sensitive growth ..
- McCann T, Guo Y, McDonald W, Tansey W. Antagonistic roles for the ubiquitin ligase Asr1 and the ubiquitin-specific protease Ubp3 in subtelomeric gene silencing. Proc Natl Acad Sci U S A. 2016;113:1309-14 pubmed publisher..We suggest that control of pol II by nonproteolytic ubiquitylation provides a mechanism to enforce silencing by transient and reversible inhibition of pol II activity at subtelomeric chromatin. ..
- Suh M, Ye P, Zhang M, Hausmann S, Shuman S, Gnatt A, et al. Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD. Proc Natl Acad Sci U S A. 2005;102:17314-9 pubmed..We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously. ..