TATA-Binding Protein Mutants That Are Lethal in the Absence of the Nhp6 High-Mobility-Group Protein

REFERENCES

• Agresti, A., and Bianchi M. E.. 2003. HMGB proteins and gene expression. Curr. Opin. Genet. Dev. 13:170–178.
   PubMed Web of Science ®Google Scholar
• Arndt, K. M., Ricupero-Hovasse S., and Winston F.. 1995. TBP mutants defective in activated transcription in vivo. EMBO J. 14:1490–1497.
   PubMedGoogle Scholar
• Arndt, K. M., Wobbe C. R., Ricupero-Hovasse S., Struhl K., and Winston F.. 1994. Equivalent mutations in the two repeats of yeast TATA-binding protein confer distinct TATA recognition specificities. Mol. Cell. Biol. 14:3719–3728.
   PubMed Web of Science ®Google Scholar
• Badarinarayana, V., Chiang Y. C., and Denis C. L.. 2000. Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast. Genetics 155:1045–1054.
   PubMed Web of Science ®Google Scholar
• Belotserkovskaya, R., Sterner D. E., Deng M., Sayre M. H., Lieberman P. M., and Berger S. L.. 2000. Inhibition of TATA-binding protein function by SAGA subunits Spt3 and Spt8 at Gcn4-activated promoters. Mol. Cell. Biol. 20:634–647.
   PubMedGoogle Scholar
• Bender, A., and Pringle J. R.. 1991. Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:1295–1305.
   PubMedGoogle Scholar
• Bhoite, L. T., Yu Y., and Stillman D. J.. 2001. The Swi5 activator recruits the Mediator complex to the HO promoter without RNA polymerase II. Genes Dev. 15:2457–2469.
   PubMed Web of Science ®Google Scholar
• Boeke, J. D., LaCroute F., and Fink G. R.. 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197:345–346.
   PubMedGoogle Scholar
• Brachmann, C. B., Davies A., Cost G. J., Caputo E., Li J., Hieter P., and Boeke J. D.. 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.
   PubMed Web of Science ®Google Scholar
• Brewster, N. K., Johnston G. C., and Singer R. A.. 2001. A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription. Mol. Cell. Biol. 21:3491–3502.
   PubMed Web of Science ®Google Scholar
• Buratowski, S., and Zhou H.. 1992. Transcription factor IID mutants defective for interaction with transcription factor IIA. Science 255:1130–1132.
   PubMedGoogle Scholar
• Cang, Y., Auble D. T., and Prelich G.. 1999. A new regulatory domain on the TATA-binding protein. EMBO J. 18:6662–6671.
   PubMedGoogle Scholar
• Collart, M. A. 1996. The NOT, SPT3, and MOT1 genes functionally interact to regulate transcription at core promoters. Mol. Cell. Biol. 16:6668–6676.
   PubMedGoogle Scholar
• Cormack, B. P., and Struhl K.. 1993. Regional codon randomization: defining a TATA-binding protein surface required for RNA polymerase III transcription. Science 262:244–248.
   PubMedGoogle Scholar
• de la Mata, M., Alonso C. R., Kadener S., Fededa J. P., Blaustein M., Pelisch F., Cramer P., Bentley D., and Kornblihtt A. R.. 2003. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12:525–532.
   PubMed Web of Science ®Google Scholar
• Desmoucelles, C., Pinson B., Saint-Marc C., and Daignan-Fornier B.. 2002. Screening the yeast “disruptome” for mutants affecting resistance to the immunosuppressive drug, mycophenolic acid. J. Biol. Chem. 277:27036–27044.
   PubMedGoogle Scholar
• Dudley, A. M., Rougeulle C., and Winston F.. 1999. The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev. 13:2940–2945.
   PubMedGoogle Scholar
• Dvir, A., Conaway J. W., and Conaway R. C.. 2001. Mechanism of transcription initiation and promoter escape by RNA polymerase II. Curr. Opin. Genet. Dev. 11:209–214.
   PubMedGoogle Scholar
• Eisenmann, D. M., Arndt K. M., Ricupero S. L., Rooney J. W., and Winston F.. 1992. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 6:1319–1331.
   PubMed Web of Science ®Google Scholar
• Exinger, F., and Lacroute F.. 1992. 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 22:9–11.
   PubMedGoogle Scholar
• Fong, Y. W., and Zhou Q.. 2001. Stimulatory effect of splicing factors on transcriptional elongation. Nature 414:929–933.
   PubMed Web of Science ®Google Scholar
• Formosa, T., Eriksson P., Wittmeyer J., Ginn J., Yu Y., and Stillman D. J.. 2001. Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. EMBO J. 20:3506–3517.
   PubMed Web of Science ®Google Scholar
• Fragiadakis, G. S., Tzamarias D., and Alexandraki D.. 2004. Nhp6 facilitates Aft1 binding and Ssn6 recruitment, both essential for FRE2 transcriptional activation. EMBO J. 23:333–342.
   PubMedGoogle Scholar
• Geiger, J. H., Hahn S., Lee S., and Sigler P. B.. 1996. Crystal structure of the yeast TFIIA/TBP/DNA complex. Science 272:830–836.
   PubMed Web of Science ®Google Scholar
• Gietz, R. D., and Sugino A.. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527–534.
   PubMed Web of Science ®Google Scholar
• Guex, N., and Peitsch M. C.. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714–2723.
   PubMed Web of Science ®Google Scholar
• Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465–503.
   PubMed Web of Science ®Google Scholar
• Hernandez, N. 1993. TBP, a universal eukaryotic transcription factor? Genes Dev. 7:1291–1308.
   PubMed Web of Science ®Google Scholar
• Hoopes, B. C., LeBlanc J. F., and Hawley D. K.. 1992. Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multistep pathway. J. Biol. Chem. 267:11539–11547.
   PubMed Web of Science ®Google Scholar
• Howe, K. J., Kane C. M., and Ares M., Jr. 2003. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9:993–1006.
   PubMed Web of Science ®Google Scholar
• Jiang, Y. W., and Stillman D. J.. 1995. Regulation of HIS4 expression by the Saccharomyces cerevisiae SIN4 transcriptional regulator. Genetics 140:103–114.
   PubMedGoogle Scholar
• Juo, Z. S., Kassavetis G. A., Wang J., Geiduschek E. P., and Sigler P. B.. 2003. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 422:534–539.
   PubMed Web of Science ®Google Scholar
• Kassavetis, G. A., Joazeiro C. A., Pisano M., Geiduschek E. P., Colbert T., Hahn S., and Blanco J. A.. 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.
   PubMed Web of Science ®Google Scholar
• Kobayashi, A., Miyake T., Ohyama Y., Kawaichi M., and Kokubo T.. 2001. Mutations in the TATA-binding protein, affecting transcriptional activation, show synthetic lethality with the TAF145 gene lacking the TAF N-terminal domain in Saccharomyces cerevisiae. J. Biol. Chem. 276:395–405.
   PubMedGoogle Scholar
• Kruppa, M., Moir R. D., Kolodrubetz D., and Willis I. M.. 2001. Nhp6, an HMG1 protein, functions in SNR6 transcription by RNA polymerase III in S. cerevisiae. Mol. Cell 7:309–318.
   PubMed Web of Science ®Google Scholar
• Kuras, L., and Struhl K.. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 399:609–613.
   PubMedGoogle Scholar
• Lee, M., and Struhl K.. 1995. Mutations on the DNA-binding surface of TATA-binding protein can specifically impair the response to acidic activators in vivo. Mol. Cell. Biol. 15:5461–5469.
   PubMedGoogle Scholar
• Lee, M., and Struhl K.. 1997. A severely defective TATA-binding protein-TFIIB interaction does not preclude transcriptional activation in vivo. Mol. Cell. Biol. 17:1336–1345.
   PubMedGoogle Scholar
• Lee, T. I., and Young R. A.. 1998. Regulation of gene expression by TBP-associated proteins. Genes Dev. 12:1398–1408.
   PubMedGoogle Scholar
• Li, X. Y., Virbasius A., Zhu X., and Green M. R.. 1999. Enhancement of TBP binding by activators and general transcription factors. Nature 399:605–609.
   PubMed Web of Science ®Google Scholar
• Lindstrom, D. L., Squazzo S. L., Muster N., Burckin T. A., Wachter K. C., Emigh C. A., McCleery J. A., Yates III J. R., and Hartzog G. A.. 2003. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23:1368–1378.
   PubMed Web of Science ®Google Scholar
• Lopez, S., Livingstone-Zatchej M., Jourdain S., Thoma F., Sentenac A., and Marsolier M. C.. 2001. High-mobility-group proteins NHP6A and NHP6B participate in activation of the RNA polymerase III SNR6 gene. Mol. Cell. Biol. 21:3096–3104.
   PubMedGoogle Scholar
• Madison, J. M., and Winston F.. 1997. Evidence that Spt3 functionally interacts with Mot1, TFIIA, and TATA-binding protein to confer promoter-specific transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:287–295.
   PubMedGoogle Scholar
• Martin, M. P., Gerlach V. L., and Brow D. A.. 2001. A novel upstream RNA polymerase III promoter element becomes essential when the chromatin structure of the yeast U6 RNA gene is altered. Mol. Cell. Biol. 21:6429–6439.
   PubMedGoogle Scholar
• Moreira, J. M., and Holmberg S.. 2000. Chromatin-mediated transcriptional regulation by the yeast architectural factors NHP6A and NHP6B. EMBO J. 19:6804–6813.
   PubMedGoogle Scholar
• Nikolov, D. B., and Burley S. K.. 1997. RNA polymerase II transcription initiation: a structural view. Proc. Natl. Acad. Sci. USA 94:15–22.
   PubMed Web of Science ®Google Scholar
• Nikolov, D. B., Chen H., Halay E. D., Hoffman A., Roeder R. G., and Burley S. K.. 1996. Crystal structure of a human TATA box-binding protein/TATA element complex. Proc. Natl. Acad. Sci. USA 93:4862–4867.
   PubMedGoogle Scholar
• Nikolov, D. B., Chen H., Halay E. D., Usheva A. A., Hisatake K., Lee D. K., Roeder R. G., and Burley S. K.. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377:119–128.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., LeRoy G., Chang C. H., Luse D. S., and Reinberg D.. 1998. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92:105–116.
   PubMed Web of Science ®Google Scholar
• Paull, T. T., Carey M., and Johnson R. C.. 1996. Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. Genes Dev. 10:2769–2781.
   PubMedGoogle Scholar
• Pokholok, D. K., Hannett N. M., and Young R. A.. 2002. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol. Cell 9:799–809.
   PubMed Web of Science ®Google Scholar
• Pugh, B. F. 2000. Control of gene expression through regulation of the TATA-binding protein. Gene 255:1–14.
   PubMed Web of Science ®Google Scholar
• Rothstein, R. 1991. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 194:281–302.
   PubMedGoogle Scholar
• Ruone, S., Rhoades A. R., and Formosa T.. 2003. Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. J. Biol. Chem. 278:45288–45295.
   PubMed Web of Science ®Google Scholar
• Sayle, R. A., and Milner-White E. J.. 1995. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20:374–376.
   PubMed Web of Science ®Google Scholar
• Sethy-Coraci, I., Moir R. D., Lopez-de-Leon A., and Willis I. M.. 1998. A differential response of wild type and mutant promoters to TFIIIB70 overexpression in vivo and in vitro. Nucleic Acids Res. 26:2344–2352.
   PubMedGoogle Scholar
• Shaw, R. J., and Reines D.. 2000. Saccharomyces cerevisiae transcription elongation mutants are defective in PUR5 induction in response to nucleotide depletion. Mol. Cell. Biol. 20:7427–7437.
   PubMedGoogle Scholar
• Shen, Y., Kassavetis G. A., Bryant G. O., and Berk A. J.. 1998. Polymerase (Pol) III TATA box-binding protein (TBP)-associated factor Brf binds to a surface on TBP also required for activated Pol II transcription. Mol. Cell. Biol. 18:1692–1700.
   PubMedGoogle Scholar
• Sherman, F. 1991. Getting started with yeast. Methods Enzymol. 194:1–21.
   PubMedGoogle Scholar
• Sikorski, R. S., and 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
• Stargell, L. A., and Struhl K.. 1996. A new class of activation-defective TATA-binding protein mutants: evidence for two steps of transcriptional activation in vivo. Mol. Cell. Biol. 16:4456–4464.
   PubMedGoogle Scholar
• Stargell, L. A., and Struhl K.. 1995. The TBP-TFIIA interaction in the response to acidic activators in vivo. Science 269:75–78.
   PubMedGoogle Scholar
• Sterner, D. E., Grant P. A., Roberts S. M., Duggan L. J., Belotserkovskaya R., Pacella L. A., Winston F., Workman J. L., and Berger S. L.. 1999. Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction. Mol. Cell. Biol. 19:86–98.
   PubMed Web of Science ®Google Scholar
• Tan, S., Hunziker Y., Sargent D. F., and Richmond T. J.. 1996. Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 381:127–151.
   PubMed Web of Science ®Google Scholar
• Thomas, B. J., and Rothstein R.. 1989. Elevated recombination rates in transcriptionally active DNA. Cell 56:619–630.
   PubMed Web of Science ®Google Scholar
• van Kempen, G. M., and van Vliet L. J.. 2000. Mean and variance of ratio estimators used in fluorescence ratio imaging. Cytometry 39:300–305.
   PubMedGoogle Scholar
• Yu, Y., Eriksson P., Bhoite L. T., and Stillman D. J.. 2003. Regulation of TATA-binding protein binding by the SAGA complex and the Nhp6 high-mobility-group protein. Mol. Cell. Biol. 23:1910–1921.
   PubMedGoogle Scholar
• Yu, Y., Eriksson P., and Stillman D. J.. 2000. Architectural transcription factors and the SAGA complex function in parallel pathways to activate transcription. Mol. Cell. Biol. 20:2350–2357.
   PubMedGoogle Scholar
• Zhao, X., and Herr W.. 2002. A regulated two-step mechanism of TBP binding to DNA: a solvent-exposed surface of TBP inhibits TATA box recognition. Cell 108:615–627.
   PubMed Web of Science ®Google Scholar