Coordinate regulation of multiple and distinct biosynthetic pathways by TOR and PKA kinases in S. cerevisiae
Tóm tắt
Từ khóa
Tài liệu tham khảo
Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL (2004) Global nucleosome occupancy in yeast. Genome Biol 5:R62
Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD (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
Breitling R, Sharif O, Hartman ML, Krisans SK (2002) Loss of compartmentalization causes misregulation of lysine biosynthesis in peroxisome-deficient yeast cells. Eukaryot Cell 1:978–86
Cardenas ME, Cutler NS, Lorenz MC, Di Como CJ, Heitman J (1999) The TOR signaling cascade regulates gene expression in response to nutrients. Genes Dev 13:3271–3279
Crauwels M, Donaton MC, Pernambuco MB, Winderickx J, de Winde JH, Thevelein JM (1997) The Sch9 protein kinase in the yeast Saccharomyces cerevisiae controls cAPK activity and is required for nitrogen activation of the fermentable-growth-medium-induced (FGM) pathway. Microbiology 143(Pt 8):2627–2637
Crespo JL, Hall MN (2003) Elucidating TOR signaling and rapamycin action: lessons from Saccharomyces cerevisiae. Microbiol Mol Biol Rev 66:579–591
Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, Roth FP, Young RA, Cairns BR, Silver PA (2002) The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell 9:563–573
Deminoff SJ, Santangelo GM (2001) Rap1p requires Gcr1p and Gcr2p homodimers to activate ribosomal protein and glycolytic genes, respectively. Genetics 158:133–143
DeRisi JL, Vishwanath IR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686
Di Como CJ, Arndt KT (1996) Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases. Genes Dev 10:1904–1916
Dilova I, Aronova S, Chen C-Y, Powers T (2004) Tor signaling and nutrient-based signals converge on Mks1p phosphorylation to regulate expression of Rtg1p/Rtg3p-dependent genes. J Biol Chem 279:46527–46535
Dilova I, Chen C-Y, Powers T (2002) Mks1 in concert with TOR signaling negatively regulates RTG target gene expression in S. cerevisiae. Curr Biol 12:389–395
Düvel K, Santhanam A, Garrett S, Schneper L, Broach JR (2003) Multiple roles of Tap42 in mediating rapamycin-induced transcriptional changes in yeast. Mol Cell 11:1467–1478
Eden A, Simchen G, Benvenisty N (1996) Two yeast homologs of ECA39, a target for c-Myc regulation, code for cytosolic and mitochondrial branched-chain amino acid aminotransferases. J Biol Chem 271:20242–20245
Fabrizio P, Pozza F, Pletcher SD, Gendron CM, Longo VD (2001) Regulation of longevity and stress resistance by Sch9 in yeast. Science 292:288–290
Feller A, Dubois E, Ramos F, Pierard A (1994) Repression of the genes for lysine biosynthesis in Saccharomyces cerevisiae is caused by limitation of Lys14-dependent transcriptional activation. Mol Cell Biol 14:6411–64118
Feller A, Ramos F, Pierard A, Dubois E (1999) In Saccharomyces cerevisae, feedback inhibition of homocitrate synthase isoenzymes by lysine modulates the activation of LYS gene expression by Lys14p. Eur J Biochem 261:163–170
Feller A, Ramos F, Pierard A, Dubois E (1997) Lys80p of Saccharomyces cerevisiae, previously proposed to as a specific repressor of Lys genes, is a pleiotropic regulatory factor identical to Mks1p. Yeast 13:1337–1346
Fingerman I, Nagaraj V, Norris D, Vershon AK (2003) Sfp1 plays a key role in yeast ribosome biogenesis. Eukaryot Cell 2:1061–1068
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241–4257
Gelling CL, Piper MD, Hong SP, Kornfeld GD, Dawes IW (2004) Identification of a novel one-carbon metabolism regulon in Saccharomyces cerevisiae. J Biol Chem 279:7072–7081
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391
Gietz RD, Woods RA (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350:87–96
Gorner W, Durchschlag E, Wolf J, Brown EL, Ammerer G, Ruis H, Schuller C (2002) Acute glucose starvation activates the nuclear localization signal of a stress-specific yeast transcription factor. Embo J 21:135–144
Grundy WN, Bailey TL, Elkan CP (1996) ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput Appl Biosci 12:303–310
Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, Schreiber SL (1999) Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc Natl Acad Sci USA 96:14866–14870
Heitman J, Movva NR, Hall MN (1991) Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253:905–909
Hinnebusch AG, Natarajan K (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
Holland MJ, Yokoi T, Holland JP, Myambo K, Innis MA (1987) The GCR1 gene encodes a positive transcriptional regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families in Saccharomyces cerevisiae. Mol Cell Biol 7:813–820
Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296:1205–1214
Humphrey EL, Shamji AF, Bernstein BE, Schreiber SL (2004) Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem Biol 11:295–299
Jacinto E, Guo B, Arndt KT, Schmelzle T, Hall MN (2001) TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway. Mol Cell 8:1017–1026
Jiang Y, Broach JR (1999) Tor proteins and protein phosphatase 2A reciprocally regulate Tap42 in controlling cell growth in yeast. EMBO J 18:2782–2792
Jones DL, Petty J, Hoyle DC, Hayes A, Ragni E, Popolo L, Oliver SG, Stateva LI (2003) Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway. Physiol Genomics 16:107–118
Jorgensen P, Rupes I, Sharom JR, Schneper L, Broach JR, Tyers M (2004) A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 18:2491–2505
Klein C, Struhl K (1994) Protein kinase A mediates growth-regulated expression of yeast ribosomal protein genes by modulating RAP1 transcriptional activity. Mol Cell Biol 14:1920–1928
Komeili A, Wedaman KP, O’Shea EO, Powers T (2000) Mechanism of metabolic control: Target of rapamycin signaling links nitrogen quality to the activity of the Rtg1 and Rtg3 transcription factors. J Cell Biol 151:863–878
Lin SJ, Kaeberlein M, Andalis AA, Sturtz LA, Defossez PA, Culotta VC, Fink GR, Guarente L (2002) Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration. Nature 418:344–348
Liu Z, Sekito T, S’pirek M, Thornton J, Butow RA (2003) Retrograde signaling is regulated by the dynamic interaction between Rtg2p and Mks1p. Mol Cell 12:410–411
Longtine MS, McKenzie III A, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953–961
Marion RM, Regev A, Segal E, Barash Y, Koller D, Friedman N, O’Shea EK (2004) Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc Natl Acad Sci U S A 101:14315–14322
Martin DE, Soulard A, and Hall MN (2004) TOR regulates ribosomal gene expression via PKA and the forkhead transcription factor FHL1. Cell
Nasmyth K, Adolf G, Lydall D, Seddon A (1990) The identiciation of a second cell cycle control on the HO promoter in yeast: Cell cycle regulation of SW15 nuclear entry. Cell 62:631–647
Natarajan K, Meyer MR, Jackson BM, Slade D, Roberts C, Hinnebusch AG, Marton MJ (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
Neuman-Silverberg FS, Bhattacharya S, Broach JR (1995) Nutrient availability and the RAS/Cyclic AMP pathway both induce expression of ribosomal protein genes in Saccharomyces cerevisiae but by different mechanisms. Mol Cell Biol 15:3187–3196
Pedruzzi I, Dubouloz F, Cameroni E, Wanke V, Roosen J, Winderickx J, De Virgilio C (2003) TOR and PKA signaling pathways converge on the protein kinase Rim15 to control entry into G0. Mol Cell 12:1607–1613
Powers T, Walter P (1999) Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae. Mol Biol Cell 10:987–1000
Rohde JR, Cardenas ME (2004) Nutrient signaling through TOR kinases controls gene expression and cellular differentiation in fungi. Curr Top Microbiol Immunol 279:53–72
Rohde JR, Cardenas ME (2003) The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation. Mol Cell Biol 23:629–635
Rolland F, Winderickx J, Thevelein JM (2002) Glucose-sensing and -signalling mechanisms in yeast. FEMS Yeast Res 2:183–201
Roosen J, Engelen K, Marchal K, Mathys J, Griffioen G, Cameroni E, Thevelein JM, De Virgilio C, De Moor B, Winderickx J (2005) PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability. Mol Microbiol 55:862–880
Rudra D, Zhao Y, Warner JR (2005) Central role of Ifh1p-Fhl1p interaction in the synthesis of yeast ribosomal proteins. Embo J 24:533–542
Schawalder SB, Kabani M, Howald I, Choudhury U, Werner M, Shore D (2004) Growth-regulated recruitment of the essential yeast ribosomal protein gene activator Ifh1. Nature 432:1058–1061
Schmelzle T, Beck T, Martin DE, Hall MN (2004) Activation of the RAS/cyclic AMP pathway suppresses a TOR deficiency in yeast. Mol Cell Biol 24:338–351
Schuller C, Mamnun YM, Mollapour M, Krapf G, Schuster M, Bauer BE, Piper PW, Kuchler K (2004) Global phenotypic analysis and transcriptional profiling defines the weak acid stress response regulon in Saccharomyces cerevisiae. Mol Biol Cell 15:706–720
Shamji AF, Kuruvilla FG, Schreiber SL (2000) Partitioning the transcriptional program induced by rapmycin among the effectors of the Tor proteins. Curr Biol 10:1574–1581
Shamji AF, Nghiem P, Schreiber SL (2003) Integration of growth factor and nutrient signaling: implications for cancer biology. Mol Cell 12:271–280
Smith A, Ward MP, Garrett S (1998) Yeast PKA represses Msn2p/Msn4p-dependent gene expression to regulate growth, stress response and glycogen accumulation. Embo J 17:3556–3564
Thevelein JM, de Winde JH (1999) Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol Microbiol 33:904–918
Tornow J, Zeng X, Gao W, Santangelo GM (1993) GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain. Embo J 12:2431–2437
Tsang CK, Bertram PG, Ai W, Drenan R, Zheng XF (2003) Chromatin-mediated regulation of nucleolar structure and RNA Pol I localization by TOR. Embo J 22:6045–6056
Wade C, Shea KA, Jensen RV, McAlear MA (2001) EBP2 is a member of the yeast RRB regulon, a transcriptionally coregulated set of genes that are required for ribosome and rRNA biosynthesis. Mol Cell Biol 21:8638–8650
Wade JT, Hall DB, Struhl K (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432:1054–1058
Wang Y, Pierce M, Schneper L, Guldal CG, Zhang X, Tavazoie S, Broach JR (2004) Ras and gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol 2:E128