Transcriptional regulation in yeast during diauxic shift and stationary phase

OMICS A Journal of Integrative Biology

Volumn 14, Issue 6, 2010, Pages 629-638

  Galdieri, Luciano ^a   Mehrotra, Swati ^a   Yu, Sean ^a   Vancura, Ales ^a  

^a ST JOHN'S UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; CYCLIC AMP DEPENDENT PROTEIN KINASE; PROTEIN RIM15P; PROTEIN SNF1P; TARGET OF RAPAMYCIN KINASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GIS1P; TRANSCRIPTION FACTOR MSN2P; TRANSCRIPTION FACTOR MSN4P; UNCLASSIFIED DRUG;

AEROBIC METABOLISM; AGING; CELL CYCLE G0 PHASE; CELL GROWTH; CHROMATIN STRUCTURE; CULTURE MEDIUM; GENE CONTROL; GENETIC TRANSCRIPTION; GLYCOLYSIS; METABOLITE; NONHUMAN; NUTRIENT; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; YEAST; YEAST CELL;

ETHANOL; GENE EXPRESSION REGULATION, FUNGAL; GLUCOSE; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EUKARYOTA;

EID: 78649701863     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2010.0069     Document Type: Review

References (135)

1. Allen, C., Büttner, S., Aragon, A.D., Thomas, J.A., Meirelles, O., Jaetao, J.E., et al. (2006). Isolation of quiescent and non-quiescent cells from yeast stationary-phase cultures. J Cell Biol 174, 89-100.
2. Beck, T., and Hall, M.N. (1999). The TOR signaling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402, 689-692.
3. Blagosklonny, M.V., and Hall, M.N. (2009). Growth and aging: a common molecular mechanism. Aging 1, 356-362.
4. Boy-Marcotte, E., Ikonomi, P., and Jacquet, M. (1996). SDC25, a dispensable RAS guanine nucleotide exchange factor of Sac-charomyces cerevisiae differes from CDC25 by its regulation. Mol Biol Cell 7, 529-539.
5. Broek, D., Toda, T., Michaeli, T., Levin, L., Birchmeier, C., Zoller, M., et al. (1987). The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell 48, 789-799.
6. Cameroni, E., Hulo, N., Roosen, J., Winderickx, J., and De Vir-gilio, C. (2004). The novel yeast PAS kinase Rim15 orchestrates G0-associated antioxidant defense mechanisms. Cell Cycle 3, 462-468.
7. Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., et al. (2001). Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12, 323-337.
8. Chang, Y.W., Howard, S.C., and Herman, P.K. (2004). The Ras/PKA signaling pathway directly targets the Srb9p protein, a component of the general RNA polymerase II transcription apparatus. Mol Cell 15, 107-116.
9. Chen, J.C., and Powers, T. (2006). Coordinate regulation of multiple and distinct biosynthetic pathways by TOR and PKA kinases in S. cerevisiae. Curr Genet 49, 281-293.
10. Chen, Q., Ding, Q., and Keller, J.N. (2005). The stationary phase model of aging in yeast for the study of oxidative stress and age-related neurodegeneration. Biogerontology 6, 1-13.
11. Chi, Y., Huddleston, M.J., Zhang, X., Young, R.A., Annan, R.S., Carr, S.A., et al. (2001). Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev 15, 1078-1092.
12. Choder, M. (1991). A general topoisomerase I-dependent tran-scriptional repression in the stationary phase in yeast. Genes Dev 5, 2315-2326.
13. Claypool, J.A., French, S.L., Johzuka, K., Eliason, K., Vu, L. Dodd, J.A., et al. (2004). Tor pathway regulates Rrn3p-de-pendent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol Biol Cell 15, 946-956.
14. Cooper, T.G. (2002). Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol Rev 26, 223-238.
15. Damak, F., Boy-Marcotte, E., Le-Roscoiuet, D., Guilbaud, R., and Jacquet, M. (1991). SDC25, a CDC25-like gene which contains a RAS-activating domain and is a disposable gene of Sac-charomyces cerevisiae. Mol Cell Biol 11, 202-212.
16. DeNobel, H., Ruiz, C., Martin, H., Morris, W., Brul, S., Molina, M., et al. (2000). Cell wall perturbations in yeast result in dual phosphorylation of the Slt2/Mpk1 MAP kinases and the Slt2-mediated increase in FKS-lacZ expression, glucanase resistance and thermotolerance. Microbiology 146, 2121-2123.
17. DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
18. De Virgilio, C., and Loewith, R. (2006). Cell growth control: little eukaryots make big contributions. Oncogene 25, 6392-6415.
19. De Wever, V., Reiter, W., Ballarini, A., Ammerer, G., and Bro-card, C. (2005). A dual role for PP1 in shaping the Msn2-dependent transcriptional response to glucose starvation. EMBO J 24, 4115-4123.
20. Di Como, C.J., and Arndt, K.T. (1996). Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases. Genes Dev 10, 1904-1916.
21. Dion, M.F., Altschuler, S.J., Wu, L.F., and Rando, O.J. (2005). Genomic characterization reveals a simple histone H4 acety-lation code. Proc Natl Acad Sci USA 102, 5501-5506.
22. Durchschlag, E., Reiter, W., Ammerer, G., and Schuller, C. (2004). Nuclear localization destabilizes the stress-regulated transcription factor Msn2. J Biol Chem 279, 55425-55432.
23. Duvel, K., and Broach, J.R. (2004). The role of phosphatases in TOR signaling in yeast. Curr Top Microbiol Immunol 279, 19-38.
24. Duvel, K., Santhanam, A., Garrett, S., Schneper, L., and Broach, J.R. (2003). Multiple roles of Tap42 in mediating rapamycin-induced transcriptional changes in yeast. Mol Cell 11, 1467-1478.
25. Estruch, F. (2000). Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiol Rev 24, 469-486.
26. Estruch, F., and Carlson, M. (1993). Two homologous zinc finger genes identified by multicopy suppression in a SNF1 protein kinase mutant of Saccharomyces cerevisiae. Mol Cell Biol 13, 3872-3881.
27. Fabrizio, P., Pozza, F., Pletcher, S.D., Gendron, C.M., and Longo, V.D. (2001). Regulation of longevity and stress resistance by Sch9 in yeast. Science 292, 288-290.
28. Fabrizio, P., Liou, L.L., Moy, V.N., Diaspro, A., Valentine, J.S., Gralla, E.B., et al. (2003). SOD2 functions downstream of Sch9 to extend longevity in yeast. Genetics 163, 35-46.
29. Friis, R.M., and Schultz, M.C. (2009). Untargeted tail acetylation of histones in chromatin: Lessons from yeast. Biochem Cell Biol 87, 107-116.
30. Friis, R.M.N., Wu, B.P., Reinke, S.N., Hockman, D.J., Stykes, B.D., and Schultz, M.C. (2009). A glycolytic burst drives glucose induction of global histone acetylation by picNuA4 and SAGA. Nucleic Acid Res 37, 3969-3980.
31. Fuge, E.K., Braun, E.L., and Werner-Washburne, M. (1994). Protein synthesis in long term stationary-phase cultures of Saccharomyces cerevisiae. J Bacteriol 176, 5802-5813.
32. Garmendia-Torres, C., Goldbeter, A., and Jacquet, M. (2007). Nucleocytoplasmic oscillations of the yeast transcription factor Msn2: evidence for periodic PKA activation. Curr Biol 17, 1044-1049.
33. Garreau, H., Hasan, R.N., Renault, G., Estruch, F., Boy-Marcotte, E., and Jacquet, M. (2000). Hyperphosphorylation of Msn2p and Msn4p in response to heat shock and the diauxic shift is inhibited by cAMP in Saccharomyces cerevisiae. Microbiology 146, 2113-2120.
34. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., et al. (2000). Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11, 4241-4257.
35. Gershon, H., and Gershon, D. (2000). The budding yeast, Sac-charomyces cerevisiae, as a model for aging research: a critical review. Mech Ageing Dev 120, 1-22.
36. 2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev 12, 586-597.
37. Görner, W., Durchslag, E., Wolf, J., Brown, E.L., Ammerer, G., Ruis, H., et al. (2002). Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor. EMBO J 21, 135-144.
38. Gray, J.V., Petsko, G.A., Johnston, G.C., Ringe, D., Singer, R.A., and Werner-Washburne, M. (2004). "Sleeping beauty": quiescence in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 68, 187-206.
39. Hahn, J.S., and Thiele, D.J. (2004). Activation of Saccharomyces cerevisiae heat shock transcription factor under glucose starvation conditions by Snf1 protein kinase. J Biol Chem 279, 5169-5176.
40. Harashima, T., and J. Heitman. (2002). The Ga protein Gpa2p controls yeast differentiation by interacting with kelch repeat proteins that mimic Gb subunits. Mol Cell 10, 163-173.
41. Harashima, T., and Heitman, J. (2005). Ga subunit Gpa2 recruits kelch repeat subunits that inhibit receptor G-protein coupling during cAMP-induced dimorphic transitions in Saccharomyces cerevisiae. Mol Biol Cell 16, 4557-4571.
42. Hardie, D.G., Carling, D., and Carlson, M. (1998). The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of the eukaryotic cell? Annu Rev Biochem 67, 821-855.
43. Hedbacker, K., and Carlson, M. (2008). SNF1/AMPK pathways in yeast. Front Biosci 13, 2408-2420.
44. Herman, P.K. (2002). Stationary phase in yeast. Curr Opin Mi-crobiol 5, 602-607.
45. Hirata, Y., Andoh, T., Asahara, T., and Kikuchi, A. (2003). Yeast glycogen synthase kinase-3 activates Msn2p-dependent transcription of stress responsive genes. Mol Biol Cell 14, 302-312.
46. Hosaka, K., and Yamashita, S. (1984). Regulatory role of phos-phatidate phosphatase in triacylglycerol synthesis in Sacchar-omyces cerevisiae. Biochim Biophys Acta, 796, 110-117.
47. Howard, S.C., Chang, Y.W., Budovskaya, Y.V., and Herman, P.K. (2001). The Ras/PKA signaling pathway of Saccharomyces cer-evisiae exhibits a functional interaction with the Sin4p complex of the RNA polymerase II holoenzyme. Genetics 159, 77-89.
48. Howard, S.C., Budovskaya, Y.V., Chang, Y.W., and Herman, P.K. (2002). The C-terminal domain of the largest subunit of RNA polymerase II is required for stationary phase entry and functionally interacts with the Ras/PKA signaling pathway. J Biol Chem 277, 19488-19497.
49. Howard, S.C., Hester, A., and Herman, P.K. (2003). The Ras/PKA signaling pathway may control RNA polymerase II elongation via the Spt4p/Spt5p complex in Saccharomyces cerevisiae. Genetics 165, 1059-1070.
50. Jacinto, E., Guo, B., Arndt, K.T., Schmelzle, T., and Hall, M.N. (2001). TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway. Mol Cell 8, 1017-1026.
51. Jacquet, M., Renault, G., Lallet, S., De Mey, J., and Goldbeter, A. (2003). Oscillatory nucleocytoplasmic shuttling of the general stress response transcriptional activators Msn2 and Msn4 in Saccharomyces cerevisiae. J Cell Biol 161, 497-505.
52. Jelinsky, S.A., Estep, P., Church, G.M., and Samson, D. (2000). Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 20, 8157-8167.
53. Jiang, Y., and Broach, J.R. (1999). Tor proteins and protein phosphatase 2A reciprocally regulate Tap42 in controlling cell growth in yeast. EMBO J 18, 2782-2792.
54. Johnson, D. (2010). New connections identify Sch9 as a central node in ribosome biosynthesis. Cell Cycle, 9, 26-27.
55. Jorgenesn, P., Nishikawa, J.L., Breitkreutz, B.J., and Tyers, M. (2002). Systematic identification of pathways that couple cell growth and division in yeast. Science 297, 395-400.
56. Jorgensen, P., Rupes, I., Sharom, J.R., Schneper, L., Broach, J.R., and Tyers, M. (2004). A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 18, 2491-2505.
57. Kamada, Y., Funakoshi, T., Shintani, T., Nagano, K., and Oh-sumi, M. (2000). Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J Cell Biol 150, 1507-1513.
58. Kraakman, L., Lemaire, K., Ma, P., Teunissen, A.W., Donaton, M.C., Van Dijck, P., et al. (1999). A Saccharomyces cerevisiae G-protein coupled receptor, Gpr1, is specifically required for glucose activation of the cAMP pathway during the transition to growth on glucose. Mol Microbiol 32, 1002-1012.
59. Krause, S.A., and Gray, J.V. (2002). The protein kinase C pathway is required for viability in quiescence in Saccharomyces cerevisiae. Curr Biol 12, 588-593.
60. Kupiec, M., Byers, B., Esposito, R.E., and Mitchell, A.P. (1997). Meiosis and sporulation. In The Molecular and Cellular Biology of the Yeast Saccharomyces. Volume III: Cell Cycle and Cell Biology. J.R. Pringle, J.R. Broach, E.W. Jones, eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 889-1036.
61. Ladurner, A.G. (2009). Chromatin places metabolism center stage. Cell 138, 18-20.
62. Lallet, S., Garreau, H., Poisier, C., and Boy-Marcotte, E. (2004). Heat-shock-induced degradation of Msn2p, a Saccharomyces cerevisiae transcription factor, occurs in the nucleus. Mol Gen Genomics 272, 353-362.
63. Lenssen, E., Oberholzer, U., Labarre, J., De Virgilio, C., and Col-lart, M.A. (2002). Saccharomyces cerevisiae Ccr4-Not complex contributes to the control of Msn2p-dependent transcription by the ras/cAMP pathway. Mol Microbiol 43, 1023-1037.
64. Lenssen, E., James, N., Pedruzzi, I., Dubouloz, F., Cameroni, E., Bisig, R., et al. (2005). The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation-via a newly identified Glc7/Bud14 type I protein phosphatase module-and TFIID promoter distribution. Mol Cell Biol 25, 488-498.
65. Li, H., Tsang, C.K., Watkins, M., Bertram, P.G., and Zheng, X.F. (2006). Nutrient regulates Tor1 nuclear localization and association with rDNA promoter. Nature 442, 1058-1061.
66. Lillie, S.H., and Pringle, J.R. (1980). Reserve carbohydrate metabolism in Saccharomyces cerevisiae: responses to nutrient limitation. J Bacteriol 143, 1384-1394.
67. Lindstrom, K.C., Vary, J.C., Jr., Parthun, M.R., Delrow, J., and Tsukiyama, T. (2006). Isw1 functions in parallel with the NuA4 and Swr1 complexes in stress-induced gene expression. Mol Cell Biol 26, 6117-6129.
68. Lo, W.S., Duggan, L., Emre, N.C., Belotserkovskya, R., Lane, W.S., Shiekhattar, R., et al. (2001). Snf1-a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription. Science 293, 1142-1146.
69. Longo, V.D. (1999). Mutations in signal transduction proteins increase stress resistance and longevity in yeast, nematodes, fruit flies, and mammalian neuronal cells. Neurobiol Aging 20, 479-486.
70. Lorenz, M.C., Pan, X.W., Harashima, T., Cardenas, M.E., Xue, Y., Hirsch, J.P., et al. (2000). The G-protein-coupled receptor Gpr1 is a nutrient sensor that regulates pseudohyphal differentiation in Saccharomyces cerevisiae. Genetics 154, 609-622.
71. Martinez-Pastor, M.T., Marchler, G., Schüller, C., Marchler-Bauer, A., Ruis, H., and Estruch, F. (1996). The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress-response element (STRE). EMBO J 15, 2227-2235.
72. Martinez, M.J., Roy, S., Archuletta, A.B., Wentzel, P.D., Anna-Arriola, S.S., Rodriquez, A.L., et al. (2004). Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes. Mol Biol Cell 15, 5295-5305.
73. Mayordomo, I., Estruch, F., and Sanz, P. (2002). Convergence of the target of rapamycin and the Snf1 protein kinase pathway in the regulation of the subcellular localization of Msn2, a transcriptional activator of STRE (Stress Response Element)-regulated genes. J Biol Chem 277, 35650-35656.
74. Moir, R.D., Lee, J., Haeusler, R.A., Desai, N., Engelke, D.R., and Willis, I.M. (2006). Protein kinase A regulates RNA polymer-ase III transcription through the nuclear localization of Maf1. Proc Natl Acad Sci USA 103, 15044-15049.
75. Mujtaba, S., Zeng, L., and Zhou M.-M. (2007). Structure and acetyl-lysine recognition of the bromodomain. Oncogene 26, 5521-5527.
76. Noda, T., and Ohsumi, Y. (1998). Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast. J Biol Chem 273, 3963-3966.
77. Oficjalska-Pham, D., Harismendy, O., Smagowicz, W.J., Gon-zales de Peredo, A., Boguta, M., Sentenac, A., et al. (2006). General repression of RNA polymerase III transcription is triggered by protein phosphatase type 2A-mediated dephos-phorylation of Maf1. Mol Cell 22, 623-632.
78. Panek, A.D., and Panek, A.C. (1990). Metabolism and thermo-tolerance function of trehalose in Saccharomyces: a current perspective. J Biotechnol 14, 229-238.
79. Pedruzzi, I., Burckert, N., Egger, P., and De Virgilio, C. (2000). Saccharomyces cerevisiae Ras/cAMP pathway controls post-diauxic shift element-dependent transcription through the zinc finger protein Gis1. EMBO J 19, 2569-2579.
80. 0. Mol Cell 12, 1607-1613.
81. 0 form. Chromosoma 67, 263-274.
82. Plesset, J., Ludwig, J.R., Cox, B.S., and McLaughlin, C.S. (1987). Effect of cell cycle position on thermotolerance in Sacchar-omyces cerevisiae. J Bacteriol 169, 779-784.
83. Powers, S., Kataoka, T., Fasano, O., Goldfarb, M., Strathern, J., Broach, J., et al. (1984). Genes in S. cerevisiae encoding proteins with domains homologous to the mammalian ras proteins. Cell 36, 607-612.
84. Powers, R.W., III, Kaeberlein, M., Caldwell, S.D., Kennedy, B.K., and Fields, S. (2006). Extension of chronological life span in yeast by decreasede TOR pathway signaling. Genes Dev 20, 174-184.
85. Radonjic, M., Andrau, J.C., Lijnzaad, P., Kemmeren, P., et al. (2005). Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol Cell 18, 171-183.
86. Ramaswamy, V., Williams, J.S., Robinson, K.M., Sopko, R.L., and Schultz, M.C. (2003). Global control of histone modification by the anaphase-promoting complex. Mol Cell Biol 23, 9136-9149.
87. Reinders, A., Burckert, N., Boller, T., Wiemken, A., and De Virgilio, C. (1998). Saccharomyces cerevisiae cAMP-dependent protein kinase controls entry into stationary phase through the Rim15p protein kinase. Genes Dev 12, 2943-2955.
88. Roberts, D.N., Wilson, B., Huff, J.T., Stewart, A.J., and Cairns, B.R. (2006). Dephosphorylation and genome-wide association of Maf1 with Pol III-transcribed genes during repression. Mol Cell 22, 633-644.
89. Rohde, J.R., Bastidas, R., Puria, R., and Cardenas, M.E. (2008). Nutritional control via Tor signaling in Saccharomyces cerevi-siae. Curr Opin Microbiol 11, 153-160.
90. Roosen, J., Engelen, K., Marchal, K., Mathys, J., Griffioen, G., Cameroni, E., et al. (2005). PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability. Mol Microbiol 55, 862-880.
91. Saldanha, A.J., Brauer, M.J., and Botstein, D. (2004). Nutritional homeostasis in batch and steady-state culture of yeast. Mol Biol Cell 15, 4089-4104.
92. Sandmeier, J.J., French, S., Osheim, Y., Cheung, W.L., Gallo, C.M., Beyer, A.L., et al. (2002). RPD3 is required for the in-activation of yeast ribosomal DNA genes in stationary phase. EMBO J 21, 4959-4968.
93. Santangelo, G.M. (2006). Glucose signaling in Saccharomyces cerevisiae. Microbiol and Mol Biol Rev 70, 253-282.
94. Sanz, P. (2003). Snflproteinkinase: a key player in the response to cellular stress in yeast. Biochem Soc Trans 31, 178-181.
95. Schafer, G., McEvoy, C.R.E., and Patterton, H.-G. (2008). The Saccharomyces cerevisiae linker histone Hho1p is essential for chromatin compaction in stationary phase and is displaced by transcription. Proc Natl Acad Sci USA 105, 14838-14843.
96. Schmelzle, T., Beck, T., Martin, D.E., and Hall, M.N. (2004). Activation of the RAS/cyclic AMP pathway suppresses a TOR deficiency in yeast. Mol Cell Biol 24, 338-351.
97. Schuller, H.J. (2003). Transcriptional control of nonfermentative metabiolism in the yeast Saccharomyces cerevisiae. Curr Genet 43, 139-160.
98. Shamji, A.F., Kuruvilla, F.G., and Schreiber, S.L. (2000). Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr Biol 10, 1574-1581.
99. Shivaswamy, S., and Iyer, V.R. (2008). Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response. Mol Cell Biol 28, 2221-2234.
100. Smith, A., Ward, M.P., and Garrett, S. (1998). Yeast PKA represses Msn2p/Msn4p-dependent gene expression to regulate growth, stress response and glycogen accumulation. EMBO J 17, 3556-3564.
101. Stevens, B. (1981). Mitochondrial structure. In The Molecular Biology of the Yeast Saccharomyces: Life Cycle and Inheritance. J. Strathern, E.W. Jones, and J.R. Broach (eds.). (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY), pp. 471-504.
102. Swinnen, E., Wanke, V., Roosen, J., Dubouloz, F., Pedruzzi, I., Cameroni, E., et al. (2006). Rim15 and the crossroads of nutrient signaling pathways in Saccharomyces cerevisiae. Cell Div 1:3.
103. Tachibana, C., Yoo, J.Y., Tagne, J.B., Kacherovsky, N., Lee, T.I., and Young, E.T. (2005). Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8. Mol Cell Biol 25, 2138-2146.
104. Takahashi, H., McCaffery, J.M., Irizarry, R.A., and Boeke, J.D. (2006). Nucleocytosolic acetyl-CoA synthetase is required for histone acetylation and global transcription. Mol Cell 23, 207-217.
105. Tanaka, K., Nakafuku, M., Satoh, T., Marshall, M.S., Gibbs, J.B., Matsumoto, K., et al. (1990). S. cerevisiae genes IRA1 and IRA2 encode proteins that may be functionally equivalent to mammalian ras GTPase activating protein. Cell 60, 803-807.
106. Tanaka, K., Lin, B.K., Wood, D.R., and Tamanoi, F. (1991). IRA2, an upstream negative regulator of RAS in yeast, is a RAS GTPase-activating protein. Proc Natl Acad Sci USA 88, 468-472.
107. Tatchell, K. (1986). RAS genes and growth control in Sacchar-omyces cerevisiae. J Bacteriol 166, 364-367.
108. Tate, J.J., Cox, K.H., Rai, R., and Cooper, T.G. (2002). Mks1p is required for negative regulation of retrograde gene expression in Saccharomyces cerevisiae but does not affect nitrogen catab-olite repression-sensitive gene expression. J Biol Chem 277, 20477-20482.
109. Taylor, F.R., and Parks, L.W. (1979). Triacylglycerol metabolism in Saccharomyces cerevisiae in relation to phospholipids synthesis. Biochim Biophys Acta 575, 204-214.
110. Thevelein, J.M. (1984). Regulation of trehalose mobilization in fungi. Microbiol Rev 48, 42-59.
111. Thevelein, J.M., and de Winde, J.H. (1999). Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol Microbiol 33, 904-918.
112. Thuriaux, P., and Sentenac, A. (1992). Yeast nuclear RNA polymerases. In The Molecular and Cellular Biology of the Yeast Saccharomyces. Volume II: Gene Expression. E.W. Jones, J.R. Pringle, J.R. Broach, eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 1-48.
113. Urban, J., Soulard, A., Huber, A., Lippman, S., Mukhopadhyay, D., Deloche, O., et al. (2007). Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell 26, 663-674.
114. Van Oevelen, C.J., van Teeffelen, H.A., van Werven, F.J., and Timmers, H.T. (2006). Snf1p-dependent Spt-Ada-Gcn5-acet-yltransferase (SAGA) recruitment and chromatin remodeling activities on the HXT2 and HXT4 promoters. J Biol Chem 281, 4523-4531.
115. Venema, J., and Tollervey, D. (1999). Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 33, 261-311.
116. Versele, M., De Winde, J.H., and Thevelein, J.M. (1999). A novel regulator of G protein signaling in yeast, Rgs2, downregulates glucose-activation of the cAMP pathway through direct inhibition of Gpa2. EMBO J 18, 5577-5591.
117. Vidan, S., and Mitchell, A.P. (1997). Stimulation of yeast meiotic gene expression by the glucose-repressible protein kinase Rim15p. Mol Cell Biol 17, 2688-2697.
118. Vignali, M., Hassan, A.H., Neely, K.E., and Workman, J.L. (2000). ATP-dependent chromatin-remodeling complexes. Mol Cell Biol 20, 1899-1910.
119. Wanke, V., Pedruzzi, I., Cameroni, E., Dubouloz, F., and De Virgilio, C. (2005). Regulation of G0 entry by the Pho80-Pho85 cyclin-CDK complex. EMBO J 24, 4271-4278.
120. Warner, J.R. (1999). The economics of ribosome biosynthesis in yeast. Trens Biochem Sci 24, 437-440.
121. Warner, J.R., Vilardell, J., and Sohn, J.H. (2001). Economics of ribosome biosynthesis. Cold Spring Harbor Symp Quant Biol 66, 67-74.
122. Wei, Y., and Zheng, X.F. (2009). Sch9 partially mediates TORC1 signaling to control ribosomal RNA synthesis. Cell Cycle 8, 4085-4090.
123. Wei, M., Fabrizio, P., Hu, J., Ge, H., Cheng, C., Li, L., et al. (2008). Life span extension by calorie restriction depends on Rim15 and transcription factors downstream of Ras/PKA, Tor, and Sch9. PLoS Genet 4, 0139-0149.
124. Werner-Washburne, M., Braun, E., Johnston, G.C., and Singer, R.A. (1993). Stationary phase in the yeast Saccharomyces cere-visiae. Microbiol Rev 57, 383-401.
125. Wiemken, A. (1990). Trehalose in yeast, stress protectant rather than reserve carbohydrate. Antonie Leeuwenhoek 58, 209-217.
126. Wilson, W.A., and Roach, P.J. (2002). Nutrient-regulated protein kinases in budding yeast. Cell 111, 155-158.
127. Woolford, J.L., and Warner, J.R. (1991). The ribosome and its synthesis. In The Molecular and Cellular Biology of the Yeast Saccharomyces. Volume I: Genome Dynamics, Protein Synthesis, and Energetics. J.R. Broach, J.R. Pringle, and E.W. Jones, eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 587-625.
128. Wullschleger, S., Loewith, R., Opliger, W., and Hall, M.N. (2005). Molecular organization of target of rapamycin complex 2. J Biol Chem 280, 30697-30704.
129. Xue, Y., Batlle, M., and Hirsch, J.P. (1998). GPR1 encodes a putative G protein-coupled receptor that associates with the Gpa2p Ga subunit and functions in a Ras-independent pathway. EMBO J 17, 1996-2007.
130. Yan, G., Shen, X., and Jiang, Y. (2006). Rapamycin activates Tap42-associated phosphatases by abrogating their association with Tor complex 1. EMBO J 25, 3546-3555.
131. Young, E.T., Dombek, K.M., Tachibana, C., and Ideker, T. (2003). Multiple pathways are coregulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J. Biol Chem 278, 26146-26158.
132. Zaman, S., Lipman, S.I., Zhao, X., and Roach, J.R. (2008). How Saccharomyces responds to nutrients. Annu Rev Genet 42, 27-81.
133. Zhang, N., and Oliver, S.G. (2010). The transcription activity of Gis1 is negatively modulated by proteasome-mediated limited proteolysis. J Biol Chem 285, 6465-6476.
134. Zhang, N., Wu, J., and Oliver, S.G. (2009). Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast. Microbiology 155, 1690-1698.
135. Zurita-Martinez, S.A., and Cardenas, M.E. (2005). Tor and cyclic AMP-protein kinase A: two parallel pathways regulating expression of genes required for cell growth. Eukaryot Cell 4, 63-71.