Rpb4 and Rpb7: multifunctional subunits of RNA polymerase II

References

• Armache KJ, Kettenberger H, Cramer P. (2003). Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci USA, 100, 6964–6968.
   PubMed Web of Science ®Google Scholar
• Armache KJ, Mitterweger S, Meinhart A, Cramer P. (2005). Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem, 280, 7131–7134.
   PubMed Web of Science ®Google Scholar
• Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L. (1998). EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes. Mol Cell Biol, 18, 1489–1497.
   PubMed Web of Science ®Google Scholar
• Brendel V, Karlin S. (1994). Applications of statistical criteria in protein sequence analysis: case study of yeast RNA polymerase II subunits. Comput Chem, 18, 251–253.
   PubMedGoogle Scholar
• Bushnell DA, Kornberg RD. (2003). Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci USA, 100, 6969–6973.
   PubMed Web of Science ®Google Scholar
• Choder M. (1993). A growth rate-limiting process in the last growth phase of the yeast life cycle involves RPB4, a subunit of RNA polymerase II. J Bacteriol, 175, 6358–6363.
   PubMed Web of Science ®Google Scholar
• Choder M. (2004). Rpb4 and Rpb7: subunits of RNA polymerase II and beyond. Trends Biochem Sci, 29, 674–681.
   PubMed Web of Science ®Google Scholar
• Choder M. (2011). mRNA imprinting: Additional level in the regulation of gene expression. Cell Logist, 1, 37–40.
   PubMedGoogle Scholar
• Choder M, Young RA. (1993). A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival. Mol Cell Biol, 13, 6984–6991.
   PubMed Web of Science ®Google Scholar
• Cojocaru M, Jeronimo C, Forget D, Bouchard A, Bergeron D, Côte P, Poirier GG, Greenblatt J, Coulombe B. (2008). Genomic location of the human RNA polymerase II general machinery: evidence for a role of TFIIF and Rpb7 at both early and late stages of transcription. Biochem J, 409, 139–147.
   PubMedGoogle Scholar
• Daulny A, Geng F, Muratani M, Geisinger JM, Salghetti SE, Tansey WP. (2008). Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc Natl Acad Sci USA, 105, 19649–19654.
   PubMed Web of Science ®Google Scholar
• Djupedal I, Portoso M, Spåhr H, Bonilla C, Gustafsson CM, Allshire RC, Ekwall K. (2005). RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev, 19, 2301–2306.
   PubMed Web of Science ®Google Scholar
• Edwards AM, Kane CM, Young RA, Kornberg RD. (1991). Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J Biol Chem, 266, 71–75.
   PubMed Web of Science ®Google Scholar
• Farago M, Nahari T, Hammel C, Cole CN, Choder M. (2003). Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell, 14, 2744–2755.
   PubMed Web of Science ®Google Scholar
• Frishman D, Argos P. (1995). Knowledge-based protein secondary structure assignment. Proteins, 23, 566–579.
   PubMed Web of Science ®Google Scholar
• Goler-Baron V, Selitrennik M, Barkai O, Haimovich G, Lotan R, Choder M. (2008). Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes Dev, 22, 2022–2027.
   PubMed Web of Science ®Google Scholar
• Grohmann D, Hirtreiter A, Werner F. (2009). RNAP subunits F/E (RPB4/7) are stably associated with archaeal RNA polymerase: using fluorescence anisotropy to monitor RNAP assembly in vitro. Biochem J, 421, 339–343.
   PubMed Web of Science ®Google Scholar
• Grohmann D, Werner F. (2010). Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination. RNA Biol, 7, 310–315.
   PubMed Web of Science ®Google Scholar
• Grohmann D, Werner F. (2011). Cycling through transcription with the RNA polymerase F/E (RPB4/7) complex: structure, function and evolution of archaeal RNA polymerase. Res Microbiol, 162, 10–18.
   PubMed Web of Science ®Google Scholar
• Harel-Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. (2010). RNA polymerase II subunits link transcription and mRNA decay to translation. Cell, 143, 552–563.
   PubMed Web of Science ®Google Scholar
• He CH, Ramotar D. (1999). An allele of the yeast RPB7 gene, encoding an essential subunit of RNA polymerase II, reduces cellular resistance to the antitumor drug bleomycin. Biochem Cell Biol, 77, 375–382.
   PubMed Web of Science ®Google Scholar
• Hirtreiter A, Grohmann D, Werner F. (2010). Molecular mechanisms of RNA polymerase–the F/E (RPB4/7) complex is required for high processivity in vitro. Nucleic Acids Res, 38, 585–596.
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. (1996). VMD: visual molecular dynamics. J Mol Graph, 14, 33–8, 27.
   PubMed Web of Science ®Google Scholar
• Jasiak AJ, Hartmann H, Karakasili E, Kalocsay M, Flatley A, Kremmer E, Strässer K, Martin DE, Söding J, Cramer P. (2008). Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J Biol Chem, 283, 26423–26427.
   PubMed Web of Science ®Google Scholar
• Katoh K, Misawa K, Kuma K, Miyata T. (2002). MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res, 30, 3059–3066.
   PubMed Web of Science ®Google Scholar
• Khazak V, Estojak J, Cho H, Majors J, Sonoda G, Testa JR, Golemis EA. (1998). Analysis of the interaction of the novel RNA polymerase II (pol II) subunit hsRPB4 with its partner hsRPB7 and with pol II. Mol Cell Biol, 18, 1935–1945.
   PubMed Web of Science ®Google Scholar
• Khazak V, Sadhale PP, Woychik NA, Brent R, Golemis EA. (1995). Human RNA polymerase II subunit hsRPB7 functions in yeast and influences stress survival and cell morphology. Mol Biol Cell, 6, 759–775.
   PubMed Web of Science ®Google Scholar
• Kimura M, Suzuki H, Ishihama A. (2002). Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol II. Mol Cell Biol, 22, 1577–1588.
   PubMed Web of Science ®Google Scholar
• Klein BS, Tebbets B. (2007). Dimorphism and virulence in fungi. Curr Opin Microbiol, 10, 314–319.
   PubMed Web of Science ®Google Scholar
• Kolodziej PA, Woychik N, Liao SM, Young RA. (1990). RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol, 10, 1915–1920.
   PubMed Web of Science ®Google Scholar
• Larivière L, Geiger S, Hoeppner S, Röther S, Strässer K, Cramer P. (2006). Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nat Struct Mol Biol, 13, 895–901.
   PubMed Web of Science ®Google Scholar
• Larkin RM, Guilfoyle TJ. (1998). Two small subunits in Arabidopsis RNA polymerase II are related to yeast RPB4 and RPB7 and interact with one another. J Biol Chem, 273, 5631–5637.
   PubMed Web of Science ®Google Scholar
• Li S, Smerdon MJ. (2002). Rpb4 and Rpb9 mediate subpathways of transcription-coupled DNA repair in Saccharomyces cerevisiae. EMBO J, 21, 5921–5929.
   PubMed Web of Science ®Google Scholar
• Linder T, Rasmussen NN, Samuelsen CO, Chatzidaki E, Baraznenok V, Beve J, Henriksen P, Gustafsson CM, Holmberg S. (2008). Two conserved modules of Schizosaccharomyces pombe Mediator regulate distinct cellular pathways. Nucleic Acids Res, 36, 2489–2504.
   PubMed Web of Science ®Google Scholar
• Lotan R, Bar-On VG, Harel-Sharvit L, Duek L, Melamed D, Choder M. (2005). The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev, 19, 3004–3016.
   PubMed Web of Science ®Google Scholar
• Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M. (2007). The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol, 178, 1133–1143.
   PubMed Web of Science ®Google Scholar
• Maillet I, Buhler JM, Sentenac A, Labarre J. (1999). Rpb4p is necessary for RNA polymerase II activity at high temperature. J Biol Chem, 274, 22586–22590.
   PubMed Web of Science ®Google Scholar
• McKune K, Richards KL, Edwards AM, Young RA, Woychik NA. (1993). RPB7, one of two dissociable subunits of yeast RNA polymerase II, is essential for cell viability. Yeast, 9, 295–299.
   PubMed Web of Science ®Google Scholar
• Mehta S, Miklos I, Sipiczki M, Sengupta S, Sharma N. (2009). The Med8 mediator subunit interacts with the Rpb4 subunit of RNA polymerase II and Ace2 transcriptional activator in Schizosaccharomyces pombe. FEBS Lett, 583, 3115–3120.
   PubMed Web of Science ®Google Scholar
• Meka H, Werner F, Cordell SC, Onesti S, Brick P. (2005). Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II. Nucleic Acids Res, 33, 6435–6444.
   PubMed Web of Science ®Google Scholar
• Miklos I, Szilagyi Z, Watt S, Zilahi E, Batta G, Antunovics Z, Enczi K, Bähler J, Sipiczki M. (2008). Genomic expression patterns in cell separation mutants of Schizosaccharomyces pombe defective in the genes sep10 (+) and sep15 (+) coding for the Mediator subunits Med31 and Med8. Mol Genet Genomics, 279, 225–238.
   PubMed Web of Science ®Google Scholar
• Mitsuzawa H, Ishihama A. (2004). RNA polymerase II transcription apparatus in Schizosaccharomyces pombe. Curr Genet, 44, 287–294.
   PubMed Web of Science ®Google Scholar
• Mitsuzawa H, Kanda E, Ishihama A. (2003). Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts. Nucleic Acids Res, 31, 4696–4701.
   PubMed Web of Science ®Google Scholar
• Mitsuzawa H, Kimura M, Kanda E, Ishihama A. (2005). Glyceraldehyde-3-phosphate dehydrogenase and actin associate with RNA polymerase II and interact with its Rpb7 subunit. FEBS Lett, 579, 48–52.
   PubMed Web of Science ®Google Scholar
• Miyao T, Barnett JD, Woychik NA. (2001). Deletion of the RNA polymerase subunit RPB4 acts as a global, not stress-specific, shut-off switch for RNA polymerase II transcription at high temperatures. J Biol Chem, 276, 46408–46413.
   PubMed Web of Science ®Google Scholar
• Na X, Duan HO, Messing EM, Schoen SR, Ryan CK, di Sant’Agnese PA, Golemis EA, Wu G. (2003). Identification of the RNA polymerase II subunit hsRPB7 as a novel target of the von Hippel-Lindau protein. EMBO J, 22, 4249–4259.
   PubMed Web of Science ®Google Scholar
• Naji S, Grünberg S, Thomm M. (2007). The RPB7 orthologue E’ is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation. J Biol Chem, 282, 11047–11057.
   PubMed Web of Science ®Google Scholar
• Naorem A, Sadhale PP. (2008). Identification and characterization of DdRPB4, a subunit of Dictyostelium discoideum RNA polymerase II. Biochem Biophys Res Commun, 377, 1141–1146.
   PubMed Web of Science ®Google Scholar
• Orlicky SM, Tran PT, Sayre MH, Edwards AM. (2001). Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem, 276, 10097–10102.
   PubMed Web of Science ®Google Scholar
• Pankotai T, Ujfaludi Z, Vámos E, Suri K, Boros IM. (2010). The dissociable RPB4 subunit of RNA Pol II has vital functions in Drosophila. Mol Genet Genomics, 283, 89–97.
   PubMed Web of Science ®Google Scholar
• Perbal B. (1999). Nuclear localisation of NOVH protein: a potential role for NOV in the regulation of gene expression. MP, Mol Pathol, 52, 84–91.
   PubMedGoogle Scholar
• Petermann R, Mossier BM, Aryee DN, Khazak V, Golemis EA, Kovar H. (1998). Oncogenic EWS-Fli1 interacts with hsRPB7, a subunit of human RNA polymerase II. Oncogene, 17, 603–610.
   PubMed Web of Science ®Google Scholar
• Pillai B, Sampath V, Sharma N, Sadhale P. (2001). Rpb4, a non-essential subunit of core RNA polymerase II of Saccharomyces cerevisiae is important for activated transcription of a subset of genes. J Biol Chem, 276, 30641–30647.
   PubMed Web of Science ®Google Scholar
• Pillai B, Verma J, Abraham A, Francis P, Kumar Y, Tatu U, Brahmachari SK, Sadhale PP. (2003). Whole genome expression profiles of yeast RNA polymerase II core subunit, Rpb4, in stress and nonstress conditions. J Biol Chem, 278, 3339–3346.
   PubMed Web of Science ®Google Scholar
• Rosenheck S, Choder M. (1998). Rpb4, a subunit of RNA polymerase II, enables the enzyme to transcribe at temperature extremes in vitro. J Bacteriol, 180, 6187–6192.
   PubMed Web of Science ®Google Scholar
• Runner VM, Podolny V, Buratowski S. (2008). The Rpb4 subunit of RNA polymerase II contributes to cotranscriptional recruitment of 3′ processing factors. Mol Cell Biol, 28, 1883–1891.
   PubMed Web of Science ®Google Scholar
• Russell RB, Barton GJ. (1992). Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins, 14, 309–323.
   PubMedGoogle Scholar
• Sakurai H, Mitsuzawa H, Kimura M, Ishihama A. (1999). The Rpb4 subunit of fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotes. Mol Cell Biol, 19, 7511–7518.
   PubMed Web of Science ®Google Scholar
• Sampath V, Balakrishnan B, Verma-Gaur J, Onesti S, Sadhale PP. (2008). Unstructured N terminus of the RNA polymerase II subunit Rpb4 contributes to the interaction of Rpb4.Rpb7 subcomplex with the core RNA polymerase II of Saccharomyces cerevisiae. J Biol Chem, 283, 3923–3931.
   PubMed Web of Science ®Google Scholar
• Sampath V, Rekha N, Srinivasan N, Sadhale P. (2003). The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae. J Biol Chem, 278, 51566–51576.
   PubMed Web of Science ®Google Scholar
• Sampath V, Sadhale P. (2005). Rpb4 and Rpb7: a sub-complex integral to multi-subunit RNA polymerases performs a multitude of functions. IUBMB Life, 57, 93–102.
   PubMed Web of Science ®Google Scholar
• Sareen A, Choudhry P, Mehta S, Sharma N. (2005). Mapping the interaction site of Rpb4 and Rpb7 subunits of RNA polymerase II in Saccharomyces cerevisiae. Biochem Biophys Res Commun, 332, 763–770.
   PubMed Web of Science ®Google Scholar
• Selitrennik M, Duek L, Lotan R, Choder M. (2006). Nucleocytoplasmic shuttling of the Rpb4p and Rpb7p subunits of Saccharomyces cerevisiae RNA polymerase II by two pathways. Eukaryotic Cell, 5, 2092–2103.
   PubMed Web of Science ®Google Scholar
• Sharma N, Marguerat S, Mehta S, Watt S, Bähler J. (2006). The fission yeast Rpb4 subunit of RNA polymerase II plays a specialized role in cell separation. Mol Genet Genomics, 276, 545–554.
   PubMed Web of Science ®Google Scholar
• Sharma, N. and Sadhale, P. P. (1999). Overexpression of the gene for Rpb7 subunit of yeast RNA polymerase II rescues the phenotypes associated with absence of the largest, nonessential subunit Rpb4. J. Genet., 78, 149–156.
   Web of Science ®Google Scholar
• Sheffer A, Varon M, Choder M. (1999). Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol Cell Biol, 19, 2672–2680.
   PubMed Web of Science ®Google Scholar
• Shen XQ, Bubulya A, Zhou XF, Khazak V, Golemis EA, Shemshedini L. (1999). Ligand-free RAR can interact with the RNA polymerase II subunit hsRPB7 and repress transcription. Endocrine, 10, 281–289.
   PubMed Web of Science ®Google Scholar
• Shpakovski GV, Gadal O, Labarre-Mariotte S, Lebedenko EN, Miklos I, Sakurai H, Proshkin SA, Van Mullem V, Ishihama A, Thuriaux P. (2000). Functional conservation of RNA polymerase II in fission and budding yeasts. J Mol Biol, 295, 1119–1127.
   PubMed Web of Science ®Google Scholar
• Singh SR, Pillai B, Balakrishnan B, Naorem A, Sadhale PP. (2007). Relative levels of RNA polII subunits differentially affect starvation response in budding yeast. Biochem Biophys Res Commun, 356, 266–272.
   PubMed Web of Science ®Google Scholar
• Singh SR, Rekha N, Pillai B, Singh V, Naorem A, Sampath V, Srinivasan N, Sadhale PP. (2004). Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation. Nucleic Acids Res, 32, 201–210.
   PubMed Web of Science ®Google Scholar
• Spåhr H, Calero G, Bushnell DA, Kornberg RD. (2009). Schizosacharomyces pombe RNA polymerase II at 3.6-A resolution. Proc Natl Acad Sci USA, 106, 9185–9190.
   PubMed Web of Science ®Google Scholar
• Tan Q, Li X, Sadhale PP, Miyao T, Woychik NA. (2000). Multiple mechanisms of suppression circumvent transcription defects in an RNA polymerase mutant. Mol Cell Biol, 20, 8124–8133.
   PubMed Web of Science ®Google Scholar
• Todone F, Brick P, Werner F, Weinzierl RO, Onesti S. (2001). Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. Mol Cell, 8, 1137–1143.
   PubMed Web of Science ®Google Scholar
• Todorova R. (2009). In vitro interaction between the N-terminus of the Ewing’s sarcoma protein and the subunit of RNA polymerase II hsRPB7. Mol Biol Rep, 36, 1269–1274.
   PubMed Web of Science ®Google Scholar
• Tombácz I, Schauer T, Juhász I, Komonyi O, Boros I. (2009). The RNA Pol II CTD phosphatase Fcp1 is essential for normal development in Drosophila melanogaster. Gene, 446, 58–67.
   PubMed Web of Science ®Google Scholar
• Ujvári A, Luse DS. (2006). RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit. Nat Struct Mol Biol, 13, 49–54.
   PubMed Web of Science ®Google Scholar
• Verma-Gaur J, Rao SN, Taya T, Sadhale P. (2008). Genomewide recruitment analysis of Rpb4, a subunit of polymerase II in Saccharomyces cerevisiae, reveals its involvement in transcription elongation. Eukaryotic Cell, 7, 1009–1018.
   PubMedGoogle Scholar
• Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. (2009). Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189–1191.
   PubMed Web of Science ®Google Scholar
• Werner F, Eloranta JJ, Weinzierl RO. (2000). Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic Acids Res, 28, 4299–4305.
   PubMed Web of Science ®Google Scholar
• Woychik NA, Hampsey M. (2002). The RNA polymerase II machinery: structure illuminates function. Cell, 108, 453–463.
   PubMed Web of Science ®Google Scholar
• Woychik NA, Lane WS, Young RA. (1991). Yeast RNA polymerase II subunit RPB9 is essential for growth at temperature extremes. J Biol Chem, 266, 19053–19055.
   PubMed Web of Science ®Google Scholar
• Woychik NA, Young RA. (1989). RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth. Mol Cell Biol, 9, 2854–2859.
   PubMed Web of Science ®Google Scholar
• Xue X, Lehming N. (2008). Nhp6p and Med3p regulate gene expression by controlling the local subunit composition of RNA polymerase II. J Mol Biol, 379, 212–230.
   PubMed Web of Science ®Google Scholar