Stimulation of RNA polymerase II transcript cleavage activity contributes to maintain transcriptional fidelity in yeast

Genes to Cells

Volumn 12, Issue 5, 2007, Pages 547-559

  Koyama, Hiroshi ^a   Ito, Takahiro ^a   Nakanishi, Toshiyuki ^b   Sekimizu, Kazuhisa ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b DAIICHI SANKYO CO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; DNA POLYMERASE; GLUTAMIC ACID; MENADIONE; RNA POLYMERASE II; TRANSCRIPTION ELONGATION FACTOR;

AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME BINDING; ENZYME DEGRADATION; GENE DISRUPTION; GENE EXPRESSION; GENE MUTATION; GENETIC TRANSCRIPTION; NONHUMAN; OXIDATIVE STRESS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; YEAST;

BASE SEQUENCE; DNA, FUNGAL; DNA-BINDING PROTEINS; DRUG RESISTANCE, FUNGAL; GENES, FUNGAL; GENES, REPORTER; LAC OPERON; MODELS, MOLECULAR; MUTATION; OXIDATIVE STRESS; PROTEIN SUBUNITS; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS; VITAMIN K 3;

EID: 34249726498     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/j.1365-2443.2007.01072.x     Document Type: Article

References (44)

1. Awrey, D.E., Shimasaki, N., Koth, C., Weilbaecher, R., Olmsted, V., Kazanis, S., Shan, X., Arellano, J., Arrowsmith, C.H., Kane, C.M. & Edwards, A.M. (1998) Yeast transcript elongation factor (TFIIS), structure and function. II: RNA polymerase binding, transcript cleavage, and read-through. J. Biol. Chem. 273, 22595-22605.
2. Awrey, D.E., Weilbaecher, R.G., Hemming, S.A., Orlicky, S.M., Kane, C.M. & Edwards, A.M. (1997) Transcription elongation through DNA arrest sites. A multistep process involving both RNA polymerase II subunit RPB9 and TFIIS. J. Biol. Chem. 272, 14747-14754.
3. Cipres-Palacin, G. & Kane, C.M. (1994) Cleavage of the nascent transcript induced by TFIIS is insufficient to promote read-through of intrinsic blocks to elongation by RNA polymerase II. Proc. Natl. Acad. Sci. USA 91, 8087-8091.
4. Erie, D.A., Hajiseyedjavadi, O., Young, M.C. & von Hippel, P.H. (1993) Multiple RNA polymerase conformations and GreA: Control of the fidelity of transcription. Science 262, 867-873.
5. Exinger, F. & Lacroute, F. (1992) 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 22, 9-11.
6. Fish, R.N. & Kane, C.M. (2002) Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta 1577, 287-307.
7. Guthrie, C. & Fink, G.R. (1991) Guide to yeast genetics and molecular biology. Methods Enzymol. 194, 1-863.
8. Hayakawa, H., Hofer, A., Thelander, L., Kitajima, S., Cai, Y., Oshiro, S., Yakushiji, H., Nakabeppu, Y., Kuwano, M. & Sekiguchi, M. (1999) Metabolic fate of oxidized guanine ribonucleotides in mammalian cells. Biochemistry 38, 3610-3614.
9. Hemming, S.A. & Edwards, A.M. (2000) Yeast RNA polymerase II subunit RPB9. Mapping of domains required for transcription elongation. J. Biol. Chem. 275, 2288-2294.
10. Hemming, S.A., Jansma, D.B., Macgregor, P.F., Goryachev, A., Friesen, J.D. & Edwards, A.M. (2000) RNA polymerase II subunit Rpb9 regulates transcription elongation in vivo. J. Biol. Chem. 275, 35506-35511.
11. Hull, M.W., McKune, K. & Woychik, N.A. (1995) RNA polymerase II subunit RPB9 is required for accurate start site selection. Genes Dev. 9, 481-490.
12. Izban, M.G. & Luse, D.S. (1992) The RNA polymerase II ternary complex cleaves the nascent transcript in a-3′→5′ direction in the presence of elongation factor SII. Genes Dev. 6, 1342-1356.
13. Jeon, C. & Agarwal, K. (1996) Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc. Natl. Acad. Sci. USA 93, 13677-13682.
14. Jeon, C., Yoon, H. & Agarwal, K. (1994) The transcription factor TFIIS zinc ribbon dipeptide Asp-Glu is critical for stimulation of elongation and RNA cleavage by RNA polymerase II. Proc. Natl. Acad. Sci. USA 91, 9106-9110.
15. Joyce, C.M. & Steitz, T.A. (1994) Function and structure relationships in DNA polymerases. Annu. Rev. Biochem. 63, 777-822.
16. Kettenberger, H., Armache, K.J. & Cramer, P. (2003) Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 114, 347-357.
17. Koyama, H., Ito, T., Nakanishi, T., Kawamura, N. & Sekimizu, K. (2003) Transcription elongation factor S-II maintains transcriptional fidelity and confers oxidative stress resistance. Genes Cells 8, 779-788.
18. Lange, U. & Hausner, W. (2004) Transcriptional fidelity and proofreading in Archaea and implications for the mechanism of TFS-induced RNA cleavage. Mol. Microbiol. 52, 1133-1143.
19. Morrison, A., Bell, J.B., Kunkel, T.A. & Sugino, A. (1991) Eukaryotic DNA polymerase amino acid sequence required for 3′→5′ exonuclease activity. Proc. Natl. Acad. Sci. USA 88, 9473-9477.
20. Nakanishi, T., Nakano, A., Nomura, K., Sekimizu, K. & Natori, S. (1992) Purification, gene cloning, and gene disruption of the transcription elongation factor S-II in Saccharomyces cerevisiae. J. Biol. Chem. 267, 13200-13204.
21. Nakanishi, T., Shimoaraiso, M., Kubo, T. & Natori, S. (1995) Structure-function relationship of yeast S-II in terms of stimulation of RNA polymerase II, arrest relief, and suppression of 6-azauracil sensitivity. J. Biol. Chem. 270, 8991-8995.
22. Natori, S., Takeuchi, K. & Mizuno, D. (1973) DNA-dependent RNA polymerase from Ehrlich ascites tumor cells. 3. Ribonuclease H and elongating activity of stimulatory factor S-II. J. Biochem. (Tokyo) 74, 1177-1182.
23. Nesser, N.K., Peterson, D.O. & Hawley, D.K. (2006) RNA polymerase II subunit Rpb9 is important for transcriptional fidelity in vivo. Proc. Natl. Acad. Sci. USA 103, 3268-3273.
24. Ohya, Y., Goebl, M., Goodman, L.E., Petersen-Bjorn, S., Friesen, J.D., Tamanoi, F. & Anraku, Y. (1991) Yeast CAL1 is a structural and functional homologue to the DPR1 (RAM) gene involved in ras processing. J. Biol. Chem. 266, 12356-12360.
25. Orlova, M., Newlands, J., Das, A., Goldfarb, A. & Borukhov, S. (1995) Intrinsic transcript cleavage activity of RNA polymerase. Proc. Natl. Acad. Sci. USA 92, 4596-4600.
26. Reines, D. (1992) Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. J. Biol. Chem. 267, 3795-3800.
27. Reines, D., Chamberlin, M.J. & Kane, C.M. (1989) Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro. J. Biol. Chem. 264, 10799-10809.
28. Saso, K., Ito, T., Natori, S. & Sekimizu, K. (2003) Identification of a novel tissue-specific transcriptional activator FESTA as a protein that interacts with the transcription elongation factor S-II. J. Biochem. (Tokyo) 133, 493-500.
29. Sekimizu, K., Nakanishi, Y., Mizuno, D. & Natori, S. (1979) Purification and preparation of antibody to RNA polymerase II stimulatory factors from Ehrlich ascites tumor cells. Biochemistry 18, 1582-1588.
30. Sekiya-Kawasaki, M., Abe, M., Saka, A., Watanabe, D., Kono, K., Minemura-Asakawa, M., Ishihara, S., Watanabe, T. & Ohya, Y. (2002) Dissection of upstream regulatory components of the Rho1p effector, 1,3-β-glucan synthase, in Saccharomyces cerevisiae. Genetics 162, 663-676.
31. Shaw, R.J. & Reines, D. (2000) Saccharomyces cerevisiae transcription elongation mutants are defective in PUR5 induction in response to nucleotide depletion. Mol. Cell. Biol. 20, 7427-7437.
32. Shimoaraiso, M., Nakanishi, T., Kubo, T. & Natori, S. (1997) Identification of the region in yeast S-II that defines species specificity in its interaction with RNA polymerase II. J. Biol. Chem. 272, 26550-26554.
33. Shimoaraiso, M., Nakanishi, T., Kubo, T. & Natori, S. (2000) Transcription elongation factor S-II confers yeast resistance to 6-azauracil by enhancing expression of the SSM1 gene. J. Biol. Chem. 275, 29623-29627.
34. Sikorski, R.S. & 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.
35. Sosunova, E., Sosunov, V., Kozlov, M., Nikiforov, V., Goldfarb, A. & Mustaev, A. (2003) Donation of catalytic residues to RNA polymerase active center by transcription factor Gre. Proc. Natl. Acad. Sci. USA 100, 15469-15474.
36. Taddei, F., Hayakawa, H., Bouton, M., Cirinesi, A., Matic, I., Sekiguchi, M. & Radman, M. (1997) Counteraction by MutT protein of transcriptional errors caused by oxidative damage. Science 278, 128-130.
37. Thomas, M.J., Platas, A.A. & Hawley, D.K. (1998) Transcriptional fidelity and proofreading by RNA polymerase II. Cell 93, 627-637.
38. Ubukata, T., Shimizu, T., Adachi, N., Sekimizu, K. & Nakanishi, T. (2002) Cleavage, but not read-through, stimulation activity is responsible for three biologic functions of transcription elongation factor S-II. J. Biol. Chem. 278, 8580-8585.
39. Van Mullem, V., Wery, M., Werner, M., Vandenhaute, J. & Thuriaux, P. (2002) The Rpb9 subunit of RNA polymerase II binds transcription factor TFIIE and interferes with the SAGA and elongator histone acetyltransferases. J. Biol. Chem. 277, 10220-10225.
40. Wang, D. & Hawley, D.K. (1993) Identification of a-3′→5′ exonuclease activity associated with human RNA polymerase II. Proc. Natl. Acad. Sci. USA 90, 843-847.
41. Wery, M., Shematorova, E., Van Driessche, B., Vandenhaute, J., Thuriaux, P. & Van Mullem, V. (2004) Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. EMBO J. 23, 4232-4242.
42. Wind, M. & Reines, D. (2000) Transcription elongation factor SII. Bioessays 22, 327-336.
43. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906.
44. Woychik, N.A., Lane, W.S. & Young, R.A. (1991) Yeast RNA polymerase II subunit RPB9 is essential for growth at temperature extremes. J. Biol. Chem. 266, 19053-19055.