A Region of Bdp1 Necessary for Transcription Initiation That Is Located within the RNA Polymerase III Active Site Cleft

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
• Vannini A, Cramer P. 2012. Conservation between the RNA polymerase I, II, and III transcription initiation machineries. Mol Cell 45:439–446. http://dx.doi.org/10.1016/j.molcel.2012.01.023.
   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
• Kassavetis GA, Bartholomew B, Blanco JA, Johnson TE, Geiduschek EP. 1991. Two essential components of the Saccharomyces cerevisiae transcription factor TFIIIB: transcription and DNA-binding properties. Proc Natl Acad Sci U S A 88:7308–7312. http://dx.doi.org/10.1073/pnas.88.16.7308.
   PubMedGoogle 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
• 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
• Persinger J, Bartholomew B. 1996. Mapping the contacts of yeast TFIIIB and RNA polymerase III at various distances from the major groove of DNA by DNA photoaffinity labeling. J Biol Chem 271:33039–33046. http://dx.doi.org/10.1074/jbc.271.51.33039.
   PubMedGoogle 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
• Persinger J, Sengupta SM, Bartholomew B. 1999. Spatial organization of the core region of yeast TFIIIB-DNA complexes. Mol Cell Biol 19:5218–5234.
   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
• Kassavetis GA, Nguyen ST, Kobayashi R, Kumar A, Geiduschek EP, Pisano M. 1995. Cloning, expression, and function of TFC5, the gene encoding the B″ component of the Saccharomyces cerevisiae RNA polymerase III transcription factor TFIIIB. Proc Natl Acad Sci U S A 92:9786–9790. http://dx.doi.org/10.1073/pnas.92.21.9786.
   PubMed Web of Science ®Google 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
• 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
• Khoo SK, Wu CC, Lin YC, Lee JC, Chen HT. 2014. Mapping the protein interaction network for TFIIB-related factor Brf1 in the RNA polymerase III preinitiation complex. Mol Cell Biol 34:551–559. http://dx.doi.org/10.1128/MCB.00910-13.
   PubMed Web of Science ®Google 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.
   PubMedGoogle Scholar
• Roberts S, Miller SJ, Lane WS, Lee S, Hahn S. 1996. Cloning and functional characterization of the gene encoding the TFIIIB90 subunit of RNA polymerase III transcription factor TFIIIB. J Biol Chem 271:14903–14909. http://dx.doi.org/10.1074/jbc.271.25.14903.
   PubMedGoogle Scholar
• Aasland R, Stewart AF, Gibson T. 1996. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem Sci 21:87–88. http://dx.doi.org/10.1016/S0968-0004(96)30009-1.
   PubMed Web of Science ®Google Scholar
• Saida 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
• Schramm L, Pendergrast PS, Sun Y, Hernandez N. 2000. Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters. Genes Dev 14:2650–2663. http://dx.doi.org/10.1101/gad.836400.
   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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• Vannini A, Ringel R, Kusser AG, Berninghausen O, Kassavetis GA, Cramer P. 2010. Molecular basis of RNA polymerase III transcription repression by Maf1. Cell 143:59–70. http://dx.doi.org/10.1016/j.cell.2010.09.002.
   PubMed Web of Science ®Google Scholar
• Fernandez-Tornero C, Bottcher B, Rashid UJ, Steuerwald U, Florchinger B, Devos DP, Lindner D, Muller CW. 2010. Conformational flexibility of RNA polymerase III during transcriptional elongation. EMBO J 29:3762–3772. http://dx.doi.org/10.1038/emboj.2010.266.
   PubMed Web of Science ®Google 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
• 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
• Rijal K, Maraia RJ. 2013. RNA polymerase III mutants in TFIIFalpha-like C37 that cause terminator readthrough with no decrease in transcription output. Nucleic Acids Res 41:139–155. http://dx.doi.org/10.1093/nar/gks985.
   PubMed Web of Science ®Google Scholar
• Landrieux E, Alic N, Ducrot C, Acker J, Riva M, Carles C. 2006. A subcomplex of RNA polymerase III subunits involved in transcription termination and reinitiation. EMBO J 25:118–128. http://dx.doi.org/10.1038/sj.emboj.7600915.
   PubMed Web of Science ®Google Scholar
• Hu P, Samudre K, Wu S, Sun Y, Hernandez N. 2004. CK2 phosphorylation of Bdp1 executes cell cycle-specific RNA polymerase III transcription repression. Mol Cell 16:81–92. http://dx.doi.org/10.1016/j.molcel.2004.09.008.
   PubMed Web of Science ®Google Scholar
• Bachman N, Gelbart ME, Tsukiyama T, Boeke JD. 2005. TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes Dev 19:955–964. http://dx.doi.org/10.1101/gad.1299105.
   PubMedGoogle Scholar
• Milliman EJ, Hu Z, Yu MC. 2012. Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions. BMC Genomics 13:728. http://dx.doi.org/10.1186/1471-2164-13-728.
   PubMedGoogle Scholar
• He Y, Fang J, Taatjes DJ, Nogales E. 2013. Structural visualization of key steps in human transcription initiation. Nature 495:481–486. http://dx.doi.org/10.1038/nature11991.
   PubMed Web of Science ®Google Scholar
• Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD. 2013. Architecture of an RNA polymerase II transcription pre-initiation complex. Science 342:1238724. http://dx.doi.org/10.1126/science.1238724.
   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
• 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
• 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
• Fernandez-Tornero C, Moreno-Morcillo M, Rashid UJ, Taylor NM, Ruiz FM, Gruene T, Legrand P, Steuerwald U, Muller CW. 2013. Crystal structure of the 14-subunit RNA polymerase I. Nature 502:644–649. http://dx.doi.org/10.1038/nature12636.
   PubMed Web of Science ®Google Scholar