Modulation of yeast genome expression in response to defective RNA polymerase III-dependent transcription

Molecular and Cellular Biology

Volumn 25, Issue 19, 2005, Pages 8631-8642

  Conesa, Christine ^a   Ruotolo, Roberta ^b   Soularue, Pascal ^c   Simms, Tiffany A ^d   Donze, David ^d   Sentenac, André ^a   Dieci, Giorgio ^b  

^a CEA SACLAY   (France)

^b UNIVERSITY OF PARMA   (Italy)

^c DIF   (France)

^d LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; GCN4P PROTEIN; GEN2 PROTEIN KINASE; PROTEIN; PROTEIN KINASE; RNA POLYMERASE II; TRANSCRIPTOME; TRANSFER RNA; TRANSFER RNA METHYLTRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; CORRELATION ANALYSIS; GCN4 GENE; GENE; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HEAT SENSITIVITY; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION;

DNA; DNA-BINDING PROTEINS; GENE DELETION; GENE DOSAGE; GENES, FUNGAL; GENES, REPORTER; GENOME, FUNGAL; HEAT; LAC OPERON; METHIONINE; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BIOSYNTHESIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; RNA POLYMERASE II; RNA POLYMERASE III; RNA, MESSENGER; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 25444501758     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.19.8631-8642.2005     Document Type: Article

References (58)

1. Allen, T. A., S. Von Kaenel, J. A. Goodrich, and J. F. Kugel. 2004. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11:816-821.
2. Andrau, J. C., A. Sentenac, and M. Werner. 1999. Mutagenesis of yeast TFIIIB70 reveals C-terminal residues critical for interaction with TBP and C34. J. Mol. Biol. 288:511-520.
3. Arrebola, R., N. Manaud, S. Rozenfeld, M. C. Marsolier, O. Lefebvre, C. Carles, P. Thuriaux, C. Conesa, and A. Sentenac. 1998. Tau91, an essential subunit of yeast transcription factor IIIC, cooperates with τ138 in DNA binding. Mol. Cell. Biol. 18:1-9.
4. Bolton, E. C., and J. D. Boeke. 2003. Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view. Genome Res. 13:254-263.
5. Boyle, E. I., S. Weng, J. Gollub, H. Jin, D. Botstein, J. M. Cherry, and G. Sherlock. 2004. GO::TermFinder: open source software for accessing Gene Ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20:3710-3715.
6. Briand, J. F., F. Navarro, O. Gadal, and P. Thuriaux. 2001. Cross talk between tRNA and rRNA synthesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 21:189-195.
7. Calvo, O., R. Cuesta, J. Anderson, N. Gutierrez, M. T. Garcia-Barrio, A. G. Hinnebusch, and M. Tamame. 1999. GCD14p, a repressor of GCN4 translation, cooperates with Gcd10p and Lhp1p in the maturation of initiator methionyl-tRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:4167-4181.
8. Causton, H. C., B. Ren, S. S. Koh, C. T. Harbison, E. Kanin, E. G. Jennings, T. I. Lee, H. L. True, E. S. Lander, and R. A. Young. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12:323-337.
9. Clarke, E. M., C. L. Peterson, A. V. Brainard, and D. L. Riggs. 1996. Regulation of the RNA polymerase I and III transcription systems in response to growth conditions. J. Biol. Chem. 271:22189-22195.
10. Colbert, T., and S. Hahn. 1992. A yeast TFIIB-related factor involved in RNA polymerase III transcription. Genes Dev. 6:1940-1949.
11. Dever, T. E., W. Yang, S. Astrom, A. S. Bystrom, and A. G. Hinnebusch. 1995. Modulation of tRNA(iMet), eIF-2, and eIF-2B expression shows that GCN4 translation is inversely coupled to the level of eIF-2.GTP. Met-tRNA(iMet) ternary complexes. Mol. Cell. Biol. 15:6351-6363.
12. Died, G., L. Duimio, G. Peracchia, and S. Ottonello. 1995. Selective inactivation of two components of the multiprotein transcription factor TFIIIB in cycloheximide growth-arrested yeast cells. J. Biol. Chem. 270:13476-13482.
13. Dieci, G., S. Hermann-Le Denmat, E. Lukhtanov, P. Thuriaux, M. Werner, and A. Sentenac. 1995. A universally conserved region of the largest subunit participates in the active site of RNA polymerase III. EMBO J. 14:3766-3776.
14. Dieci, G., and A. Sentenac. 2003. Detours and shortcuts to transcription reinitiation. Trends Biochem. Sci. 28:202-209.
15. Donze, D., and R. T. Kamakaka. 2001. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20:520-531.
16. Drysdale, C. M., E. Duenas, B. M. Jackson, U. Reusser, G. H. Braus, and A. G. Hinnebusch. 1995. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol. Cell. Biol. 15:1220-1233.
17. Fauchon, M., G. Lagniel, J. C. Aude, L. Lombardia, P. Soularue, C. Petat, G. Marguerie, A. Sentenac, M. Werner, and J. Labarre. 2002. Sulfur sparing in the yeast proteome in response to sulfur demand. Mol. Cell 9:713-723.
18. Ferrari, R., C. Rivetti, J. Acker, and G. Dieci. 2004. Distinct roles of transcription factors TFIIIB and TFIIIC in RNA polymerase III transcription reinitiation. Proc. Natl. Acad. Sci. USA 101:13442-13447.
19. Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241-4257.
20. Geiduschek, E. P., and G. A. Kassavetis. 2001. The RNA polymerase III transcription apparatus. J. Mol. Biol. 310:1-26.
21. Ghavidel, A., and M. C. Schultz. 2001. TATA binding protein-associated CK2 transduces DNA damage signals to the RNA polymerase III transcriptional machinery. Cell 106:575-584.
22. Goossens, A., T. E. Dever, A. Pascual-Ahuir, and R. Serrano. 2001. The protein kinase Gcn2p mediates sodium toxicity in yeast. J. Biol. Chem. 276:30753-30760.
23. Gustin, M. C., J. Albertyn, M. Alexander, and K. Davenport. 1998. MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 62:1264-1300.
24. Harismendy, O., C. G. Gendrel, P. Soularue, X. Gidrol, A. Sentenac, M. Werner, and O. Lefebvre. 2003. Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J. 22:4738-4747.
25. Heinisch, J. J., A. Lorberg, H. P. Schmitz, and J. J. Jacoby. 1999. The protein kinase C-mediated MAP kinase pathway involved in the maintenance of cellular integrity in Saccharomyces cerevisiae. Mol. Microbiol. 32:671-680.
26. Hinnebusch, A. G., and K. Natarajan. 2002. Gcn4p, a master regulator of gene expression, is controlled at multiple levels by diverse signals of starvation and stress. Eukaryot. Cell 1:22-32.
27. Hull, M. W., J. Erickson, M. Johnston, and D. R. Engelke. 1994. tRNA genes as transcriptional repressor elements. Mol. Cell. Biol. 14:1266-1277.
28. Jia, M. H., R. A. Larossa, J. M. Lee, A. Rafalski, E. Derose, G. Gonye, and Z. Xue. 2000. Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol. Genomics 3:83-92.
29. Jourdain, S., J. Acker, C. Ducrol, A. Sentenac, and O. Lefebvre. 2003. The tau95 subunrt of yeast TFIIIC influences upstream and downstream functions of TFIIIC.DNA complexes. J. Biol. Chem. 278:10450-10457.
30. Kendall, A., M. W. Hull, E. Bertrand, P. D. Good, R. H. Singer, and D. R. Engelke. 2000. A CBF5 mutation that disrupts nucleolar localization of early tRNA biosynthesis in yeast also suppresses tRNA gene-mediated transcriptional silencing. Proc. Natl. Acad. Sci. USA 97:13108-13113.
31. Kinsey, P. T., and S. B. Sandmeyer. 1991. Adjacent pol II and pol III promoters: transcription of the yeast retrotransposon Ty3 and a target tRNA gene. Nucleic Acids Res. 19:1317-1324.
32. Lagorce, A., N. C. Hauser, D. Labourdette, C. Rodriguez, H. Martin-Yken, J. Arroyo, J. D. Hoheisel, and J. Francois. 2003. Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 278:20345-20357.
33. Lefebvre, O., J. Ruth, and A. Sentenac. 1994. A mutation in the largest subunit of yeast TFIIIC affects tRNA and 5S RNA synthesis. J. Biol. Chem. 269:23373-23381.
34. Li, Y., R. D. Moir, I. K. Sethy-Coraci, J. R. Warner, and I. M. Willis. 2000. Repression of ribosome and tRNA synthesis in secretion-defective cells is signaled by a novel branch of the cell integrity pathway. Mol. Cell. Biol. 20:3843-3851.
35. 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.
36. Lussier, M., A. M. White, J. Sheraton, T. di Paolo, J. Treadwell, S. B. Southard, C. I. Horenstein, J. Chen-Weiner, A. F. Ram, J. C. Kapteyn, T. W. Roemer, D. H. Vo, D. C. Bondoc, J. Hall, W. W. Zhong, A. M. Sdicu, J. Davies, F. M. Klis, P. W. Robbins, and H. Bussey. 1997. Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147:435-450.
37. Manaud, N., R. Arrebola, B. Buffin-Meyer, O. Lefebvre, H. Voss, M. Riva, C. Conesa, and A. Sentenac. 1998. A chimeric subunit of yeast transcription factor IIIC forms a subcomplex with τ95. Mol. Cell. Biol. 18:3191-3200.
38. Moqtaderi, Z., and K. Struhl. 2004. Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol. Cell. Biol. 24:4118-4127.
39. Mueller, P. P., S. Harashima, and A. G. Hinnebusch. 1987. A segment of GCN4 mRNA containing the upstream AUG codons confers translational control upon a heterologous yeast transcript. Proc. Natl. Acad. Sci. USA 84:2863-2867.
40. Natarajan, K., M. R. Meyer, B. M. Jackson, D. Slade, C. Roberts, A. G. Hinnebusch, and M. J. Marton. 2001. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21:4347-4368.
41. Nierras, C. R., and J. R. Warner. 1999. Protein kinase C enables the regulatory circuit that connects membrane synthesis to ribosome synthesis in Saccharomyces cerevisiae. J. Biol. Chem. 274:13235-13241.
42. Powers, T., and P. Walter. 1999. Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae. Mol. Biol. Cell 10:987-1000.
43. Qiu, H., C. Hu, J. Anderson, G. R. Bjork, S. Sarkar, A. K. Hopper, and A. G. Hinnebusch. 2000. Defects in tRNA processing and nuclear export induce GCN4 translation independently of phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2. Mol. Cell. Biol. 20:2505-2516.
44. Rep, M., M. Krantz, J. M. Thevelein, and S. Hohmann. 2000. The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J. Biol. Chem. 275:8290-8300.
45. Ririe, K. M., R. P. Rasmussen, and C. T. Wittwer. 1997. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245:154-160.
46. Roberts, D. N., A. J. Stewart, J. T. Huff, and B. R. Cairns. 2003. The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc. Natl. Acad. Sci. USA 100:14695-14700.
47. Ruepp, A., A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Guldener, G. Mannhaupt, M. Munsterkotter, and H. W. Mewes. 2004. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32:5539-5545.
48. Sentenac, A. 1985. Eukaryotic RNA polymerases. CRC Crit. Rev. Biochem. 18:31-90.
49. Sethy, I., R. D. Moir, M. Librizzi, and I. M. Willis. 1995. In vitro evidence for growth regulation of tRNA gene transcription in yeast. A role for transcription factor (TF) IIIB70 and TFIIIC. J. Biol. Chem. 270:28463-28470.
50. Shulman, R. W., C. E. Sripati, and J. R. Warner. 1977. Noncoordinated transcription in the absence of protein synthesis in yeast. J. Biol. Chem. 252:1344-1349.
51. Simms, T. A., E. C. Miller, N. P. Buisson, N. Jambunathan, and D. Donze. 2004. The Saccharomyces cerevisiae TRT2 tRNA Thr gene upstream of STE6 is a barrier to repression in MATα cells and exerts a potential tRNA position effect in MATa cells. Nucleic Acids Res. 32:5206-5213.
52. Upadhya, R., J. Lee, and I. M. Willis. 2002. Mail is an essential mediator of diverse signals that repress RNA polymerase III transcription. Mol. Cell 10:1489-1494.
53. Warner, J. R. 1999. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24:437-440.
54. Werner, M., N. Chaussivert, I. M. Willis, and A. Sentenac. 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.
55. Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Bocke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. El Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, N. Liebundguth, D. J. Lockhart, A. Lucau-Danila, M. Lussier, N. M'Rabet, P. Menard, M. Mittmann, C. Pai, C. Rebischung, J. L. Revuelta, L. Riles, C. J. Roberts, P. Ross-MacDonald, B. Scherens, M. Snyder, S. Sookhai-Mahadeo, R. K. Storms, S. Veronneau, M. Voet, G. Volckaert, T. R. Ward, R. Wysocki, G. S. Yen, K. Yu, K. Zimmermann, P. Philippsen, M. Johnston, and R. W. Davis. 1999. Functional characterization of the Saccharomyces cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
56. Wu, L., J. Pan, V. Thoroddsen, D. R. Wysong, R. K. Blackman, C. E. Bulawa, A. E. Gould, T. D. Ocain, L. R. Dick, P. Errada, P. K. Dorr, T. Parkinson, T. Wood, D. Kornitzer, Z. Weissman, I. M. Willis, and K. McGovern. 2003. Novel small-molecule inhibitors of RNA polymerase III. Eukaryot. Cell 2:256-264.
57. Yale, J., and H. J. Bohnert. 2001. Transcript expression in Saccharomyces cerevisiae at high salinity. J. Biol. Chem. 276:15996-16007.
58. Zaragoza, D., A. Ghavidel, J. Heitman, and M. C. Schultz. 1998. Rapamycin induces the G0 program of transcriptional repression in yeast by interfering with the TOR signaling pathway. Mol. Cell. Biol. 18:4463-4470.