Current Genetics

, Volume 56, Issue 1, pp 1–32 | Cite as

Life in the midst of scarcity: adaptations to nutrient availability in Saccharomyces cerevisiae

  • Bart Smets
  • Ruben Ghillebert
  • Pepijn De Snijder
  • Matteo Binda
  • Erwin Swinnen
  • Claudio De Virgilio
  • Joris Winderickx
Review

Abstract

Cells of all living organisms contain complex signal transduction networks to ensure that a wide range of physiological properties are properly adapted to the environmental conditions. The fundamental concepts and individual building blocks of these signalling networks are generally well-conserved from yeast to man; yet, the central role that growth factors and hormones play in the regulation of signalling cascades in higher eukaryotes is executed by nutrients in yeast. Several nutrient-controlled pathways, which regulate cell growth and proliferation, metabolism and stress resistance, have been defined in yeast. These pathways are integrated into a signalling network, which ensures that yeast cells enter a quiescent, resting phase (G0) to survive periods of nutrient scarceness and that they rapidly resume growth and cell proliferation when nutrient conditions become favourable again. A series of well-conserved nutrient-sensory protein kinases perform key roles in this signalling network: i.e. Snf1, PKA, Tor1 and Tor2, Sch9 and Pho85–Pho80. In this review, we provide a comprehensive overview on the current understanding of the signalling processes mediated via these kinases with a particular focus on how these individual pathways converge to signalling networks that ultimately ensure the dynamic translation of extracellular nutrient signals into appropriate physiological responses.

Keywords

Nutrient sensing Signal transduction Yeast TOR PKA Sch9 

References

  1. Ahuatzi D, Herrero P, de la Cera T, Moreno F (2004) The glucose-regulated nuclear localization of hexokinase 2 in Saccharomyces cerevisiae is Mig1-dependent. J Biol Chem 279:14440–14446PubMedGoogle Scholar
  2. Ahuatzi D, Riera A, Pelaez R, Herrero P, Moreno F (2007) Hxk2 regulates the phosphorylation state of Mig1 and therefore its nucleocytoplasmic distribution. J Biol Chem 282:4485–4493PubMedGoogle Scholar
  3. Almaguer C, Mantella D, Perez E, Patton-Vogt J (2003) Inositol and phosphate regulate GIT1 transcription and glycerophosphoinositol incorporation in Saccharomyces cerevisiae. Eukaryot Cell 2:729–736PubMedGoogle Scholar
  4. Araki T, Uesono Y, Oguchi T, Toh EA (2005) LAS24/KOG1, a component of the TOR complex 1 (TORC1), is needed for resistance to local anesthetic tetracaine and normal distribution of actin cytoskeleton in yeast. Genes Genet Syst 80:325–343PubMedGoogle Scholar
  5. Arguelles JC, Mbonyi K, Van Aelst L, Vanhalewyn M, Jans AW, Thevelein JM (1990) Absence of glucose-induced cAMP signaling in the Saccharomyces cerevisiae mutants cat1 and cat3 which are deficient in derepression of glucose-repressible proteins. Arch Microbiol 154:199–205PubMedGoogle Scholar
  6. Arndt KT, Styles CA, Fink GR (1989) A suppressor of a HIS4 transcriptional defect encodes a protein with homology to the catalytic subunit of protein phosphatases. Cell 56:527–537PubMedGoogle Scholar
  7. Aronova S, Wedaman K, Anderson S, Yates J 3rd, Powers T (2007) Probing the membrane environment of the TOR kinases reveals functional interactions between TORC1, actin, and membrane trafficking in Saccharomyces cerevisiae. Mol Biol Cell 18:2779–2794PubMedGoogle Scholar
  8. Aronova S, Wedaman K, Aronov PA, Fontes K, Ramos K, Hammock BD, Powers T (2008) Regulation of ceramide biosynthesis by TOR complex 2. Cell Metab 7:148–158PubMedGoogle Scholar
  9. Audhya A, Loewith R, Parsons AB, Gao L, Tabuchi M, Zhou H, Boone C, Hall MN, Emr SD (2004) Genome-wide lethality screen identifies new PI4, 5P2 effectors that regulate the actin cytoskeleton. EMBO J 23:3747–3757PubMedGoogle Scholar
  10. Auesukaree C, Homma T, Kaneko Y, Harashima S (2003) Transcriptional regulation of phosphate-responsive genes in low-affinity phosphate-transporter-defective mutants in Saccharomyces cerevisiae. Biochem Biophys Res Commun 306:843–850PubMedGoogle Scholar
  11. Auesukaree C, Homma T, Tochio H, Shirakawa M, Kaneko Y, Harashima S (2004) Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccharomyces cerevisiae. J Biol Chem 279:17289–17294PubMedGoogle Scholar
  12. Auesukaree C, Tochio H, Shirakawa M, Kaneko Y, Harashima S (2005) Plc1p, Arg82p, and Kcs1p, enzymes involved in inositol pyrophosphate synthesis, are essential for phosphate regulation and polyphosphate accumulation in Saccharomyces cerevisiae. J Biol Chem 280:25127–25133PubMedGoogle Scholar
  13. Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32:878–887PubMedGoogle Scholar
  14. Barbet NC, Schneider U, Helliwell SB, Stansfield I, Tuite MF, Hall MN (1996) TOR controls translation initiation and early G1 progression in yeast. Mol Biol Cell 7:25–42PubMedGoogle Scholar
  15. Batlle M, Lu A, Green DA, Xue Y, Hirsch JP (2003) Krh1p and Krh2p act downstream of the Gpa2p G(alpha) subunit to negatively regulate haploid invasive growth. J Cell Sci 116:701–710PubMedGoogle Scholar
  16. Beck T, Hall MN (1999) The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402:689–692PubMedGoogle Scholar
  17. Beck T, Schmidt A, Hall MN (1999) Starvation induces vacuolar targeting and degradation of the tryptophan permease in yeast. J Cell Biol 146:1227–1238PubMedGoogle Scholar
  18. Berchtold D, Walther TC (2009) TORC2 plasma membrane localization is essential for cell viability and restricted to a distinct domain. Mol Biol Cell 20:1565–1575PubMedGoogle Scholar
  19. Berger AB, Decourty L, Badis G, Nehrbass U, Jacquier A, Gadal O (2007) Hmo1 is required for TOR-dependent regulation of ribosomal protein gene transcription. Mol Cell Biol 27:8015–8026PubMedGoogle Scholar
  20. Berset C, Trachsel H, Altmann M (1998) The TOR (target of rapamycin) signal transduction pathway regulates the stability of translation initiation factor eIF4G in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci USA 95:4264–4269PubMedGoogle Scholar
  21. Bertram PG, Choi JH, Carvalho J, Chan TF, Ai W, Zheng XF (2002) Convergence of TOR-nitrogen and Snf1-glucose signaling pathways onto Gln3. Mol Cell Biol 22:1246–1252PubMedGoogle Scholar
  22. Beullens M, Mbonyi K, Geerts L, Gladines D, Detremerie K, Jans AW, Thevelein JM (1988) Studies on the mechanism of the glucose-induced cAMP signal in glycolysis and glucose repression mutants of the yeast Saccharomyces cerevisiae. Eur J Biochem 172:227–231PubMedGoogle Scholar
  23. Bharucha N, Ma J, Dobry CJ, Lawson SK, Yang Z, Kumar A (2008) Analysis of the yeast kinome reveals a network of regulated protein localization during filamentous growth. Mol Biol Cell 19:2708–2717PubMedGoogle Scholar
  24. Bhoite LT, Stillman DJ (1998) Residues in the Swi5 zinc finger protein that mediate cooperative DNA binding with the Pho2 homeodomain protein. Mol Cell Biol 18:6436–6446PubMedGoogle Scholar
  25. Bhoite LT, Allen JM, Garcia E, Thomas LR, Gregory ID, Voth WP, Whelihan K, Rolfes RJ, Stillman DJ (2002) Mutations in the pho2 (bas2) transcription factor that differentially affect activation with its partner proteins bas1, pho4, and swi5. J Biol Chem 277:37612–37618PubMedGoogle Scholar
  26. Bickle M, Delley PA, Schmidt A, Hall MN (1998) Cell wall integrity modulates RHO1 activity via the exchange factor ROM2. EMBO J 17:2235–2245PubMedGoogle Scholar
  27. Binda M, Peli-Gulli MP, Bonfils G, Panchaud N, Urban J, Sturgill TW, Loewith R, De Virgilio C (2009) The Vam6 GEF controls TORC1 by activating the EGO complex. Mol Cell 35:563–573PubMedGoogle Scholar
  28. Boustany LM, Cyert MS (2002) Calcineurin-dependent regulation of Crz1p nuclear export requires Msn5p and a conserved calcineurin docking site. Genes Dev 16:608–619PubMedGoogle Scholar
  29. Boy-Marcotte E, Perrot M, Bussereau F, Boucherie H, Jacquet M (1998) Msn2p and Msn4p control a large number of genes induced at the diauxic transition which are repressed by cyclic AMP in Saccharomyces cerevisiae. J Bacteriol 180:1044–1052PubMedGoogle Scholar
  30. Broek D, Toda T, Michaeli T, Levin L, Birchmeier C, Zoller M, Powers S, Wigler M (1987) The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell 48:789–799PubMedGoogle Scholar
  31. Bruun AW, Svendsen I, Sorensen SO, Kielland-Brandt MC, Winther JR (1998) A high-affinity inhibitor of yeast carboxypeptidase Y is encoded by TFS1 and shows homology to a family of lipid binding proteins. Biochemistry 37:3351–3357PubMedGoogle Scholar
  32. Budovskaya YV, Stephan JS, Reggiori F, Klionsky DJ, Herman PK (2004) The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. J Biol Chem 279:20663–20671PubMedGoogle Scholar
  33. Budovskaya YV, Stephan JS, Deminoff SJ, Herman PK (2005) An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase. Proc Natl Acad Sci USA 102:13933–13938PubMedGoogle Scholar
  34. Butow RA, Avadhani NG (2004) Mitochondrial signaling: the retrograde response. Mol Cell 14:1–15PubMedGoogle Scholar
  35. Caesar R, Blomberg A (2004) The stress-induced Tfs1p requires NatB-mediated acetylation to inhibit carboxypeptidase Y and to regulate the protein kinase A pathway. J Biol Chem 279:38532–38543PubMedGoogle Scholar
  36. Cafferkey R, Young PR, McLaughlin MM, Bergsma DJ, Koltin Y, Sathe GM, Faucette L, Eng WK, Johnson RK, Livi GP (1993) Dominant missense mutations in a novel yeast protein related to mammalian phosphatidylinositol 3-kinase and VPS34 abrogate rapamycin cytotoxicity. Mol Cell Biol 13:6012–6023PubMedGoogle Scholar
  37. Cameroni E, Hulo N, Roosen J, Winderickx J, De Virgilio C (2004) The novel yeast PAS kinase Rim 15 orchestrates G0-associated antioxidant defense mechanisms. Cell Cycle 3:462–468PubMedGoogle Scholar
  38. Camonis JH, Jacquet M (1988) A new RAS mutation that suppresses the CDC25 gene requirement for growth of Saccharomyces cerevisiae. Mol Cell Biol 8:2980–2983PubMedGoogle Scholar
  39. Camus C, Boy-Marcotte E, Jacquet M (1994) Two subclasses of guanine exchange factor (GEF) domains revealed by comparison of activities of chimeric genes constructed from CDC25, SDC25 and BUD5 in Saccharomyces cerevisiae. Mol Gen Genet 245:167–176PubMedGoogle Scholar
  40. Cardenas ME, Heitman J (1995) FKBP12-rapamycin target TOR2 is a vacuolar protein with an associated phosphatidylinositol-4 kinase activity. EMBO J 14:5892–5907PubMedGoogle Scholar
  41. 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 13:3271–3279PubMedGoogle Scholar
  42. Casamayor A, Torrance PD, Kobayashi T, Thorner J, Alessi DR (1999) Functional counterparts of mammalian protein kinases PDK1 and SGK in budding yeast. Curr Biol 9:186–197PubMedGoogle Scholar
  43. Casperson GF, Walker N, Brasier AR, Bourne HR (1983) A guanine nucleotide-sensitive adenylate cyclase in the yeast Saccharomyces cerevisiae. J Biol Chem 258:7911–7914PubMedGoogle Scholar
  44. Casperson GF, Walker N, Bourne HR (1985) Isolation of the gene encoding adenylate cyclase in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 82:5060–5063PubMedGoogle Scholar
  45. Cazzaniga P, Pescini D, Besozzi D, Mauri G, Colombo S, Martegani E (2008) Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools. J Biotechnol 133:377–385PubMedGoogle Scholar
  46. Celenza JL, Carlson M (1989) Mutational analysis of the Saccharomyces cerevisiae SNF1 protein kinase and evidence for functional interaction with the SNF4 protein. Mol Cell Biol 9:5034–5044PubMedGoogle Scholar
  47. Celenza JL, Eng FJ, Carlson M (1989) Molecular analysis of the SNF4 gene of Saccharomyces cerevisiae: evidence for physical association of the SNF4 protein with the SNF1 protein kinase. Mol Cell Biol 9:5045–5054PubMedGoogle Scholar
  48. Chang YY, Juhasz G, Goraksha-Hicks P, Arsham AM, Mallin DR, Muller LK, Neufeld TP (2009) Nutrient-dependent regulation of autophagy through the target of rapamycin pathway. Biochem Soc Trans 37:232–236PubMedGoogle Scholar
  49. Chautard H, Jacquet M, Schoentgen F, Bureaud N, Benedetti H (2004) Tfs1p, a member of the PEBP family, inhibits the Ira2p but not the Ira1p Ras GTPase-activating protein in Saccharomyces cerevisiae. Eukaryot Cell 3:459–470PubMedGoogle Scholar
  50. Chen EJ, Kaiser CA (2002) Amino acids regulate the intracellular trafficking of the general amino acid permease of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99:14837–14842PubMedGoogle Scholar
  51. Chen EJ, Kaiser CA (2003) LST8 negatively regulates amino acid biosynthesis as a component of the TOR pathway. J Cell Biol 161:333–347PubMedGoogle Scholar
  52. Cherkasova VA, Hinnebusch AG (2003) Translational control by TOR and TAP42 through dephosphorylation of eIF2alpha kinase GCN2. Genes Dev 17:859–872PubMedGoogle Scholar
  53. Chevtzoff C, Vallortigara J, Averet N, Rigoulet M, Devin A (2005) The yeast cAMP protein kinase Tpk3p is involved in the regulation of mitochondrial enzymatic content during growth. Biochim Biophys Acta 1706:117–125PubMedGoogle Scholar
  54. Claypool JA, French SL, Johzuka K, Eliason K, Vu L, Dodd JA, Beyer AL, Nomura M (2004) Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol Biol Cell 15:946–956PubMedGoogle Scholar
  55. Coffman JA, Rai R, Cooper TG (1995) Genetic evidence for Gln3p-independent, nitrogen catabolite repression-sensitive gene expression in Saccharomyces cerevisiae. J Bacteriol 177:6910–6918PubMedGoogle Scholar
  56. Coffman JA, Rai R, Cunningham T, Svetlov V, Cooper TG (1996) Gat1p, a GATA family protein whose production is sensitive to nitrogen catabolite repression, participates in transcriptional activation of nitrogen-catabolic genes in Saccharomyces cerevisiae. Mol Cell Biol 16:847–858PubMedGoogle Scholar
  57. Coffman JA, Rai R, Loprete DM, Cunningham T, Svetlov V, Cooper TG (1997) Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J Bacteriol 179:3416–3429PubMedGoogle Scholar
  58. Cohen A, Perzov N, Nelson H, Nelson N (1999) A novel family of yeast chaperons involved in the distribution of V-ATPase and other membrane proteins. J Biol Chem 274:26885–26893PubMedGoogle Scholar
  59. Colombo S, Ma P, Cauwenberg L, Winderickx J, Crauwels M, Teunissen A, Nauwelaers D, de Winde JH, Gorwa MF, Colavizza D, Thevelein JM (1998) Involvement of distinct G-proteins, Gpa2 and Ras, in glucose- and intracellular acidification-induced cAMP signalling in the yeast Saccharomyces cerevisiae. EMBO J 17:3326–3341PubMedGoogle Scholar
  60. Colombo S, Ronchetti D, Thevelein JM, Winderickx J, Martegani E (2004) Activation state of the Ras2 protein and glucose-induced signaling in Saccharomyces cerevisiae. J Biol Chem 279:46715–46722PubMedGoogle Scholar
  61. Cooper TG (2002) Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol Rev 26:223–238PubMedGoogle Scholar
  62. Corradetti MN, Guan KL (2006) Upstream of the mammalian target of rapamycin: do all roads pass through mTOR? Oncogene 25:6347–6360PubMedGoogle Scholar
  63. Crauwels M, Donaton MC, Pernambuco MB, Winderickx J, de Winde JH, Thevelein JM (1997a) 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):2627–2637PubMedGoogle Scholar
  64. Crauwels M, Winderickx J, de Winde JH, Thevelein JM (1997b) Identification of genes with nutrient-controlled expression by PCR-mapping in the yeast Saccharomyces cerevisiae. Yeast 13:973–984PubMedGoogle Scholar
  65. Crespo JL, Powers T, Fowler B, Hall MN (2002) The TOR-controlled transcription activators GLN3, RTG1, and RTG3 are regulated in response to intracellular levels of glutamine. Proc Natl Acad Sci USA 99:6784–6789PubMedGoogle Scholar
  66. Cytrynska M, Frajnt M, Jakubowicz T (2001) Saccharomyces cerevisiae pyruvate kinase Pyk1 is PKA phosphorylation substrate in vitro. FEMS Microbiol Lett 203:223–227PubMedGoogle Scholar
  67. Daignan-Fornier B, Fink GR (1992) Coregulation of purine and histidine biosynthesis by the transcriptional activators BAS1 and BAS2. Proc Natl Acad Sci USA 89:6746–6750PubMedGoogle Scholar
  68. Danaie P, Altmann M, Hall MN, Trachsel H, Helliwell SB (1999) CLN3 expression is sufficient to restore G1-to-S-phase progression in Saccharomyces cerevisiae mutants defective in translation initiation factor eIF4E. Biochem J 340(Pt 1):135–141PubMedGoogle Scholar
  69. De Craene JO, Soetens O, Andre B (2001) The Npr1 kinase controls biosynthetic and endocytic sorting of the yeast Gap1 permease. J Biol Chem 276:43939–43948PubMedGoogle Scholar
  70. De Virgilio C, Loewith R (2006a) Cell growth control: little eukaryotes make big contributions. Oncogene 25:6392–6415PubMedGoogle Scholar
  71. De Virgilio C, Loewith R (2006b) The TOR signalling network from yeast to man. Int J Biochem Cell Biol 38:1476–1481PubMedGoogle Scholar
  72. De Vit MJ, Johnston M (1999) The nuclear exportin Msn5 is required for nuclear export of the Mig1 glucose repressor of Saccharomyces cerevisiae. Curr Biol 9:1231–1241Google Scholar
  73. De Vit MJ, Waddle JA, Johnston M (1997) Regulated nuclear translocation of the Mig1 glucose repressor. Mol Biol Cell 8:1603–1618PubMedGoogle Scholar
  74. De Winde JH, Crauwels M, Hohmann S, Thevelein JM, Winderickx J (1996) Differential requirement of the yeast sugar kinases for sugar sensing in establishing the catabolite-repressed state. Eur J Biochem 241:633–643PubMedGoogle Scholar
  75. Devasahayam G, Ritz D, Helliwell SB, Burke DJ, Sturgill TW (2006) Pmr1, a Golgi Ca2+/Mn2+-ATPase, is a regulator of the target of rapamycin (TOR) signaling pathway in yeast. Proc Natl Acad Sci USA 103:17840–17845PubMedGoogle Scholar
  76. Devasahayam G, Burke DJ, Sturgill TW (2007) Golgi manganese transport is required for rapamycin signaling in Saccharomyces cerevisiae. Genetics 177:231–238PubMedGoogle Scholar
  77. Dever TE, Feng L, Wek RC, Cigan AM, Donahue TF, Hinnebusch AG (1992) Phosphorylation of initiation factor 2 alpha by protein kinase GCN2 mediates gene-specific translational control of GCN4 in yeast. Cell 68:585–596PubMedGoogle Scholar
  78. Di Como CJ, Arndt KT (1996) Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases. Genes Dev 10:1904–1916PubMedGoogle Scholar
  79. Dihazi H, Kessler R, Eschrich K (2003) Glucose-induced stimulation of the Ras-cAMP pathway in yeast leads to multiple phosphorylations and activation of 6-phosphofructo-2-kinase. Biochemistry 42:6275–6282PubMedGoogle Scholar
  80. Dilova I, Chen CY, Powers T (2002) Mks1 in concert with TOR signaling negatively regulates RTG target gene expression in S. cerevisiae. Curr Biol 12:389–395PubMedGoogle Scholar
  81. Dilova I, Aronova S, Chen JC, Powers T (2004) Tor signaling and nutrient-based signals converge on Mks1p phosphorylation to regulate expression of Rtg1.Rtg3p-dependent target genes. J Biol Chem 279:46527–46535PubMedGoogle Scholar
  82. Dubouloz F, Deloche O, Wanke V, Cameroni E, De Virgilio C (2005) The TOR and EGO protein complexes orchestrate microautophagy in yeast. Mol Cell 19:15–26PubMedGoogle Scholar
  83. Duvel K, Broach JR (2004) The role of phosphatases in TOR signaling in yeast. Curr Top Microbiol Immunol 279:19–38PubMedGoogle Scholar
  84. Duvel K, Santhanam A, Garrett S, Schneper L, Broach JR (2003) Multiple roles of Tap42 in mediating rapamycin-induced transcriptional changes in yeast. Mol Cell 11:1467–1478PubMedGoogle Scholar
  85. Entian KD (1980) Genetic and biochemical evidence for hexokinase PII as a key enzyme involved in carbon catabolite repression in yeast. Mol Gen Genet 178:633–637PubMedGoogle Scholar
  86. Entian KD, Zimmermann FK (1980) Glycolytic enzymes and intermediates in carbon catabolite repression mutants of Saccharomyces cerevisiae. Mol Gen Genet 177:345–350PubMedGoogle Scholar
  87. Estruch F, Carlson M (1993) Two homologous zinc finger genes identified by multicopy suppression in a SNF1 protein kinase mutant of Saccharomyces cerevisiae. Mol Cell Biol 13:3872–3881PubMedGoogle Scholar
  88. Estruch F, Treitel MA, Yang X, Carlson M (1992) N-terminal mutations modulate yeast SNF1 protein kinase function. Genetics 132:639–650PubMedGoogle Scholar
  89. Fadri M, Daquinag A, Wang S, Xue T, Kunz J (2005) The pleckstrin homology domain proteins Slm1 and Slm2 are required for actin cytoskeleton organization in yeast and bind phosphatidylinositol-4,5-bisphosphate and TORC2. Mol Biol Cell 16:1883–1900PubMedGoogle Scholar
  90. Fayard E, Tintignac LA, Baudry A, Hemmings BA (2005) Protein kinase B/Akt at a glance. J Cell Sci 118:5675–5678PubMedGoogle Scholar
  91. Ferguson SB, Anderson ES, Harshaw RB, Thate T, Craig NL, Nelson HC (2005) Protein kinase A regulates constitutive expression of small heat-shock genes in an Msn2/4p-independent and Hsf1p-dependent manner in Saccharomyces cerevisiae. Genetics 169:1203–1214PubMedGoogle Scholar
  92. Field J, Nikawa J, Broek D, MacDonald B, Rodgers L, Wilson IA, Lerner RA, Wigler M (1988) Purification of a RAS-responsive adenylyl cyclase complex from Saccharomyces cerevisiae by use of an epitope addition method. Mol Cell Biol 8:2159–2165PubMedGoogle Scholar
  93. Flick JS, Thorner J (1998) An essential function of a phosphoinositide-specific phospholipase C is relieved by inhibition of a cyclin-dependent protein kinase in the yeast Saccharomyces cerevisiae. Genetics 148:33–47PubMedGoogle Scholar
  94. Forsberg H, Ljungdahl PO (2001) Sensors of extracellular nutrients in Saccharomyces cerevisiae. Curr Genet 40:91–109PubMedGoogle Scholar
  95. Friant S, Lombardi R, Schmelzle T, Hall MN, Riezman H (2001) Sphingoid base signaling via Pkh kinases is required for endocytosis in yeast. EMBO J 20:6783–6792PubMedGoogle Scholar
  96. Funakoshi T, Matsuura A, Noda T, Ohsumi Y (1997) Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae. Gene 192:207–213PubMedGoogle Scholar
  97. Gancedo JM (1998) Yeast carbon catabolite repression. Microbiol Mol Biol Rev 62:334–361PubMedGoogle Scholar
  98. Gancedo JM (2008) The early steps of glucose signalling in yeast. FEMS Microbiol Rev 32:673–704PubMedGoogle Scholar
  99. Gancedo JM, Mazon MJ, Gancedo C (1983) Fructose 2,6-bisphosphate activates the cAMP-dependent phosphorylation of yeast fructose-1,6-bisphosphatase in vitro. J Biol Chem 258:5998–5999PubMedGoogle Scholar
  100. Gander S, Bonenfant D, Altermatt P, Martin DE, Hauri S, Moes S, Hall MN, Jenoe P (2008) Identification of the rapamycin-sensitive phosphorylation sites within the Ser/Thr-rich domain of the yeast Npr1 protein kinase. Rapid Commun Mass Spectrom 22:3743–3753PubMedGoogle Scholar
  101. Gao M, Kaiser CA (2006) A conserved GTPase-containing complex is required for intracellular sorting of the general amino-acid permease in yeast. Nat Cell Biol 8:657–667PubMedGoogle Scholar
  102. Garreau H, Hasan RN, Renault G, Estruch F, Boy-Marcotte E, 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(Pt 9):2113–2120PubMedGoogle Scholar
  103. Garrett S, Broach J (1989) Loss of Ras activity in Saccharomyces cerevisiae is suppressed by disruptions of a new kinase gene, YAKI, whose product may act downstream of the cAMP-dependent protein kinase. Genes Dev 3:1336–1348PubMedGoogle Scholar
  104. Garrett S, Menold MM, Broach JR (1991) The Saccharomyces cerevisiae YAK1 gene encodes a protein kinase that is induced by arrest early in the cell cycle. Mol Cell Biol 11:4045–4052PubMedGoogle Scholar
  105. 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 11:4241–4257PubMedGoogle Scholar
  106. Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B (2008) Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Mol Microbiol 68:1583–1594PubMedGoogle Scholar
  107. Georis I, Tate JJ, Cooper TG, Dubois E (2008) Tor pathway control of the nitrogen-responsive DAL5 gene bifurcates at the level of Gln3 and Gat1 regulation in Saccharomyces cerevisiae. J Biol Chem 283:8919–8929PubMedGoogle Scholar
  108. Geyskens I, Kumara SHMC, Donaton MCV, Bergsma JCT, Thevelein JM, Wera S (2001) Expression of mammalian PKB complements deletion of the yeast protein kinase Sch9. Nato Sci Ser A316:117–126Google Scholar
  109. Gilliquet V, Berben G (1993) Positive and negative regulators of the Saccharomyces cerevisiae ‘PHO system’ participate in several cell functions. FEMS Microbiol Lett 108:333–339PubMedGoogle Scholar
  110. Godard P, Urrestarazu A, Vissers S, Kontos K, Bontempi G, van Helden J, Andre B (2007) Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Mol Cell Biol 27:3065–3086PubMedGoogle Scholar
  111. Gorner W, Durchschlag E, Martinez-Pastor MT, Estruch F, Ammerer G, Hamilton B, Ruis H, Schuller C (1998) Nuclear localization of the C2H2 zinc finger protein Msn2p is regulated by stress and protein kinase A activity. Genes Dev 12:586–597PubMedGoogle Scholar
  112. 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 21:135–144PubMedGoogle Scholar
  113. Griffioen G, Mager WH, Planta RJ (1994) Nutritional upshift response of ribosomal protein gene transcription in Saccharomyces cerevisiae. FEMS Microbiol Lett 123:137–144PubMedGoogle Scholar
  114. Griffioen G, Anghileri P, Imre E, Baroni MD, Ruis H (2000) Nutritional control of nucleocytoplasmic localization of cAMP-dependent protein kinase catalytic and regulatory subunits in Saccharomyces cerevisiae. J Biol Chem 275:1449–1456PubMedGoogle Scholar
  115. Griffioen G, Branduardi P, Ballarini A, Anghileri P, Norbeck J, Baroni MD, Ruis H (2001) Nucleocytoplasmic distribution of budding yeast protein kinase A regulatory subunit Bcy1 requires Zds1 and is regulated by Yak1-dependent phosphorylation of its targeting domain. Mol Cell Biol 21:511–523PubMedGoogle Scholar
  116. Hahn JS, Thiele DJ (2004) Activation of the Saccharomyces cerevisiae heat shock transcription factor under glucose starvation conditions by Snf1 protein kinase. J Biol Chem 279:5169–5176PubMedGoogle Scholar
  117. Hahn JS, Hu Z, Thiele DJ, Iyer VR (2004) Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol 24:5249–5256PubMedGoogle Scholar
  118. Hall DB, Wade JT, Struhl K (2006) An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol 26:3672–3679PubMedGoogle Scholar
  119. Harashima T, Heitman J (2002) The Galpha protein Gpa2 controls yeast differentiation by interacting with kelch repeat proteins that mimic Gbeta subunits. Mol Cell 10:163–173PubMedGoogle Scholar
  120. Harashima T, Heitman J (2005) Galpha subunit Gpa2 recruits kelch repeat subunits that inhibit receptor-G protein coupling during cAMP-induced dimorphic transitions in Saccharomyces cerevisiae. Mol Biol Cell 16:4557–4571PubMedGoogle Scholar
  121. Harashima T, Anderson S, Yates JR 3rd, Heitman J (2006) The kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with the yeast RasGAP neurofibromin homologs Ira1 and Ira2. Mol Cell 22:819–830PubMedGoogle Scholar
  122. Hardie DG (2007) AMP-activated/SNF1 protein kinases: conserved guardians of cellular energy. Nat Rev Mol Cell Biol 8:774–785PubMedGoogle Scholar
  123. 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 96:14866–14870PubMedGoogle Scholar
  124. Hardy TA, Roach PJ (1993) Control of yeast glycogen synthase-2 by COOH-terminal phosphorylation. J Biol Chem 268:23799–23805PubMedGoogle Scholar
  125. Hartley AD, Ward MP, Garrett S (1994) The Yak1 protein kinase of Saccharomyces cerevisiae moderates thermotolerance and inhibits growth by an Sch9 protein kinase-independent mechanism. Genetics 136:465–474PubMedGoogle Scholar
  126. Healy AM, Zolnierowicz S, Stapleton AE, Goebl M, DePaoli-Roach AA, Pringle JR (1991) CDC55, a Saccharomyces cerevisiae gene involved in cellular morphogenesis: identification, characterization, and homology to the B subunit of mammalian type 2A protein phosphatase. Mol Cell Biol 11:5767–5780PubMedGoogle Scholar
  127. Hedbacker K, Carlson M (2006) Regulation of the nucleocytoplasmic distribution of Snf1-Gal83 protein kinase. Eukaryot Cell 5:1950–1956PubMedGoogle Scholar
  128. Hedbacker K, Carlson M (2008) SNF1/AMPK pathways in yeast. Front Biosci 13:2408–2420PubMedGoogle Scholar
  129. Hedbacker K, Hong SP, Carlson M (2004) Pak1 protein kinase regulates activation and nuclear localization of Snf1-Gal83 protein kinase. Mol Cell Biol 24:8255–8263PubMedGoogle Scholar
  130. Hedges D, Proft M, Entian KD (1995) CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae. Mol Cell Biol 15:1915–1922PubMedGoogle Scholar
  131. Heitman J, Movva NR, Hall MN (1991) Targets for cell cycle arrest by the immunosuppressant rapamycin in yeast. Science 253:905–909PubMedGoogle Scholar
  132. Helliwell SB, Wagner P, Kunz J, Deuter-Reinhard M, Henriquez R, Hall MN (1994) TOR1 and TOR2 are structurally and functionally similar but not identical phosphatidylinositol kinase homologues in yeast. Mol Biol Cell 5:105–118PubMedGoogle Scholar
  133. Helliwell SB, Schmidt A, Ohya Y, Hall MN (1998) The Rho1 effector Pkc1, but not Bni1, mediates signalling from Tor2 to the actin cytoskeleton. Curr Biol 8:1211–1214PubMedGoogle Scholar
  134. Helliwell SB, Losko S, Kaiser CA (2001) Components of a ubiquitin ligase complex specify polyubiquitination and intracellular trafficking of the general amino acid permease. J Cell Biol 153:649–662PubMedGoogle Scholar
  135. Herrero P, Martinez-Campa C, Moreno F (1998) The hexokinase 2 protein participates in regulatory DNA-protein complexes necessary for glucose repression of the SUC2 gene in Saccharomyces cerevisiae. FEBS Lett 434:71–76PubMedGoogle Scholar
  136. Herruer MH, Mager WH, Woudt LP, Nieuwint RT, Wassenaar GM, Groeneveld P, Planta RJ (1987) Transcriptional control of yeast ribosomal protein synthesis during carbon-source upshift. Nucleic Acids Res 15:10133–10144PubMedGoogle Scholar
  137. Hiesinger M, Roth S, Meissner E, Schuller HJ (2001) Contribution of Cat8 and Sip4 to the transcriptional activation of yeast gluconeogenic genes by carbon source-responsive elements. Curr Genet 39:68–76PubMedGoogle Scholar
  138. Hinnebusch AG (2005) Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 59:407–450PubMedGoogle Scholar
  139. Ho HL, Lee HY, Liao HC, Chen MY (2008) Involvement of Saccharomyces cerevisiae Avo3p/Tsc11p in maintaining TOR complex 2 integrity and coupling to downstream signaling. Eukaryot Cell 7:1328–1343PubMedGoogle Scholar
  140. Hohmann S, Winderickx J, de Winde JH, Valckx D, Cobbaert P, Luyten K, de Meirsman C, Ramos J, Thevelein JM (1999) Novel alleles of yeast hexokinase PII with distinct effects on catalytic activity and catabolite repression of SUC2. Microbiology 145(Pt 3):703–714PubMedGoogle Scholar
  141. Hohmann S, Krantz M, Nordlander B (2007) Yeast osmoregulation. Methods Enzymol 428:29–45PubMedGoogle Scholar
  142. Holsbeeks I, Lagatie O, Van Nuland A, Van de Velde S, Thevelein JM (2004) The eukaryotic plasma membrane as a nutrient-sensing device. Trends Biochem Sci 29:556–564PubMedGoogle Scholar
  143. Hong SP, Momcilovic M, Carlson M (2005) Function of mammalian LKB1 and Ca2+/calmodulin-dependent protein kinase kinase alpha as Snf1-activating kinases in yeast. J Biol Chem 280:21804–21809PubMedGoogle Scholar
  144. Huang S, O’Shea EK (2005) A systematic high-throughput screen of a yeast deletion collection for mutants defective in PHO5 regulation. Genetics 169:1859–1871PubMedGoogle Scholar
  145. Huang D, Chun KT, Goebl MG, Roach PJ (1996) Genetic interactions between REG1/HEX2 and GLC7, the gene encoding the protein phosphatase type 1 catalytic subunit in Saccharomyces cerevisiae. Genetics 143:119–127PubMedGoogle Scholar
  146. Huang S, Jeffery DA, Anthony MD, O’Shea EK (2001) Functional analysis of the cyclin-dependent kinase inhibitor Pho81 identifies a novel inhibitory domain. Mol Cell Biol 21:6695–6705PubMedGoogle Scholar
  147. Huang D, Moffat J, Andrews B (2002) Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrity. Mol Cell Biol 22:5076–5088PubMedGoogle Scholar
  148. Huang D, Friesen H, Andrews B (2007a) Pho85, a multifunctional cyclin-dependent protein kinase in budding yeast. Mol Microbiol 66:303–314PubMedGoogle Scholar
  149. Huang K, Ferrin-O’Connell I, Zhang W, Leonard GA, O’Shea EK, Quiocho FA (2007b) Structure of the Pho85–Pho80 CDK–cyclin complex of the phosphate-responsive signal transduction pathway. Mol Cell 28:614–623PubMedGoogle Scholar
  150. Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R (2009) Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev 23:1929–1943PubMedGoogle Scholar
  151. Hurlimann HC, Stadler-Waibel M, Werner TP, Freimoser FM (2007) Pho91 Is a vacuolar phosphate transporter that regulates phosphate and polyphosphate metabolism in Saccharomyces cerevisiae. Mol Biol Cell 18:4438–4445PubMedGoogle Scholar
  152. Hurlimann HC, Pinson B, Stadler-Waibel M, Zeeman SC, Freimoser FM (2009) The SPX domain of the yeast low-affinity phosphate transporter Pho90 regulates transport activity. EMBO Rep 10:1003–1008PubMedGoogle Scholar
  153. Iyengar R (1996) Gating by cyclic AMP: expanded role for an old signaling pathway. Science 271:461–463PubMedGoogle Scholar
  154. Jacinto E, Guo B, Arndt KT, Schmelzle T, Hall MN (2001) TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway. Mol Cell 8:1017–1026PubMedGoogle Scholar
  155. Jiang Y, Broach JR (1999) Tor proteins and protein phosphatase 2A reciprocally regulate Tap42 in controlling cell growth in yeast. EMBO J 18:2782–2792PubMedGoogle Scholar
  156. Jiang R, Carlson M (1996) Glucose regulates protein interactions within the yeast SNF1 protein kinase complex. Genes Dev 10:3105–3115PubMedGoogle Scholar
  157. Jiang R, Carlson M (1997) The Snf1 protein kinase and its activating subunit, Snf4, interact with distinct domains of the Sip1/Sip2/Gal83 component in the kinase complex. Mol Cell Biol 17:2099–2106PubMedGoogle Scholar
  158. Jones S, Vignais ML, Broach JR (1991) The CDC25 protein of Saccharomyces cerevisiae promotes exchange of guanine nucleotides bound to ras. Mol Cell Biol 11:2641–2646PubMedGoogle Scholar
  159. Jordan JD, Iyengar R (1998) Modes of interactions between signaling pathways. Biochem Pharmacol 55:1347–1352PubMedGoogle Scholar
  160. Jorgensen P, Nishikawa JL, Breitkreutz BJ, Tyers M (2002) Systematic identification of pathways that couple cell growth and division in yeast. Science 297:395–400PubMedGoogle Scholar
  161. 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 18:2491–2505PubMedGoogle Scholar
  162. Kafadar KA, Cyert MS (2004) Integration of stress responses: modulation of calcineurin signaling in Saccharomyces cerevisiae by protein kinase A. Eukaryot Cell 3:1147–1153PubMedGoogle Scholar
  163. Kafadar KA, Zhu H, Snyder M, Cyert MS (2003) Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I. Genes Dev 17:2698–2708PubMedGoogle Scholar
  164. Kaffman A, Rank NM, O’Neill EM, Huang LS, O’Shea EK (1998a) The receptor Msn5 exports the phosphorylated transcription factor Pho4 out of the nucleus. Nature 396:482–486PubMedGoogle Scholar
  165. Kaffman A, Rank NM, O’Shea EK (1998b) Phosphorylation regulates association of the transcription factor Pho4 with its import receptor Pse1/Kap121. Genes Dev 12:2673–2683PubMedGoogle Scholar
  166. Kamada Y, Funakoshi T, Shintani T, Nagano K, Ohsumi M, Ohsumi Y (2000) Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J Cell Biol 150:1507–1513PubMedGoogle Scholar
  167. Kamada Y, Fujioka Y, Suzuki NN, Inagaki F, Wullschleger S, Loewith R, Hall MN, Ohsumi Y (2005) Tor2 directly phosphorylates the AGC kinase Ypk2 to regulate actin polarization. Mol Cell Biol 25:7239–7248PubMedGoogle Scholar
  168. Kataoka T, Broek D, Wigler M (1985) DNA sequence and characterization of the S. cerevisiae gene encoding adenylate cyclase. Cell 43:493–505PubMedGoogle Scholar
  169. Keith CT, Schreiber SL (1995) PIK-related kinases: DNA repair, recombination, and cell cycle checkpoints. Science 270:50–51PubMedGoogle Scholar
  170. Keleher CA, Redd MJ, Schultz J, Carlson M, Johnson AD (1992) Ssn6-Tup1 is a general repressor of transcription in yeast. Cell 68:709–719PubMedGoogle Scholar
  171. Kim EM, Jang YK, Park SD (2002) Phosphorylation of Rph1, a damage-responsive repressor of PHR1 in Saccharomyces cerevisiae, is dependent upon Rad53 kinase. Nucleic Acids Res 30:643–648PubMedGoogle Scholar
  172. Kim MD, Hong SP, Carlson M (2005) Role of Tos3, a Snf1 protein kinase kinase, during growth of Saccharomyces cerevisiae on nonfermentable carbon sources. Eukaryot Cell 4:861–866PubMedGoogle Scholar
  173. Kim E, Goraksha-Hicks P, Li L, Neufeld TP, Guan KL (2008) Regulation of TORC1 by Rag GTPases in nutrient response. Nat Cell Biol 10:935–945PubMedGoogle Scholar
  174. Klionsky DJ, Emr SD (1989) Membrane protein sorting: biosynthesis, transport and processing of yeast vacuolar alkaline phosphatase. EMBO J 8:2241–2250PubMedGoogle Scholar
  175. Knight JP, Daly TM, Bergman LW (2004) Regulation by phosphorylation of Pho81p, a cyclin-dependent kinase inhibitor in Saccharomyces cerevisiae. Curr Genet 46:10–19PubMedGoogle Scholar
  176. Komeili A, Wedaman KP, O’Shea EK, 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 151:863–878PubMedGoogle Scholar
  177. Konrad M (1988) Analysis and in vivo disruption of the gene coding for adenylate kinase (ADK1) in the yeast Saccharomyces cerevisiae. J Biol Chem 263:19468–19474PubMedGoogle Scholar
  178. Kraakman LS, Griffioen G, Zerp S, Groeneveld P, Thevelein JM, Mager WH, Planta RJ (1993) Growth-related expression of ribosomal protein genes in Saccharomyces cerevisiae. Mol Gen Genet 239:196–204PubMedGoogle Scholar
  179. Kraakman L, Lemaire K, Ma P, Teunissen AW, Donaton MC, Van Dijck P, Winderickx J, de Winde JH, Thevelein JM (1999a) 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 32:1002–1012PubMedGoogle Scholar
  180. Kraakman LS, Winderickx J, Thevelein JM, De Winde JH (1999b) Structure–function analysis of yeast hexokinase: structural requirements for triggering cAMP signalling and catabolite repression. Biochem J 343:159–168PubMedGoogle Scholar
  181. Kubler E, Mosch HU, Rupp S, Lisanti MP (1997) Gpa2p, a G-protein alpha-subunit, regulates growth and pseudohyphal development in Saccharomyces cerevisiae via a cAMP-dependent mechanism. J Biol Chem 272:20321–20323PubMedGoogle Scholar
  182. Kubota H, Obata T, Ota K, Sasaki T, Ito T (2003) Rapamycin-induced translational derepression of GCN4 mRNA involves a novel mechanism for activation of the eIF2 alpha kinase GCN2. J Biol Chem 278:20457–20460PubMedGoogle Scholar
  183. Kuepfer L, Peter M, Sauer U, Stelling J (2007) Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol 25:1001–1006PubMedGoogle Scholar
  184. Kunz J, Henriquez R, Schneider U, Deuter-Reinhard M, Movva NR, Hall MN (1993) Target of rapamycin in yeast, TOR2, is an essential phosphatidylinositol kinase homolog required for G1 progression. Cell 73:585–596PubMedGoogle Scholar
  185. Kunz J, Schneider U, Howald I, Schmidt A, Hall MN (2000) HEAT repeats mediate plasma membrane localization of Tor2p in yeast. J Biol Chem 275:37011–37020PubMedGoogle Scholar
  186. Kuret J, Johnson KE, Nicolette C, Zoller MJ (1988) Mutagenesis of the regulatory subunit of yeast cAMP-dependent protein kinase. Isolation of site-directed mutants with altered binding affinity for catalytic subunit. J Biol Chem 263:9149–9154PubMedGoogle Scholar
  187. Kuruvilla FG, Shamji AF, Schreiber SL (2001) Carbon- and nitrogen-quality signaling to translation are mediated by distinct GATA-type transcription factors. Proc Natl Acad Sci USA 98:7283–7288PubMedGoogle Scholar
  188. Lecoq K, Belloc I, Desgranges C, Daignan-Fornier B (2001) Role of adenosine kinase in Saccharomyces cerevisiae: identification of the ADO1 gene and study of the mutant phenotypes. Yeast 18:335–342PubMedGoogle Scholar
  189. Lee M, O’Regan S, Moreau JL, Johnson AL, Johnston LH, Goding CR (2000) Regulation of the Pcl7–Pho85 cyclin–cdk complex by Pho81. Mol Microbiol 38:411–422PubMedGoogle Scholar
  190. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799–804PubMedGoogle Scholar
  191. Lee YS, Mulugu S, York JD, O’Shea EK (2007) Regulation of a cyclin–CDK–CDK inhibitor complex by inositol pyrophosphates. Science 316:109–112PubMedGoogle Scholar
  192. Lee P, Cho BR, Joo HS, Hahn JS (2008a) Yeast Yak1 kinase, a bridge between PKA and stress-responsive transcription factors, Hsf1 and Msn2/Msn4. Mol Microbiol 70:882–895PubMedGoogle Scholar
  193. Lee YS, Huang K, Quiocho FA, O’Shea EK (2008b) Molecular basis of cyclin–CDK–CKI regulation by reversible binding of an inositol pyrophosphate. Nat Chem Biol 4:25–32PubMedGoogle Scholar
  194. Lee J, Moir RD, Willis IM (2009) Regulation of RNA polymerase III transcription involves SCH9-dependent and -independent branches of the TOR pathway. J Biol Chem 284:12604–12608PubMedGoogle Scholar
  195. Lemaire K, Van de Velde S, Van Dijck P, Thevelein JM (2004) Glucose and sucrose act as agonist and mannose as antagonist ligands of the G protein-coupled receptor Gpr1 in the yeast Saccharomyces cerevisiae. Mol Cell 16:293–299PubMedGoogle Scholar
  196. Lemmon MA (2008) Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol 9:99–111PubMedGoogle Scholar
  197. Lempiainen H, Uotila A, Urban J, Dohnal I, Ammerer G, Loewith R, Shore D (2009) Sfp1 interaction with TORC1 and Mrs6 reveals feedback regulation on TOR signaling. Mol Cell 33:704–716PubMedGoogle Scholar
  198. Lenburg ME, O’Shea EK (1996) Signaling phosphate starvation. Trends Biochem Sci 21:383–387PubMedGoogle Scholar
  199. Lenssen E, Oberholzer U, Labarre J, De Virgilio C, Collart MA (2002) Saccharomyces cerevisiae Ccr4-not complex contributes to the control of Msn2p-dependent transcription by the Ras/cAMP pathway. Mol Microbiol 43:1023–1037PubMedGoogle Scholar
  200. Lenssen E, James N, Pedruzzi I, Dubouloz F, Cameroni E, Bisig R, Maillet L, Werner M, Roosen J, Petrovic K, Winderickx J, Collart MA, De Virgilio C (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 25:488–498PubMedGoogle Scholar
  201. Lesage P, Yang X, Carlson M (1996) Yeast SNF1 protein kinase interacts with SIP4, a C6 zinc cluster transcriptional activator: a new role for SNF1 in the glucose response. Mol Cell Biol 16:1921–1928PubMedGoogle Scholar
  202. Levin DE (2005) Cell wall integrity signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 69:262–291PubMedGoogle Scholar
  203. Li H, Tsang CK, Watkins M, Bertram PG, Zheng XF (2006) Nutrient regulates Tor1 nuclear localization and association with rDNA promoter. Nature 442:1058–1061PubMedGoogle Scholar
  204. Liko D, Slattery MG, Heideman W (2007) Stb3 binds to ribosomal RNA processing element motifs that control transcriptional responses to growth in Saccharomyces cerevisiae. J Biol Chem 282:26623–26628PubMedGoogle Scholar
  205. Liu Z, Butow RA (2006) Mitochondrial retrograde signaling. Annu Rev Genet 40:159–185PubMedGoogle Scholar
  206. Liu C, Yang Z, Yang J, Xia Z, Ao S (2000) Regulation of the yeast transcriptional factor PHO2 activity by phosphorylation. J Biol Chem 275:31972–31978PubMedGoogle Scholar
  207. Liu Z, Sekito T, Spirek M, Thornton J, Butow RA (2003) Retrograde signaling is regulated by the dynamic interaction between Rtg2p and Mks1p. Mol Cell 12:401–411PubMedGoogle Scholar
  208. Liu K, Zhang X, Lester RL, Dickson RC (2005a) The sphingoid long chain base phytosphingosine activates AGC-type protein kinases in Saccharomyces cerevisiae including Ypk1, Ypk2, and Sch9. J Biol Chem 280:22679–22687PubMedGoogle Scholar
  209. Liu K, Zhang X, Sumanasekera C, Lester RL, Dickson RC (2005b) Signalling functions for sphingolipid long-chain bases in Saccharomyces cerevisiae. Biochem Soc Trans 33:1170–1173PubMedGoogle Scholar
  210. Lo WS, Duggan L, Emre NC, Belotserkovskya R, Lane WS, Shiekhattar R, Berger SL (2001) Snf1—a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription. Science 293:1142–1146PubMedGoogle Scholar
  211. Loewith R, Jacinto E, Wullschleger S, Lorberg A, Crespo JL, Bonenfant D, Oppliger W, Jenoe P, Hall MN (2002) Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol Cell 10:457–468PubMedGoogle Scholar
  212. Lorenz MC, Heitman J (1997) Yeast pseudohyphal growth is regulated by GPA2, a G protein alpha homolog. EMBO J 16:7008–7018PubMedGoogle Scholar
  213. Lorenz MC, Pan X, Harashima T, Cardenas ME, Xue Y, Hirsch JP, Heitman J (2000) The G protein-coupled receptor gpr1 is a nutrient sensor that regulates pseudohyphal differentiation in Saccharomyces cerevisiae. Genetics 154:609–622PubMedGoogle Scholar
  214. Lu A, Hirsch JP (2005) Cyclic AMP-independent regulation of protein kinase A substrate phosphorylation by Kelch repeat proteins. Eukaryot Cell 4:1794–1800PubMedGoogle Scholar
  215. Ludin K, Jiang R, Carlson M (1998) Glucose-regulated interaction of a regulatory subunit of protein phosphatase 1 with the Snf1 protein kinase in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 95:6245–6250PubMedGoogle Scholar
  216. Luke MM, Della Seta F, Di Como CJ, Sugimoto H, Kobayashi R, Arndt KT (1996) The SAP, a new family of proteins, associate and function positively with the SIT4 phosphatase. Mol Cell Biol 16:2744–2755PubMedGoogle Scholar
  217. Lundin M, Nehlin JO, Ronne H (1994) Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1. Mol Cell Biol 14:1979–1985PubMedGoogle Scholar
  218. Ma H, Bloom LM, Walsh CT, Botstein D (1989) The residual enzymatic phosphorylation activity of hexokinase II mutants is correlated with glucose repression in Saccharomyces cerevisiae. Mol Cell Biol 9:5643–5649PubMedGoogle Scholar
  219. Magasanik B, Kaiser CA (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290:1–18PubMedGoogle Scholar
  220. Magbanua JP, Ogawa N, Harashima S, Oshima Y (1997) The transcriptional activators of the PHO regulon, Pho4p and Pho2p, interact directly with each other and with components of the basal transcription machinery in Saccharomyces cerevisiae. J Biochem 121:1182–1189PubMedGoogle Scholar
  221. Mai B, Breeden L (1997) Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family. Mol Cell Biol 17:6491–6501PubMedGoogle Scholar
  222. 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 USA 101:14315–14322PubMedGoogle Scholar
  223. Martin DE, Soulard A, Hall MN (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119:969–979PubMedGoogle Scholar
  224. Martinez-Pastor MT, Marchler G, Schuller C, Marchler-Bauer A, Ruis H, 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 15:2227–2235PubMedGoogle Scholar
  225. Matheos DP, Kingsbury TJ, Ahsan US, Cunningham KW (1997) Tcn1p/Crz1p, a calcineurin-dependent transcription factor that differentially regulates gene expression in Saccharomyces cerevisiae. Genes Dev 11:3445–3458PubMedGoogle Scholar
  226. Matsumoto K, Uno I, Ishikawa T (1983) Initiation of meiosis in yeast mutants defective in adenylate cyclase and cyclic AMP-dependent protein kinase. Cell 32:417–423PubMedGoogle Scholar
  227. Matsumoto K, Uno I, Ishikawa T (1984) Identification of the structural gene and nonsense alleles for adenylate cyclase in Saccharomyces cerevisiae. J Bacteriol 157:277–282PubMedGoogle Scholar
  228. Mayordomo I, Sanz P (2001) Hexokinase PII: structural analysis and glucose signalling in the yeast Saccharomyces cerevisiae. Yeast 18:923–930PubMedGoogle Scholar
  229. Mayordomo I, Estruch F, Sanz P (2002) Convergence of the target of rapamycin and the Snf1 protein kinase pathways in the regulation of the subcellular localization of Msn2, a transcriptional activator of STRE (Stress Response Element)-regulated genes. J Biol Chem 277:35650–35656PubMedGoogle Scholar
  230. Mbonyi K, Beullens M, Detremerie K, Geerts L, Thevelein JM (1988) Requirement of one functional RAS gene and inability of an oncogenic ras variant to mediate the glucose-induced cyclic AMP signal in the yeast Saccharomyces cerevisiae. Mol Cell Biol 8:3051–3057PubMedGoogle Scholar
  231. Mbonyi K, van Aelst L, Arguelles JC, Jans AW, Thevelein JM (1990) Glucose-induced hyperaccumulation of cyclic AMP and defective glucose repression in yeast strains with reduced activity of cyclic AMP-dependent protein kinase. Mol Cell Biol 10:4518–4523PubMedGoogle Scholar
  232. McCartney RR, Schmidt MC (2001) Regulation of Snf1 kinase. Activation requires phosphorylation of threonine 210 by an upstream kinase as well as a distinct step mediated by the Snf4 subunit. J Biol Chem 276:36460–36466PubMedGoogle Scholar
  233. McCartney RR, Rubenstein EM, Schmidt MC (2005) Snf1 kinase complexes with different beta subunits display stress-dependent preferences for the three Snf1-activating kinases. Curr Genet 47:335–344PubMedGoogle Scholar
  234. Measday V, Moore L, Retnakaran R, Lee J, Donoviel M, Neiman AM, Andrews B (1997) A family of cyclin-like proteins that interact with the Pho85 cyclin-dependent kinase. Mol Cell Biol 17:1212–1223PubMedGoogle Scholar
  235. Minehart PL, Magasanik B (1991) Sequence and expression of GLN3, a positive nitrogen regulatory gene of Saccharomyces cerevisiae encoding a protein with a putative zinc finger DNA-binding domain. Mol Cell Biol 11:6216–6228PubMedGoogle Scholar
  236. Mitchelhill KI, Stapleton D, Gao G, House C, Michell B, Katsis F, Witters LA, Kemp BE (1994) Mammalian AMP-activated protein kinase shares structural and functional homology with the catalytic domain of yeast Snf1 protein kinase. J Biol Chem 269:2361–2364PubMedGoogle Scholar
  237. Moir RD, Lee J, Haeusler RA, Desai N, Engelke DR, Willis IM (2006) Protein kinase A regulates RNA polymerase III transcription through the nuclear localization of Maf1. Proc Natl Acad Sci USA 103:15044–15049PubMedGoogle Scholar
  238. Momcilovic M, Iram SH, Liu Y, Carlson M (2008) Roles of the glycogen-binding domain and Snf4 in glucose inhibition of SNF1 protein kinase. J Biol Chem 283:19521–19529PubMedGoogle Scholar
  239. Moriya H, Shimizu-Yoshida Y, Omori A, Iwashita S, Katoh M, Sakai A (2001) Yak1p, a DYRK family kinase, translocates to the nucleus and phosphorylates yeast Pop2p in response to a glucose signal. Genes Dev 15:1217–1228PubMedGoogle Scholar
  240. Moskvina E, Schuller C, Maurer CT, Mager WH, Ruis H (1998) A search in the genome of Saccharomyces cerevisiae for genes regulated via stress response elements. Yeast 14:1041–1050PubMedGoogle Scholar
  241. Nakafuku M, Obara T, Kaibuchi K, Miyajima I, Miyajima A, Itoh H, Nakamura S, Arai K, Matsumoto K, Kaziro Y (1988) Isolation of a second yeast Saccharomyces cerevisiae gene (GPA2) coding for guanine nucleotide-binding regulatory protein: studies on its structure and possible functions. Proc Natl Acad Sci USA 85:1374–1378PubMedGoogle Scholar
  242. 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 21:4347–4368PubMedGoogle Scholar
  243. Nehlin JO, Ronne H (1990) Yeast MIG1 repressor is related to the mammalian early growth response and Wilms’ tumour finger proteins. EMBO J 9:2891–2898PubMedGoogle Scholar
  244. Niederacher D, Entian KD (1991) Characterization of Hex2 protein, a negative regulatory element necessary for glucose repression in yeast. Eur J Biochem 200:311–319PubMedGoogle Scholar
  245. Nikawa J, Cameron S, Toda T, Ferguson KM, Wigler M (1987a) Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae. Genes Dev 1:931–937PubMedGoogle Scholar
  246. Nikawa J, Sass P, Wigler M (1987b) Cloning and characterization of the low-affinity cyclic AMP phosphodiesterase gene of Saccharomyces cerevisiae. Mol Cell Biol 7:3629–3636PubMedGoogle Scholar
  247. Nishizawa M, Kanaya Y, Toh EA (1999) Mouse cyclin-dependent kinase (Cdk) 5 is a functional homologue of a yeast Cdk, pho85 kinase. J Biol Chem 274:33859–33862PubMedGoogle Scholar
  248. Nishizawa M, Katou Y, Shirahige K, Toh-e A (2004) Yeast Pho85 kinase is required for proper gene expression during the diauxic shift. Yeast 21:903–918PubMedGoogle Scholar
  249. Nishizawa M, Komai T, Katou Y, Shirahige K, Ito T, Toh EA (2008a) Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast. PLoS Biol 6:2817–2830PubMedGoogle Scholar
  250. Nishizawa M, Komai T, Morohashi N, Shimizu M, Toh-e A (2008b) Transcriptional repression by the Pho4 transcription factor controls the timing of SNZ1 expression. Eukaryot Cell 7:949–957PubMedGoogle Scholar
  251. O’Neill EM, Kaffman A, Jolly ER, O’Shea EK (1996) Regulation of PHO4 nuclear localization by the PHO80–PHO85 cyclin–CDK complex. Science 271:209–212PubMedGoogle Scholar
  252. Oficjalska-Pham D, Harismendy O, Smagowicz WJ, Gonzalez de Peredo A, Boguta M, Sentenac A, Lefebvre O (2006) General repression of RNA polymerase III transcription is triggered by protein phosphatase type 2A-mediated dephosphorylation of Maf1. Mol Cell 22:623–632PubMedGoogle Scholar
  253. Ogawa N, DeRisi J, Brown PO (2000) New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 11:4309–4321PubMedGoogle Scholar
  254. Pan X, Heitman J (1999) Cyclic AMP-dependent protein kinase regulates pseudohyphal differentiation in Saccharomyces cerevisiae. Mol Cell Biol 19:4874–4887PubMedGoogle Scholar
  255. Panek AC, de Araujo PS, Moura Neto V, Panek AD (1987) Regulation of the trehalose-6-phosphate synthase complex in Saccharomyces. I. Interconversion of forms by phosphorylation. Curr Genet 11:459–465PubMedGoogle Scholar
  256. Papamichos-Chronakis M, Gligoris T, Tzamarias D (2004) The Snf1 kinase controls glucose repression in yeast by modulating interactions between the Mig1 repressor and the Cyc8-Tup1 co-repressor. EMBO Rep 5:368–372PubMedGoogle Scholar
  257. Park JI, Grant CM, Dawes IW (2005) The high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae is the major determinant of cAMP levels in stationary phase: involvement of different branches of the Ras-cyclic AMP pathway in stress responses. Biochem Biophys Res Commun 327:311–319PubMedGoogle Scholar
  258. Pascual-Ahuir A, Proft M (2007) The Sch9 kinase is a chromatin-associated transcriptional activator of osmostress-responsive genes. EMBO J 26:3098–3108PubMedGoogle Scholar
  259. Pedruzzi I, Burckert N, Egger P, De Virgilio C (2000) Saccharomyces cerevisiae Ras/cAMP pathway controls post-diauxic shift element-dependent transcription through the zinc finger protein Gis1. EMBO J 19:2569–2579PubMedGoogle Scholar
  260. 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 12:1607–1613PubMedGoogle Scholar
  261. Peeters T, Louwet W, Gelade R, Nauwelaers D, Thevelein JM, Versele M (2006) Kelch-repeat proteins interacting with the Galpha protein Gpa2 bypass adenylate cyclase for direct regulation of protein kinase A in yeast. Proc Natl Acad Sci USA 103:13034–13039PubMedGoogle Scholar
  262. Persson BL, Lagerstedt JO, Pratt JR, Pattison-Granberg J, Lundh K, Shokrollahzadeh S, Lundh F (2003) Regulation of phosphate acquisition in Saccharomyces cerevisiae. Curr Genet 43:225–244PubMedGoogle Scholar
  263. Pike BL, Yongkiettrakul S, Tsai MD, Heierhorst J (2004) Mdt1, a novel Rad53 FHA1 domain-interacting protein, modulates DNA damage tolerance and G(2)/M cell cycle progression in Saccharomyces cerevisiae. Mol Cell Biol 24:2779–2788PubMedGoogle Scholar
  264. Pinson B, Vaur S, Sagot I, Coulpier F, Lemoine S, Daignan-Fornier B (2009) Metabolic intermediates selectively stimulate transcription factor interaction and modulate phosphate and purine pathways. Genes Dev 23:1399–1407PubMedGoogle Scholar
  265. Piper RC (2006) Successful transporter gets an EGO boost. Dev Cell 11:6–7PubMedGoogle Scholar
  266. Planta RJ (1997) Regulation of ribosome synthesis in yeast. Yeast 13:1505–1518PubMedGoogle Scholar
  267. Polizotto RS, Cyert MS (2001) Calcineurin-dependent nuclear import of the transcription factor Crz1p requires Nmd5p. J Cell Biol 154:951–960PubMedGoogle Scholar
  268. Popova Iu G, Padkina MV, Sambuk EV (2000) Effect of mutations in PHO85 and PHO4 genes on utilization of proline in Saccharomyces cerevisiae yeasts. Genetika 36:1622–1628PubMedGoogle Scholar
  269. Portela P, Moreno S (2006) Glucose-dependent activation of protein kinase A activity in Saccharomyces cerevisiae and phosphorylation of its TPK1 catalytic subunit. Cell Signal 18:1072–1086PubMedGoogle Scholar
  270. Portela P, Howell S, Moreno S, Rossi S (2002) In vivo and in vitro phosphorylation of two isoforms of yeast pyruvate kinase by protein kinase A. J Biol Chem 277:30477–30487PubMedGoogle Scholar
  271. Pruyne D, Bretscher A (2000a) Polarization of cell growth in yeast. J Cell Sci 113(Pt 4):571–585PubMedGoogle Scholar
  272. Pruyne D, Bretscher A (2000b) Polarization of cell growth in yeast. I. Establishment and maintenance of polarity states. J Cell Sci 113(Pt 3):365–375PubMedGoogle Scholar
  273. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M (2005) Global analysis of protein phosphorylation in yeast. Nature 438:679–684PubMedGoogle Scholar
  274. Rahner A, Scholer A, Martens E, Gollwitzer B, Schuller HJ (1996) Dual influence of the yeast Cat1p (Snf1p) protein kinase on carbon source-dependent transcriptional activation of gluconeogenic genes by the regulatory gene CAT8. Nucleic Acids Res 24:2331–2337PubMedGoogle Scholar
  275. Randez-Gil F, Bojunga N, Proft M, Entian KD (1997) Glucose derepression of gluconeogenic enzymes in Saccharomyces cerevisiae correlates with phosphorylation of the gene activator Cat8p. Mol Cell Biol 17:2502–2510PubMedGoogle Scholar
  276. Randez-Gil F, Herrero P, Sanz P, Prieto JA, Moreno F (1998) Hexokinase PII has a double cytosolic-nuclear localisation in Saccharomyces cerevisiae. FEBS Lett 425:475–478PubMedGoogle Scholar
  277. Rebora K, Desmoucelles C, Borne F, Pinson B, Daignan-Fornier B (2001) Yeast AMP pathway genes respond to adenine through regulated synthesis of a metabolic intermediate. Mol Cell Biol 21:7901–7912PubMedGoogle Scholar
  278. Rebora K, Laloo B, Daignan-Fornier B (2005) Revisiting purine-histidine cross-pathway regulation in Saccharomyces cerevisiae: a central role for a small molecule. Genetics 170:61–70PubMedGoogle Scholar
  279. Reinders A, Burckert N, Boller T, Wiemken A, De Virgilio C (1998) Saccharomyces cerevisiae cAMP-dependent protein kinase controls entry into stationary phase through the Rim15p protein kinase. Genes Dev 12:2943–2955PubMedGoogle Scholar
  280. Reinke A, Anderson S, McCaffery JM, Yates J 3rd, Aronova S, Chu S, Fairclough S, Iverson C, Wedaman KP, Powers T (2004) TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae. J Biol Chem 279:14752–14762PubMedGoogle Scholar
  281. Rittenhouse J, Moberly L, Marcus F (1987) Phosphorylation in vivo of yeast (Saccharomyces cerevisiae) fructose-1,6-bisphosphatase at the cyclic AMP-dependent site. J Biol Chem 262:10114–10119PubMedGoogle Scholar
  282. Roberg KJ, Rowley N, Kaiser CA (1997) Physiological regulation of membrane protein sorting late in the secretory pathway of Saccharomyces cerevisiae. J Cell Biol 137:1469–1482PubMedGoogle Scholar
  283. Roberts DN, Wilson B, Huff JT, Stewart AJ, Cairns BR (2006) Dephosphorylation and genome-wide association of Maf1 with Pol III-transcribed genes during repression. Mol Cell 22:633–644PubMedGoogle Scholar
  284. Robertson LS, Fink GR (1998) The three yeast A kinases have specific signaling functions in pseudohyphal growth. Proc Natl Acad Sci USA 95:13783–13787PubMedGoogle Scholar
  285. Robertson LS, Causton HC, Young RA, Fink GR (2000) The yeast A kinases differentially regulate iron uptake and respiratory function. Proc Natl Acad Sci USA 97:5984–5988PubMedGoogle Scholar
  286. Robinson LC, Tatchell K (1991) TFS1: a suppressor of cdc25 mutations in Saccharomyces cerevisiae. Mol Gen Genet 230:241–250PubMedGoogle Scholar
  287. Roelants FM, Torrance PD, Thorner J (2004) Differential roles of PDK1- and PDK2-phosphorylation sites in the yeast AGC kinases Ypk1, Pkc1 and Sch9. Microbiology 150:3289–3304PubMedGoogle Scholar
  288. Rohde JR, Campbell S, Zurita-Martinez SA, Cutler NS, Ashe M, Cardenas ME (2004) TOR controls transcriptional and translational programs via Sap-Sit4 protein phosphatase signaling effectors. Mol Cell Biol 24:8332–8341PubMedGoogle Scholar
  289. Rohde JR, Bastidas R, Puria R, Cardenas ME (2008) Nutritional control via Tor signaling in Saccharomyces cerevisiae. Curr Opin Microbiol 11:153–160PubMedGoogle Scholar
  290. Rolland F, De Winde JH, Lemaire K, Boles E, Thevelein JM, Winderickx J (2000) Glucose-induced cAMP signalling in yeast requires both a G-protein coupled receptor system for extracellular glucose detection and a separable hexose kinase-dependent sensing process. Mol Microbiol 38:348–358PubMedGoogle Scholar
  291. Ronne H (1995) Glucose repression in fungi. Trends Genet 11:12–17PubMedGoogle Scholar
  292. Ronne H, Carlberg M, Hu GZ, Nehlin JO (1991) Protein phosphatase 2A in Saccharomyces cerevisiae: effects on cell growth and bud morphogenesis. Mol Cell Biol 11:4876–4884PubMedGoogle Scholar
  293. Roosen J, Oesterhelt C, Pardons K, Swinnen E, Winderickx J (2004) Integration of nutrient signalling pathways in the yeast Saccharomyces cerevisiae. In: Winderickx J, Taylor PM (eds) Topics in current genetics. Nutrient-induced responses in eukaryotic cells, vol 7. Springer, Heidelberg, pp 277–318Google Scholar
  294. 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 55:862–880PubMedGoogle Scholar
  295. Rose M, Albig W, Entian KD (1991) Glucose repression in Saccharomyces cerevisiae is directly associated with hexose phosphorylation by hexokinases PI and PII. Eur J Biochem 199:511–518PubMedGoogle Scholar
  296. Rubenstein EM, McCartney RR, Zhang C, Shokat KM, Shirra MK, Arndt KM, Schmidt MC (2008) Access denied: Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase. J Biol Chem 283:222–230PubMedGoogle Scholar
  297. Rudoni S, Colombo S, Coccetti P, Martegani E (2001) Role of guanine nucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae. Biochim Biophys Acta 1538:181–189PubMedGoogle Scholar
  298. Rudra D, Zhao Y, Warner JR (2005) Central role of Ifh1p–Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J 24:533–542PubMedGoogle Scholar
  299. Sancak Y, Peterson TR, Shaul YD, Lindquist RA, Thoreen CC, Bar-Peled L, Sabatini DM (2008) The Rag GTPases bind raptor and mediate amino acid signaling to mTORC1. Science 320:1496–1501PubMedGoogle Scholar
  300. Santangelo GM (2006) Glucose signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 70:253–282PubMedGoogle Scholar
  301. Santhanam A, Hartley A, Duvel K, Broach JR, Garrett S (2004) PP2A phosphatase activity is required for stress and Tor kinase regulation of yeast stress response factor Msn2p. Eukaryot Cell 3:1261–1271PubMedGoogle Scholar
  302. Sanz P, Alms GR, Haystead TA, Carlson M (2000) Regulatory interactions between the Reg1-Glc7 protein phosphatase and the Snf1 protein kinase. Mol Cell Biol 20:1321–1328PubMedGoogle Scholar
  303. Sass P, Field J, Nikawa J, Toda T, Wigler M (1986) Cloning and characterization of the high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 83:9303–9307PubMedGoogle Scholar
  304. 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 432:1058–1061PubMedGoogle Scholar
  305. Schmelzle T, Helliwell SB, Hall MN (2002) Yeast protein kinases and the RHO1 exchange factor TUS1 are novel components of the cell integrity pathway in yeast. Mol Cell Biol 22:1329–1339PubMedGoogle Scholar
  306. 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 24:338–351PubMedGoogle Scholar
  307. Schmidt A, Kunz J, Hall MN (1996) TOR2 is required for organization of the actin cytoskeleton in yeast. Proc Natl Acad Sci USA 93:13780–13785PubMedGoogle Scholar
  308. Schmidt A, Beck T, Koller A, Kunz J, Hall MN (1998) The TOR nutrient signalling pathway phosphorylates NPR1 and inhibits turnover of the tryptophan permease. EMBO J 17:6924–6931PubMedGoogle Scholar
  309. Schmitt AP, McEntee K (1996) Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 93:5777–5782PubMedGoogle Scholar
  310. Schuller HJ (2003) Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr Genet 43:139–160PubMedGoogle Scholar
  311. Serrano R, Ruiz A, Bernal D, Chambers JR, Arino J (2002) The transcriptional response to alkaline pH in Saccharomyces cerevisiae: evidence for calcium-mediated signalling. Mol Microbiol 46:1319–1333PubMedGoogle Scholar
  312. Shamji AF, Kuruvilla FG, Schreiber SL (2000) Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr Biol 10:1574–1581PubMedGoogle Scholar
  313. Shao D, Creasy CL, Bergman LW (1998) A cysteine residue in helixII of the bHLH domain is essential for homodimerization of the yeast transcription factor Pho4p. Nucleic Acids Res 26:710–714PubMedGoogle Scholar
  314. Singh KK, Rasmussen AK, Rasmussen LJ (2004) Genome-wide analysis of signal transducers and regulators of mitochondrial dysfunction in Saccharomyces cerevisiae. Ann N Y Acad Sci 1011:284–298PubMedGoogle Scholar
  315. Smets B, De Snijder P, Engelen K, Joossens E, Ghillebert R, Thevissen K, Marchal K, Winderickx J (2008) Genome-wide expression analysis reveals TORC1-dependent and -independent functions of Sch9. FEMS Yeast Res 8:1276–1288PubMedGoogle Scholar
  316. 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 17:3556–3564PubMedGoogle Scholar
  317. Smith FC, Davies SP, Wilson WA, Carling D, Hardie DG (1999) The SNF1 kinase complex from Saccharomyces cerevisiae phosphorylates the transcriptional repressor protein Mig1p in vitro at four sites within or near regulatory domain 1. FEBS Lett 453:219–223PubMedGoogle Scholar
  318. Sneddon AA, Cohen PT, Stark MJ (1990) Saccharomyces cerevisiae protein phosphatase 2A performs an essential cellular function and is encoded by two genes. EMBO J 9:4339–4346PubMedGoogle Scholar
  319. Soetens O, De Craene JO, Andre B (2001) Ubiquitin is required for sorting to the vacuole of the yeast general amino acid permease, Gap1. J Biol Chem 276:43949–43957PubMedGoogle Scholar
  320. Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, Andrews B (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell 21:319–330PubMedGoogle Scholar
  321. Springael JY, Andre B (1998) Nitrogen-regulated ubiquitination of the Gap1 permease of Saccharomyces cerevisiae. Mol Biol Cell 9:1253–1263PubMedGoogle Scholar
  322. Springael JY, Nikko E, Andre B, Marini AM (2002) Yeast Npi3/Bro1 is involved in ubiquitin-dependent control of permease trafficking. FEBS Lett 517:103–109PubMedGoogle Scholar
  323. Stathopoulos AM, Cyert MS (1997) Calcineurin acts through the CRZ1/TCN1-encoded transcription factor to regulate gene expression in yeast. Genes Dev 11:3432–3444PubMedGoogle Scholar
  324. Stathopoulos-Gerontides A, Guo JJ, Cyert MS (1999) Yeast calcineurin regulates nuclear localization of the Crz1p transcription factor through dephosphorylation. Genes Dev 13:798–803PubMedGoogle Scholar
  325. Steger DJ, Haswell ES, Miller AL, Wente SR, O’Shea EK (2003) Regulation of chromatin remodeling by inositol polyphosphates. Science 299:114–116PubMedGoogle Scholar
  326. Sturgill TW, Cohen A, Diefenbacher M, Trautwein M, Martin DE, Hall MN (2008) TOR1 and TOR2 have distinct locations in live cells. Eukaryot Cell 7:1819–1830PubMedGoogle Scholar
  327. Subramanian M, Qiao WB, Khanam N, Wilkins O, Der SD, Lalich JD, Bognar AL (2005) Transcriptional regulation of the one-carbon metabolism regulon in Saccharomyces cerevisiae by Bas1p. Mol Microbiol 57:53–69PubMedGoogle Scholar
  328. Sutherland CM, Hawley SA, McCartney RR, Leech A, Stark MJ, Schmidt MC, Hardie DG (2003) Elm1p is one of three upstream kinases for the Saccharomyces cerevisiae SNF1 complex. Curr Biol 13:1299–1305PubMedGoogle Scholar
  329. Swinnen E, Rosseels J, Winderickx J (2005) The minimum domain of Pho81 is not sufficient to control the Pho85-Rim15 effector branch involved in phosphate starvation-induced stress responses. Curr Genet 48:18–33PubMedGoogle Scholar
  330. Swinnen E, Wanke V, Roosen J, Smets B, Dubouloz F, Pedruzzi I, Cameroni E, De Virgilio C, Winderickx J (2006) Rim15 and the crossroads of nutrient signalling pathways in Saccharomyces cerevisiae. Cell Div 1:3PubMedGoogle Scholar
  331. Tamaki H (2007) Glucose-stimulated cAMP-protein kinase A pathway in yeast Saccharomyces cerevisiae. J Biosci Bioeng 104:245–250PubMedGoogle Scholar
  332. Tanaka K, Matsumoto K, Toh EA (1989) IRA1, an inhibitory regulator of the RAS-cyclic AMP pathway in Saccharomyces cerevisiae. Mol Cell Biol 9:757–768PubMedGoogle Scholar
  333. Tanaka K, Nakafuku M, Satoh T, Marshall MS, Gibbs JB, Matsumoto K, Kaziro Y, Toh-e A (1990a) S. cerevisiae genes IRA1 and IRA2 encode proteins that may be functionally equivalent to mammalian ras GTPase activating protein. Cell 60:803–807PubMedGoogle Scholar
  334. Tanaka K, Nakafuku M, Tamanoi F, Kaziro Y, Matsumoto K, Toh-e A (1990b) IRA2, a second gene of Saccharomyces cerevisiae that encodes a protein with a domain homologous to mammalian ras GTPase-activating protein. Mol Cell Biol 10:4303–4313PubMedGoogle Scholar
  335. Tanaka K, Lin BK, Wood DR, Tamanoi F (1991) IRA2, an upstream negative regulator of RAS in yeast, is a RAS GTPase-activating protein. Proc Natl Acad Sci USA 88:468–472PubMedGoogle Scholar
  336. Tate JJ, Cox KH, Rai R, Cooper TG (2002) Mks1p is required for negative regulation of retrograde gene expression in Saccharomyces cerevisiae but does not affect nitrogen catabolite repression-sensitive gene expression. J Biol Chem 277:20477–20482PubMedGoogle Scholar
  337. Tate JJ, Georis I, Feller A, Dubois E, Cooper TG (2009) Rapamycin-induced Gln3 dephosphorylation is insufficient for nuclear localization: Sit4 and PP2A phosphatases are regulated and function differently. J Biol Chem 284:2522–2534PubMedGoogle Scholar
  338. Tennyson CN, Lee J, Andrews BJ (1998) A role for the Pcl9–Pho85 cyclin–cdk complex at the M/G1 boundary in Saccharomyces cerevisiae. Mol Microbiol 28:69–79PubMedGoogle Scholar
  339. Thevelein JM (1994) Signal transduction in yeast. Yeast 10:1753–1790PubMedGoogle Scholar
  340. Thevelein JM, Cauwenberg L, Colombo S, De Winde JH, Donation M, Dumortier F, Kraakman L, Lemaire K, Ma P, Nauwelaers D, Rolland F, Teunissen A, Van Dijck P, Versele M, Wera S, Winderickx J (2000) Nutrient-induced signal transduction through the protein kinase A pathway and its role in the control of metabolism, stress resistance, and growth in yeast. Enzyme Microb Technol 26:819–825PubMedGoogle Scholar
  341. Timblin BK, Tatchell K, Bergman LW (1996) Deletion of the gene encoding the cyclin-dependent protein kinase Pho85 alters glycogen metabolism in Saccharomyces cerevisiae. Genetics 143:57–66PubMedGoogle Scholar
  342. Toda T, Uno I, Ishikawa T, Powers S, Kataoka T, Broek D, Cameron S, Broach J, Matsumoto K, Wigler M (1985) In yeast, RAS proteins are controlling elements of adenylate cyclase. Cell 40:27–36PubMedGoogle Scholar
  343. Toda T, Cameron S, Sass P, Zoller M, Scott JD, McMullen B, Hurwitz M, Krebs EG, Wigler M (1987a) Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae. Mol Cell Biol 7:1371–1377PubMedGoogle Scholar
  344. Toda T, Cameron S, Sass P, Zoller M, Wigler M (1987b) Three different genes in S. cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase. Cell 50:277–287PubMedGoogle Scholar
  345. Toda T, Cameron S, Sass P, Wigler M (1988) SCH9, a gene of Saccharomyces cerevisiae that encodes a protein distinct from, but functionally and structurally related to, cAMP-dependent protein kinase catalytic subunits. Genes Dev 2:517–527PubMedGoogle Scholar
  346. Treitel MA, Carlson M (1995) Repression by SSN6-TUP1 is directed by MIG1, a repressor/activator protein. Proc Natl Acad Sci USA 92:3132–3136PubMedGoogle Scholar
  347. Treitel MA, Kuchin S, Carlson M (1998) Snf1 protein kinase regulates phosphorylation of the Mig1 repressor in Saccharomyces cerevisiae. Mol Cell Biol 18:6273–6280PubMedGoogle Scholar
  348. Tu J, Carlson M (1994) The GLC7 type 1 protein phosphatase is required for glucose repression in Saccharomyces cerevisiae. Mol Cell Biol 14:6789–6796PubMedGoogle Scholar
  349. Tu J, Carlson M (1995) REG1 binds to protein phosphatase type 1 and regulates glucose repression in Saccharomyces cerevisiae. EMBO J 14:5939–5946PubMedGoogle Scholar
  350. Tung KS, Norbeck LL, Nolan SL, Atkinson NS, Hopper AK (1992) SRN1, a yeast gene involved in RNA processing, is identical to HEX2/REG1, a negative regulator in glucose repression. Mol Cell Biol 12:2673–2680PubMedGoogle Scholar
  351. Uno I, Matsumoto K, Adachi K, Ishikawa T (1983) Genetic and biochemical evidence that trehalase is a substrate of cAMP-dependent protein kinase in yeast. J Biol Chem 258:10867–10872PubMedGoogle Scholar
  352. Urban J, Soulard A, Huber A, Lippman S, Mukhopadhyay D, Deloche O, Wanke V, Anrather D, Ammerer G, Riezman H, Broach JR, De Virgilio C, Hall MN, Loewith R (2007) Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell 26:663–674PubMedGoogle Scholar
  353. Valenzuela L, Aranda C, Gonzalez A (2001) TOR modulates GCN4-dependent expression of genes turned on by nitrogen limitation. J Bacteriol 183:2331–2334PubMedGoogle Scholar
  354. Van Hoof C, Janssens V, De Baere I, Stark MJ, de Winde JH, Winderickx J, Thevelein JM, Merlevede W, Goris J (2001) The Saccharomyces cerevisiae phosphotyrosyl phosphatase activator proteins are required for a subset of the functions disrupted by protein phosphatase 2A mutations. Exp Cell Res 264:372–387PubMedGoogle Scholar
  355. van Oevelen CJ, van Teeffelen HA, van Werven FJ, Timmers HT (2006) Snf1p-dependent Spt-Ada-Gcn5-acetyltransferase (SAGA) recruitment and chromatin remodeling activities on the HXT2 and HXT4 promoters. J Biol Chem 281:4523–4531PubMedGoogle Scholar
  356. van Zyl W, Huang W, Sneddon AA, Stark M, Camier S, Werner M, Marck C, Sentenac A, Broach JR (1992) Inactivation of the protein phosphatase 2A regulatory subunit A results in morphological and transcriptional defects in Saccharomyces cerevisiae. Mol Cell Biol 12:4946–4959PubMedGoogle Scholar
  357. Vanrobays E, Leplus A, Osheim YN, Beyer AL, Wacheul L, Lafontaine DL (2008) TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export. Rna 14:2061–2073PubMedGoogle Scholar
  358. Vaseghi S, Macherhammer F, Zibek S, Reuss M (2001) Signal transduction dynamics of the protein kinase-A/phosphofructokinase-2 system in Saccharomyces cerevisiae. Metab Eng 3:163–172PubMedGoogle Scholar
  359. Versele M, de Winde JH, Thevelein JM (1999) A novel regulator of G protein signalling in yeast, Rgs2, downregulates glucose-activation of the cAMP pathway through direct inhibition of Gpa2. EMBO J 18:5577–5591PubMedGoogle Scholar
  360. Vidan S, Mitchell AP (1997) Stimulation of yeast meiotic gene expression by the glucose-repressible protein kinase Rim15p. Mol Cell Biol 17:2688–2697PubMedGoogle Scholar
  361. Vincent O, Carlson M (1998) Sip4, a Snf1 kinase-dependent transcriptional activator, binds to the carbon source-responsive element of gluconeogenic genes. EMBO J 17:7002–7008PubMedGoogle Scholar
  362. Vincent O, Townley R, Kuchin S, Carlson M (2001) Subcellular localization of the Snf1 kinase is regulated by specific beta subunits and a novel glucose signaling mechanism. Genes Dev 15:1104–1114PubMedGoogle Scholar
  363. Wade JT, Hall DB, Struhl K (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432:1054–1058PubMedGoogle Scholar
  364. Wang Z, Wilson WA, Fujino MA, Roach PJ (2001) Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p. Mol Cell Biol 21:5742–5752PubMedGoogle Scholar
  365. 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:E128PubMedGoogle Scholar
  366. Wanke V, Pedruzzi I, Cameroni E, Dubouloz F, De Virgilio C (2005) Regulation of G0 entry by the Pho80–Pho85 cyclin–CDK complex. EMBO J 24:4271–4278PubMedGoogle Scholar
  367. Wanke V, Cameroni E, Uotila A, Piccolis M, Urban J, Loewith R, De Virgilio C (2008) Caffeine extends yeast lifespan by targeting TORC1. Mol Microbiol 69:277–285PubMedGoogle Scholar
  368. Wedaman KP, Reinke A, Anderson S, Yates J 3rd, McCaffery JM, Powers T (2003) Tor kinases are in distinct membrane-associated protein complexes in Saccharomyces cerevisiae. Mol Biol Cell 14:1204–1220PubMedGoogle Scholar
  369. Wei Y, Tsang CK, Zheng XF (2009) Mechanisms of regulation of RNA polymerase III-dependent transcription by TORC1. EMBO J 28:2220–2230PubMedGoogle Scholar
  370. Werner-Washburne M, Brown D, Braun E (1991) Bcy1, the regulatory subunit of cAMP-dependent protein kinase in yeast, is differentially modified in response to the physiological status of the cell. J Biol Chem 266:19704–19709PubMedGoogle Scholar
  371. Willis IM, Moir RD (2007) Integration of nutritional and stress signaling pathways by Maf1. Trends Biochem Sci 32:51–53PubMedGoogle Scholar
  372. Wilson RB, Tatchell K (1988) SRA5 encodes the low-Km cyclic AMP phosphodiesterase of Saccharomyces cerevisiae. Mol Cell Biol 8:505–510PubMedGoogle Scholar
  373. Wilson WA, Hawley SA, Hardie DG (1996) Glucose repression/derepression in budding yeast: SNF1 protein kinase is activated by phosphorylation under derepressing conditions, and this correlates with a high AMP:ATP ratio. Curr Biol 6:1426–1434PubMedGoogle Scholar
  374. Winderickx J, Holsbeeks I, Lagatie O, Giots F, Thevelein JM, de Winde H (2003) From feast to famine: adaptation to nutrient availability in yeast. In: Hohmann S, Mager PWH (eds) Topics in current genetics. Yeast stress response, vol 1. Springer, Heidelberg, pp 305–386Google Scholar
  375. Wingender-Drissen R, Becker JU (1983) Regulation of yeast phosphorylase by phosphorylase kinase and cAMP-dependent protein kinase. FEBS Lett 163:33–36PubMedGoogle Scholar
  376. Woods A, Munday MR, Scott J, Yang X, Carlson M, Carling D (1994) Yeast SNF1 is functionally related to mammalian AMP-activated protein kinase and regulates acetyl-CoA carboxylase in vivo. J Biol Chem 269:19509–19515PubMedGoogle Scholar
  377. Wullschleger S, Loewith R, Oppliger W, Hall MN (2005) Molecular organization of target of rapamycin complex 2. J Biol Chem 280:30697–30704PubMedGoogle Scholar
  378. Wurmser AE, Sato TK, Emr SD (2000) New component of the vacuolar class C-Vps complex couples nucleotide exchange on the Ypt7 GTPase to SNARE-dependent docking and fusion. J Cell Biol 151:551–562PubMedGoogle Scholar
  379. Wykoff DD, Rizvi AH, Raser JM, Margolin B, O’Shea EK (2007) Positive feedback regulates switching of phosphate transporters in S. cerevisiae. Mol Cell 27:1005–1013PubMedGoogle Scholar
  380. Wysocki R, Javaheri A, Kristjansdottir K, Sha F, Kron SJ (2006) CDK Pho85 targets CDK inhibitor Sic1 to relieve yeast G1 checkpoint arrest after DNA damage. Nat Struct Mol Biol 13:908–914PubMedGoogle Scholar
  381. Xia ZX, Ao SZ (1999) Analysis of interaction between PHO4 and PHO2 protein by real time BIA. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 31:145–149Google Scholar
  382. Xue Y, Batlle M, Hirsch JP (1998) GPR1 encodes a putative G protein-coupled receptor that associates with the Gpa2p Galpha subunit and functions in a Ras-independent pathway. EMBO J 17:1996–2007PubMedGoogle Scholar
  383. Yan G, Shen X, Jiang Y (2006) Rapamycin activates Tap42-associated phosphatases by abrogating their association with Tor complex 1. EMBO J 25:3546–3555PubMedGoogle Scholar
  384. Yang X, Jiang R, Carlson M (1994) A family of proteins containing a conserved domain that mediates interaction with the yeast SNF1 protein kinase complex. EMBO J 13:5878–5886PubMedGoogle Scholar
  385. Yorimitsu T, Klionsky DJ (2005) Autophagy: molecular machinery for self-eating. Cell Death Differ 12(Suppl 2):1542–1552PubMedGoogle Scholar
  386. Yorimitsu T, Zaman S, Broach JR, Klionsky DJ (2007) Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae. Mol Biol Cell 18:4180–4189PubMedGoogle Scholar
  387. Yorimitsu T, He C, Wang K, Klionsky DJ (2009) Tap42-associated protein phosphatase type 2A negatively regulates induction of autophagy. Autophagy 5:616–624Google Scholar
  388. Yun CW, Tamaki H, Nakayama R, Yamamoto K, Kumagai H (1997) G-protein coupled receptor from yeast Saccharomyces cerevisiae. Biochem Biophys Res Commun 240:287–292PubMedGoogle Scholar
  389. Zabrocki P, Van Hoof C, Goris J, Thevelein JM, Winderickx J, Wera S (2002) Protein phosphatase 2A on track for nutrient-induced signalling in yeast. Mol Microbiol 43:835–842PubMedGoogle Scholar
  390. Zaman S, Lippman SI, Zhao X, Broach JR (2008) How Saccharomyces responds to nutrients. Annu Rev Genet 42:27–81PubMedGoogle Scholar
  391. Zappacosta F, Huddleston MJ, Karcher RL, Gelfand VI, Carr SA, Annan RS (2002) Improved sensitivity for phosphopeptide mapping using capillary column HPLC and microionspray mass spectrometry: comparative phosphorylation site mapping from gel-derived proteins. Anal Chem 74:3221–3231PubMedGoogle Scholar
  392. Zeller CE, Parnell SC, Dohlman HG (2007) The RACK1 ortholog Asc1 functions as a G-protein beta subunit coupled to glucose responsiveness in yeast. J Biol Chem 282:25168–25176PubMedGoogle Scholar
  393. Zhang F, Kirouac M, Zhu N, Hinnebusch AG, Rolfes RJ (1997) Evidence that complex formation by Bas1p and Bas2p (Pho2p) unmasks the activation function of Bas1p in an adenine-repressible step of ADE gene transcription. Mol Cell Biol 17:3272–3283PubMedGoogle Scholar
  394. Zhang N, Wu J, Oliver SG (2009) Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast. Microbiology 155:1690–1698PubMedGoogle Scholar
  395. Zhao Y, Boguslawski G, Zitomer RS, DePaoli-Roach AA (1997) Saccharomyces cerevisiae homologs of mammalian B and B’ subunits of protein phosphatase 2A direct the enzyme to distinct cellular functions. J Biol Chem 272:8256–8262PubMedGoogle Scholar
  396. Zhao Y, McIntosh KB, Rudra D, Schawalder S, Shore D, Warner JR (2006) Fine-structure analysis of ribosomal protein gene transcription. Mol Cell Biol 26:4853–4862PubMedGoogle Scholar
  397. Zheng Y, Jiang Y (2005) The yeast phosphotyrosyl phosphatase activator is part of the Tap42-phosphatase complexes. Mol Biol Cell 16:2119–2127PubMedGoogle Scholar
  398. Zheng XF, Florentino D, Chen J, Crabtree GR, Schreiber SL (1995) TOR kinase domains are required for two distinct functions, only one of which is inhibited by rapamycin. Cell 82:121–130PubMedGoogle Scholar
  399. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M (2000) Analysis of yeast protein kinases using protein chips. Nat Genet 26:283–289PubMedGoogle Scholar
  400. Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19:556–566PubMedGoogle Scholar
  401. Zimmermann FK, Scheel I (1977) Mutants of Saccharomyces cerevisiae resistant to carbon catabolite repression. Mol Gen Genet 154:75–82PubMedGoogle Scholar
  402. Zurita-Martinez SA, Puria R, Pan X, Boeke JD, Cardenas ME (2007) Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae. Genetics 176:2139–2150PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Bart Smets
    • 1
  • Ruben Ghillebert
    • 1
  • Pepijn De Snijder
    • 1
  • Matteo Binda
    • 2
  • Erwin Swinnen
    • 1
  • Claudio De Virgilio
    • 2
  • Joris Winderickx
    • 1
  1. 1.Laboratory of Functional BiologyKatholieke Universiteit LeuvenHeverleeBelgium
  2. 2.Division of Biochemistry, Department of MedicineUniversity of FribourgFribourgSwitzerland

Personalised recommendations