42
Views
241
CrossRef citations to date
0
Altmetric
Transcriptional Regulation

Proteomics of the Eukaryotic Transcription Machinery: Identification of Proteins Associated with Components of Yeast TFIID by Multidimensional Mass Spectrometry

, , , &
Pages 4723-4738 | Received 08 Jan 2002, Accepted 27 Mar 2002, Published online: 27 Mar 2023

REFERENCES

  • Albright, S. R., and R. Tjian. 2000. TAFs revisited: more data reveal new twists and confirm old ideas. Gene 242: 1–13.
  • Amerik, A. Y., S. J. Li, and M. Hochstrasser. 2000. Analysis of the deubiquitinating enzymes of the yeast Saccharomyces cerevisiae. Biol. Chem. 381: 981–992.
  • Angus-Hill, M. L., A. Schlichter, D. Roberts, H. Erdjument-Bromage, P. Tempst, and B. R. Cairns. 2001. A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. Mol. Cell 7: 741–751.
  • Bell, B., and L. Tora. 1999. Regulation of gene expression by multiple forms of TFIID and other novel TAFII-containing complexes. Exp. Cell Res. 246: 11–19.
  • Bell, B., E. Scheer, and L. Tora. 2001. Identification of hTAF(II)80δ links apoptotic signaling pathways to transcription factor TFIID function. Mol. Cell 8: 591–600.
  • Bhaumik, S. R., and M. R. Green. 2001. SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes Dev. 15: 1935–1945.
  • Brachmann, C. B., A. Davies, G. J. Cost, E. Caputo, J. Li, P. Hieter, and J. D. Boeke. 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.
  • Cairns, B. R., A. Schlichter, H. Erdjument-Bromage, P. Tempst, R. D. Kornberg, and F. Winston. 1999. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4: 715–723.
  • Cairns, B. R., N. L. Henry, and R. D. Kornberg. 1996. TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9. Mol. Cell. Biol. 16: 3308–3316.
  • Chi, Y., M. J. Huddleston, X. Zhang, R. A. Young, R. S. Annan, S. A. Carr, and R. J. Deshaies 2001. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15: 1078–1092.
  • Costanzo, M. C., M. E. Crawford, J. E. Hirschman, J. E. Kranz, P. Olsen, L. S. Robertson, M. S. Skrzypek, B. R. Braun, K. L. Hopkins, P. Kondu, C. Lengieza, J. E. Lew-Smith, M. Tillberg, and J. I. Garrels. 2001. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 29: 75–79.
  • Dantonel, J. C., K. G. Murthy, J. L. Manley, and L. Tora. 1997. Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA. Nature 389: 399–402.
  • Drysdale, C. M., B. M. Jackson, R. McVeigh, E. R. Klebanow, Y. Bai, T. Kokubo, M. Swanson, Y. Nakatani, P. A. Weil, and A. G. Hinnebusch. 1998. The Gcn4p activation domain interacts specifically in vitro with RNA polymerase II holoenzyme, TFIID, and the Adap-Gcn5p coactivator complex. Mol. Cell. Biol. 18: 1711–1724.
  • Eisenmann, D. M., K. M. Arndt, S. L. Ricupero, J. W. Rooney, and F. Winston. 1992. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 6: 1319–1331.
  • Eng, J. K., A. L. McCormack, and J. R. Yates III. 1994. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom. 5: 976–989.
  • Gangloff, Y. G., J. C. Pointud, S. Thuault, L. Carre, C. Romier, S. Muratoglu, M. Brand, L. Tora, J. L. Couderc, and I. Davidson. 2001. The tfiid components human taf(ii)140 and Drosophila bip2 (taf(ii)155) are novel metazoan homologues of yeast taf(ii)47 containing a histone fold and a phd finger. Mol. Cell. Biol. 21: 5109–5121.
  • Gangloff, Y., C. Romier, S. Thuault, S. Werten, and I. Davidson. 2001. The histone fold is a key structural motif of transcription factor TFIID. Trends Biochem. Sci. 26: 250–257.
  • Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M. A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147.
  • Good, P. 2000. Permutation tests: a pratical guide to resampling methods for testing hypotheses, 2nd ed. Springer-Verlag, New York, N.Y.
  • Grant, P. A., D. Schieltz, M. G. Pray-Grant, D. J. Steger, J. C. Reese, J. R. Yates III, and J. L. Workman. 1998. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94: 45–53.
  • Green, M. R. 2000. TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem. Sci. 25: 59–63.
  • Guthrie, C., and G. R. Fink. 1991. Guide to yeast genetics and molecular biology. Methods Enzymol. 194: 1–933.
  • Hartzog, G. A., T. Wada, H. Handa, and F. Winston. 1998. Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12: 357–369.
  • Henry, N. L., A. M. Campbell, W. J. Feaver, D. Poon, P. A. Weil, and R. D. Kornberg. 1994. TFIIF-TAF-RNA polymerase II connection. Genes Dev. 8: 2868–2878.
  • Ho, Y., A. Gruhler, A. Heilbut, G. D. Bader, L. Moore, S. L. Adams, A. Millar, P. Taylor, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.
  • Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science 293: 1074–1080.
  • John, S., L. Howe, S. T. Tafrov, P. A. Grant, R. Sternglanz, and J. L. Workman. 2000. The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev. 14: 1196–1208.
  • Kaiser, P., K. Flick, C. Wittenberg, and S. I. Reed. 2000. Regulation of transcription by ubiquitination without proteolysis: Cdc34/SCF(Met30)-mediated inactivation of the transcription factor Met4. Cell 102: 303–314.
  • Kirchner, J., S. L. Sanders, E. Klebanow, and P. A. Weil. 2001. Molecular genetic dissection of TAF25, an essential yeast gene encoding a subunit shared by TFIID and SAGA multiprotein transcription factors. Mol. Cell. Biol. 21: 6668–6680.
  • Klebanow, E. R., D. Poon, S. Zhou, and P. A. Weil. 1996. Isolation and characterization of TAF25, an essential yeast gene that encodes an RNA polymerase II-specific TATA-binding protein-associated factor. J. Biol. Chem. 271: 13706–13715.
  • Kuras, L., P. Kosa, M. Mencia, and K. Struhl. 2000. TAF-containing and TAF-independent forms of transcriptionally active TBP in vivo. Science 288: 1244–1248.
  • Larschan, E., and F. Winston. 2001. The Saccharomyces cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev. 15: 1946–1956.
  • Lee, T. I., and R. A. Young. 1998. Regulation of gene expression by TBP-associated proteins. Genes Dev. 12: 1398–1408.
  • Li, X. Y., S. R. Bhaumik, and M. R. Green. 2000. Distinct classes of yeast promoters revealed by differential TAF recruitment. Science 288: 1242–1244.
  • Link, A. J., J. Eng, D. M. Schieltz, E. Carmack, G. J. Mize, D. R. Morris, B. M. Garvik, and J. R. Yates III. 1999. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17: 676–682.
  • Longtine, M. S., A. McKenzie III, D. J. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953–961.
  • Macpherson, N., V. Measday, L. Moore, and B. Andrews. 2000. A yeast taf17 mutant requires the Swi6 transcriptional activator for viability and shows defects in cell cycle-regulated transcription. Genetics 154: 1561–1576.
  • Matangkasombut, O., R. M. Buratowski, N. W. Swilling, and S. Buratowski 2000. Bromodomain factor 1 corresponds to a missing piece of yeast. TFIID Genes Dev. 14: 951–962.
  • Poon, D., and P. A. Weil. 1993. Immunopurification of yeast TATA-binding protein and associated factors: presence of transcription factor IIIB transcriptional activity. J. Biol. Chem. 268: 15325–15328.
  • Poon, D., A. M. Campbell, Y. Bai, and P. A. Weil. 1994. Yeast Taf170 is encoded by MOT1 and exists in a TATA box-binding protein (TBP)-TBP-associated factor complex distinct from transcription factor IID. J. Biol. Chem. 269: 23135–23140.
  • Rigaut, G., A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17: 1030–1032.
  • Roberts, S. M., and F. Winston. 1997. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 147: 451–465.
  • Saleh, A., V. Lang, R. Cook, and C. J. Brandl. 1997. Identification of native complexes containing the yeast coactivator/repressor proteins NGG1/ADA3 and ADA2. J. Biol. Chem. 272: 5571–5578.
  • Salghetti, S. E., A. A. Caudy, J. G. Chenoweth, and W. P. Tansey. 2001. Regulation of transcriptional activation domain function by ubiquitin. Science 293: 1651–1653.
  • Sanders, S. L., and P. A. Weil. 2000. Identification of two novel TAF subunits of the yeast Saccharomyces cerevisiae TFIID complex. J. Biol. Chem. 275: 13895–13900.
  • Sanders, S. L., E. R. Klebanow, and P. A. Weil. 1999. TAF25p, a non-histone-like subunit of TFIID and SAGA complexes, is essential for total mRNA gene transcription in vivo. J. Biol. Chem. 274: 18847–18850.
  • Saurin, A. J., Z. Shao, H. Erdjument-Bromage, P. Tempst, and R. E. Kingston. 2001. A Drosophila polycomb group complex includes Zeste and dTAFII proteins. Nature 412: 655–660.
  • Shen, X., G. Mizuguchi, A. Hamiche, and C. Wu. 2000. A chromatin remodeling complex involved in transcription and DNA processing. Nature 406: 541–544.
  • Shevchenko, A., M. Wilm, O. Vorm, and M. Mann. 1996. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68: 850–858.
  • Simon, I., J. Barnett, N. Hannett, C. T. Harbison, N. J. Rinaldi, T. L. Volkert, J. J. Wyrick, J. Zeitlinger, D. K. Gifford, T. S. Jaakkola, and R. A. Young. 2001. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106: 697–708.
  • Sullivan, S., D. W. Sink, K. L. Trout, I. Makalowska, P. M. Taylor, A. D. Baxevanis, and D. Landsman. 2002. The histone database. Nucleic Acids Res. 30: 341–342.
  • Tansey, W. P. 2001. Transcriptional activation: risky business. Genes Dev. 15: 1045–1050.
  • Uetz, P., L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J. M. Rothberg. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623–627.
  • Verma, R., S. Chen, R. Feldman, D. Schieltz, J. Yates, J. Dohmen, and R. J. Deshaies. 2000. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Biol. Cell 11: 3425–3439.
  • Wada, T., T. Takagi, Y. Yamaguchi, A. Ferdous, T. Imai, S. Hirose, S. Sugimoto, K. Yano, G. A. Hartzog, F. Winston, S. Buratowski, and H. Handa. 1998. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12: 343–356.
  • Washburn, M. P., and J. R. Yates III. 2000. Analysis of the microbial proteome. Curr. Opin. Microbiol. 3: 292–297.
  • Washburn, M. P., D. Wolters, and J. R. Yates III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19: 242–247.
  • Wilcoxon, F. 1945. Individual comparisons by ranking methods. Biometrics 1: 50–83.
  • Zhu, H., M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, and M. Snyder. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101–2105.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.