Mapping the Protein Interaction Network for TFIIB-Related Factor Brf1 in the RNA Polymerase III Preinitiation Complex

REFERENCES

• Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A. 2007. The expanding RNA polymerase III transcriptome. Trends Genet. 23:614–622. http://dx.doi.org/10.1016/j.tig.2007.09.001.
   PubMed Web of Science ®Google Scholar
• Geiduschek EP, Kassavetis GA. 2001. The RNA polymerase III transcription apparatus. J. Mol. Biol. 310:1–26. http://dx.doi.org/10.1006/jmbi.2001.4732.
   PubMed Web of Science ®Google Scholar
• Schramm L, Hernandez N. 2002. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16:2593–2620. http://dx.doi.org/10.1101/gad.1018902.
   PubMed Web of Science ®Google Scholar
• Ishiguro A, Kassavetis GA, Geiduschek EP. 2002. Essential roles of Bdp1, a subunit of RNA polymerase III initiation factor TFIIIB, in transcription and tRNA processing. Mol. Cell. Biol. 22:3264–3275. http://dx.doi.org/10.1128/MCB.22.10.3264-3275.2002.
   PubMedGoogle Scholar
• Kassavetis GA, Bardeleben C, Kumar A, Ramirez E, Geiduschek EP. 1997. Domains of the Brf component of RNA polymerase III transcription factor IIIB (TFIIIB): functions in assembly of TFIIIB-DNA complexes and recruitment of RNA polymerase to the promoter. Mol. Cell. Biol. 17:5299–5306.
   PubMedGoogle Scholar
• Kassavetis GA, Driscoll R, Geiduschek EP. 2006. Mapping the principal interaction site of the Brf1 and Bdp1 subunits of Saccharomyces cerevisiae TFIIIB. J. Biol. Chem. 281:14321–14329. http://dx.doi.org/10.1074/jbc.M601702200.
   PubMedGoogle Scholar
• Kumar A, Grove A, Kassavetis GA, Geiduschek EP. 1998. Transcription factor IIIB: the architecture of its DNA complex, and its roles in initiation of transcription by RNA polymerase III. Cold Spring Harb. Symp. Quant. Biol. 63:121–129. http://dx.doi.org/10.1101/sqb.1998.63.121.
   PubMedGoogle Scholar
• Kumar A, Kassavetis GA, Geiduschek EP, Hambalko M, Brent CJ. 1997. Functional dissection of the B″ component of RNA polymerase III transcription factor IIIB: a scaffolding protein with multiple roles in assembly and initiation of transcription. Mol. Cell. Biol. 17:1868–1880.
   PubMedGoogle Scholar
• Librizzi MD, Brenowitz M, Willis IM. 1998. The TATA element and its context affect the cooperative interaction of TATA-binding protein with the TFIIB-related factor, TFIIIB70. J. Biol. Chem. 273:4563–4568. http://dx.doi.org/10.1074/jbc.273.8.4563.
   PubMed Web of Science ®Google Scholar
• Saïda F. 2008. Structural characterization of the interaction between TFIIIB components Bdp1 and Brf1. Biochemistry 47:13197–13206. http://dx.doi.org/10.1021/bi801406z.
   PubMedGoogle Scholar
• Kassavetis GA, Kumar A, Letts GA, Geiduschek EP. 1998. A post-recruitment function for the RNA polymerase III transcription-initiation factor IIIB. Proc. Natl. Acad. Sci. U. S. A. 95:9196–9201. http://dx.doi.org/10.1073/pnas.95.16.9196.
   PubMedGoogle Scholar
• Kassavetis GA, Kumar A, Ramirez E, Geiduschek EP. 1998. Functional and structural organization of Brf, the TFIIB-related component of the RNA polymerase III transcription initiation complex. Mol. Cell. Biol. 18:5587–5599.
   PubMedGoogle Scholar
• Hahn S, Roberts S. 2000. The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation. Genes Dev. 14:719–730. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC316465/.
   PubMedGoogle Scholar
• Wu CC, Lin YC, Chen HT. 2011. The TFIIF-like Rpc37/53 dimer lies at the center of a protein network to connect TFIIIC, Bdp1, and the RNA polymerase III active center. Mol. Cell. Biol. 31:2715–2728. http://dx.doi.org/10.1128/MCB.05151-11.
   PubMed Web of Science ®Google Scholar
• Chen HT, Hahn S. 2004. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell 119:169–180. http://dx.doi.org/10.1016/j.cell.2004.09.028.
   PubMed Web of Science ®Google Scholar
• Chen HT, Hahn S. 2003. Binding of TFIIB to RNA polymerase II: mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex. Mol. Cell 12:437–447. http://dx.doi.org/10.1016/S1097-2765(03)00306-X.
   PubMed Web of Science ®Google Scholar
• Bushnell DA, Westover KD, Davis RE, Kornberg RD. 2004. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 angstroms. Science 303:983–988. http://dx.doi.org/10.1126/science.1090838.
   PubMed Web of Science ®Google Scholar
• Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD. 2010. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327:206–209. http://dx.doi.org/10.1126/science.1182015.
   PubMedGoogle Scholar
• Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, Cramer P. 2009. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462:323–330. http://dx.doi.org/10.1038/nature08548.
   PubMed Web of Science ®Google Scholar
• Sainsbury S, Niesser J, Cramer P. 2013. Structure and function of the initially transcribing RNA polymerase II-TFIIB complex. Nature 493:437–440. http://dx.doi.org/10.1038/nature11715.
   PubMed Web of Science ®Google Scholar
• Colbert T, Hahn S. 1992. A yeast TFIIB-related factor involved in RNA polymerase III transcription. Genes Dev. 6:1940–1949. http://dx.doi.org/10.1101/gad.6.10.1940.
   PubMedGoogle Scholar
• Khoo B, Brophy B, Jackson SP. 1994. Conserved functional domains of the RNA polymerase III general transcription factor BRF. Genes Dev. 8:2879–2890. http://dx.doi.org/10.1101/gad.8.23.2879.
   PubMed Web of Science ®Google Scholar
• Naidu S, Friedrich JK, Russell J, Zomerdijk JC. 2011. TAF1B is a TFIIB-like component of the basal transcription machinery for RNA polymerase I. Science 333:1640–1642. http://dx.doi.org/10.1126/science.1207656.
   PubMedGoogle Scholar
• Knutson BA, Hahn S. 2011. Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors. Science 333:1637–1640. http://dx.doi.org/10.1126/science.1207699.
   PubMed Web of Science ®Google Scholar
• Martinez MJ, Sprague KU. 2003. Cloning of a putative Bombyx mori TFIIB-related factor (BRF). Arch. Insect Biochem. Physiol. 54:55–67. http://dx.doi.org/10.1002/arch.10120.
   PubMedGoogle Scholar
• Kassavetis GA, Joazeiro CA, Pisano M, Geiduschek EP, Colbert T, Hahn S, Blanco JA. 1992. The role of the TATA-binding protein in the assembly and function of the multisubunit yeast RNA polymerase III transcription factor, TFIIIB. Cell 71:1055–1064. http://dx.doi.org/10.1016/0092-8674(92)90399-W.
   PubMed Web of Science ®Google Scholar
• Colbert T, Lee S, Schimmack G, Hahn S. 1998. Architecture of protein and DNA contacts within the TFIIIB-DNA complex. Mol. Cell. Biol. 18:1682–1691.
   PubMed Web of Science ®Google Scholar
• Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler PB. 2003. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 422:534–539. http://dx.doi.org/10.1038/nature01534.
   PubMed Web of Science ®Google Scholar
• Andrau JC, Sentenac A, Werner M. 1999. Mutagenesis of yeast TFIIIB70 reveals C-terminal residues critical for interaction with TBP and C34. J. Mol. Biol. 288:511–520. http://dx.doi.org/10.1006/jmbi.1999.2724.
   PubMedGoogle Scholar
• Ferri ML, Peyroche G, Siaut M, Lefebvre O, Carles C, Conesa C, Sentenac A. 2000. A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70. Mol. Cell. Biol. 20:488–495. http://dx.doi.org/10.1128/MCB.20.2.488-495.2000.
   PubMedGoogle Scholar
• Moir RD, Puglia KV, Willis IM. 2000. Interactions between the tetratricopeptide repeat-containing transcription factor TFIIIC131 and its ligand, TFIIIB70. Evidence for a conformational change in the complex. J. Biol. Chem. 275:26591–26598. http://dx.doi.org/10.1074/jbc.M003991200.
   PubMedGoogle Scholar
• Moir RD, Puglia KV, Willis IM. 2002. Autoinhibition of TFIIIB70 binding by the tetratricopeptide repeat-containing subunit of TFIIIC. J. Biol. Chem. 277:694–701. http://dx.doi.org/10.1074/jbc.M108924200.
   PubMedGoogle Scholar
• Moir RD, Sethy-Coraci I, Puglia K, Librizzi MD, Willis IM. 1997. A tetratricopeptide repeat mutation in yeast transcription factor IIIC131 (TFIIIC131) facilitates recruitment of TFIIB-related factor TFIIIB70. Mol. Cell. Biol. 17:7119–7125.
   PubMedGoogle Scholar
• Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14:115–132. http://dx.doi.org/10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2.
   PubMed Web of Science ®Google Scholar
• Wach A, Brachat A, Pohlmann R, Philippsen P. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10:1793–1808. http://dx.doi.org/10.1002/yea.320101310.
   PubMed Web of Science ®Google Scholar
• Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P. 1992. Multifunctional yeast high-copy-number shuttle vectors. Gene 110:119–122. http://dx.doi.org/10.1016/0378-1119(92)90454-W.
   PubMed Web of Science ®Google Scholar
• Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG. 2003. An expanded eukaryotic genetic code. Science 301:964–967. http://dx.doi.org/10.1126/science.1084772.
   PubMed Web of Science ®Google Scholar
• Sikorski RS, Hieter P. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19–27.
   PubMed Web of Science ®Google Scholar
• Wu CC, Herzog F, Jennebach S, Lin YC, Pai CY, Aebersold R, Cramer P, Chen HT. 2012. RNA polymerase III subunit architecture and implications for open promoter complex formation. Proc. Natl. Acad. Sci. U. S. A. 109:19232–19237. http://dx.doi.org/10.1073/pnas.1211665109.
   PubMed Web of Science ®Google Scholar
• Chen HT, Warfield L, Hahn S. 2007. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat. Struct. Mol. Biol. 14:696–703. http://dx.doi.org/10.1038/nsmb1272.
   PubMed Web of Science ®Google Scholar
• Jasiak AJ, Armache KJ, Martens B, Jansen RP, Cramer P. 2006. Structural biology of RNA polymerase III: subcomplex C17/25 X-ray structure and 11 subunit enzyme model. Mol. Cell 23:71–81. http://dx.doi.org/10.1016/j.molcel.2006.05.013.
   PubMed Web of Science ®Google Scholar
• Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake K, Lee DK, Roeder RG, Burley SK. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377:119–128. http://dx.doi.org/10.1038/377119a0.
   PubMed Web of Science ®Google Scholar
• Werner M, Chaussivert N, Willis IM, Sentenac A. 1993. Interaction between a complex of RNA polymerase III subunits and the 70-kDa component of transcription factor IIIB. J. Biol. Chem. 268:20721–20724.
   PubMed Web of Science ®Google Scholar
• Brun I, Sentenac A, Werner M. 1997. Dual role of the C34 subunit of RNA polymerase III in transcription initiation. EMBO J. 16:5730–5741. http://dx.doi.org/10.1093/emboj/16.18.5730.
   PubMed Web of Science ®Google Scholar
• Tate JJ, Persinger J, Bartholomew B. 1998. Survey of four different photoreactive moieties for DNA photoaffinity labeling of yeast RNA polymerase III transcription complexes. Nucleic Acids Res. 26:1421–1426. http://dx.doi.org/10.1093/nar/26.6.1421.
   PubMed Web of Science ®Google Scholar
• Tsai FT, Sigler PB. 2000. Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J. 19:25–36. http://dx.doi.org/10.1093/emboj/19.1.25.
   PubMedGoogle Scholar
• Kassavetis GA, Letts GA, Geiduschek EP. 1999. A minimal RNA polymerase III transcription system. EMBO J. 18:5042–5051. http://dx.doi.org/10.1093/emboj/18.18.5042.
   PubMedGoogle Scholar
• Kassavetis GA, Letts GA, Geiduschek EP. 2001. The RNA polymerase III transcription initiation factor TFIIIB participates in two steps of promoter opening. EMBO J. 20:2823–2834. http://dx.doi.org/10.1093/emboj/20.11.2823.
   PubMed Web of Science ®Google Scholar
• Bartholomew B, Durkovich D, Kassavetis GA, Geiduschek EP. 1993. Orientation and topography of RNA polymerase III in transcription complexes. Mol. Cell. Biol. 13:942–952.
   PubMed Web of Science ®Google Scholar
• Bartholomew B, Kassavetis GA, Geiduschek EP. 1991. Two components of Saccharomyces cerevisiae transcription factor IIIB (TFIIIB) are stereospecifically located upstream of a tRNA gene and interact with the second-largest subunit of TFIIIC. Mol. Cell. Biol. 11:5181–5189.
   PubMedGoogle Scholar