Mitochondrial retrograde signaling

Annual Review of Genetics

Volumn 40, Issue , 2006, Pages 159-185

  Liu, Zhengchang ^a   Butow, Ronald A ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Mitochondria; Nutrient sensing; Retrograde response; RTG pathway; Signaling

Indexed keywords

ADENOSINE TRIPHOSPHATE; GLUTAMIC ACID; HELIX LOOP HELIX PROTEIN; MITOCHONDRIAL DNA; NICOTINAMIDE ADENINE DINUCLEOTIDE; REACTIVE OXYGEN METABOLITE; TARGET OF RAPAMYCIN KINASE; UBIQUITIN PROTEIN LIGASE E3;

AGING; CATABOLITE REPRESSION; CITRIC ACID CYCLE; GENE EXPRESSION; GENETIC CONSERVATION; MITOCHONDRION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; NUTRIENT; OXIDATIVE PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; REVIEW; RNA INTERFERENCE; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

CELL AGING; CELL NUCLEUS; DNA, MITOCHONDRIAL; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; METABOLIC NETWORKS AND PATHWAYS; MITOCHONDRIA; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 33845656956     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.40.110405.090613     Document Type: Review

References (150)

1. Bakker BM, Bro C, Kotter P, Luttik MA, van Dijken JP, Pronk JT. 2000. The mitochondrial alcohol dehydrogenase Adh3p is involved in a redox shuttle in Saccbaramyces cerevisiae. J. Bacteriol. 182:4730-37
2. Balzi E, Goffeau A. 1995. Yeast multidrug resistance: the PDR network. J. Bioenerg. Biomembr. 27:71-76
3. Balzi E, Wang M, Leterme S, Van Dyck L, Goffeau A. 1994. PDR5, a novel yeast multidrug resistance conferring transporter controlled by the transcription regulator PDR1. J. Biol. Chem. 269:2206-14
4. Barral Y, Jentsch S, Mann C. 1995. G1 cyclin turnover and nutrient uptake are controlled by a common pathway in yeast. Genes Dev. 9:399-409
5. Bhattacharyya S, Rolfsmeierv ML, Dixon MJ, Wagoner K, Lahue RS. 2002. Identification of RTG2 as a modifier gene for CTG*CAG repeat instability in Saccbaromyces cerevisiae. Genetics 162:579-89
6. Bissinger PH, Kuchler K. 1994. Molecular cloning and expression of the Saccharomyces cerevisiae STS1 gene product. A yeast ABC transporter conferring mycotoxin resistance. J. Biol. Chem. 269:4180-86
7. 2+ signaling in C2C12 skeletal myocytes in response to mitochondrial genetic and metabolic stress: a novel mode of interorganelle crosstalk. EMBO J. 18:522-33
8. Biswas G, Anandatheerthavarada HK, Zaidi M, Avadhani NG. 2003. Mitochondria to nucleus stress signaling: a distinctive mechanism of NFκB/Rel activation through calcineurin-mediated inactivation of IκBbeta. J. Cell Biol. 161:507-19
9. Borghouts C, Benguria A, Wawryn J, Jazwinski SM. 2004. Rtg2 protein links metabolism and genome stability in yeast longevity. Genetics 166:765-77
10. Bork P, Sander C, Valencia A. 1992. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. USA 89:7290-4
11. Burns N, Grimwade B, Ross-Macdonald PB, Choi EY, Finberg K, et al. 1994. Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8:1087-105
12. Butow RA, Avadhani NG. 2004. Mitochondrial signaling: the retrograde response. Mol. Cell 14:1-15
13. 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. 13:3271-79
14. Chelstowska A, Butow RA. 1995. RTG genes in yeast that function in communication between mitochondria and the nucleus are also required for expression of genes encoding peroxisomal proteins. J. Biol. Chem. 270:18141-46
15. Chelstowska A, Liu Z, Jia Y, Amberg D, Butow RA. 1999. Signalling between mitochondria and the nucleus regulates the expression of a new D-lactate dehydrogenase activity in yeast. Yeast 15:1377-91
16. 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 99:14837-42
17. Chen EJ, Kaiser CA. 2003. LST8 negatively regulates amino acid biosynthesis as a component of the TOR pathway. J. Cell Biol. 161:333-47
18. Chen XJ, Butow RA. 2005. The organization and inheritance of the mitochondrial genome. Nat. Rev. Genet. 6:815-25
19. Chen XJ, Wang X, Kaufman BA, Butow RA. 2005. Aconitase couples metabolic regulation to mitochondrial DNA maintenance. Science 307:714-17
20. Conlan RS, Gounalaki N, Hatzis P, Tzamarias D. 1999. The Tupl-Cyc8 protein complex can shift from a transcriptional corepressor to a transcriptional coactivator. J. Biol. Chem. 274:205-10
21. Conrad-Webb H, Butow RA. 1995. A polymerase switch in the synthesis of rRNA in Saccharomyces cerevisiae. Mol. Cell Biol. 15:2420-28
22. 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 99:6784-89
23. Dennis PB, Jaeschke A, Saitoh M, Fowler B, Kozma SC, Thomas G. 2001. Mammalian TOR: a homeostatic ATP sensor. Science 294:1102-5
24. Deshaies RJ. 1999. SCF and Cullin/Ring H2-based ubiquitin ligases. Annu. Rev. Cell Dev. Biol. 15:435-67
25. Devaux F, Carvajal E, Moye-Rowley S, Jacq C. 2002. Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast. FEBS Lett. 515:25-28
26. Dillin A, Hsu AL, Arantes-Oliveira N, Lehrer-Graiwer J, Hsin H, et al. 2002. Rates of behavior and aging specified by mitochondrial function during development. Science 298:2398-401
27. 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. 279:46527-35
28. Dilova I, Chen CY, Powers T. 2002. Mks1 in concert with TOR signaling negatively regulates RTG target gene expression in S. cerevisiae. Curr. Biol. 12:389-95
29. Dougherty MK, Morrison DK. 2004. Unlocking the code of 14-3-3. J. Cell Sci. 117:1875-84
30. Edskes HK, Wickner RB. 2000. A protein required for prion generation: [URE3] induction requires the Ras-regulated Mks1 protein. Proc. Natl. Acad. Sci. USA 97:6625-29
31. Eisenstein RS. 2000. Iron regulatory proteins and the molecular control of mammalian iron metabolism. Annu. Rev. Nutr. 20:627-62
32. Elgersma Y, van Roermund CW, Wanders RJ, Tabak HF. 1995. Peroxisomal and mitochondrial carnitine acetyltransferases of Saccharomyces cerevisiae are encoded by a single gene. EMBO J. 14:3472-79
33. Epstein CB, Waddle JA, Hale W IV, Davé V, Thornton J, et al. 2001. Genome-wide responses to mitochondrial dysfunction. Mol. Biol. Cell 12:297-308
34. Felkai S, Ewbank JJ, Lemieux J, Labbe JC, Brown GG, Hekimi S. 1999. CLK-1 controls respiration, behavior and aging in the nematode Caenorhabditis elegans. EMBO J. 18:1783-92
35. 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. 14:6411-18
36. Feller A, Ramos F, Pierard A, Dubois E. 1997. Lys80p of Saccharomyces cerevisiae, previously proposed as a specific repressor of LYS genes, is a pleiotropic regulatory factor identical to Mks1p. Yeast 13:1337-46
37. Flick KM, Spielewoy N, Kalashnikova TI, Guaderrama M, Zhu Q, et al. 2003. Grr1-dependent inactivation of Mth1 mediates glucose-induced dissociation of Rgt1 from HXT gene promoters. Mol. Biol. Cell 14:3230-41
38. Forsberg H, Ljungdahl PO. 2001. Sensors of extracellular nutrients in Saccharomyces cerevisiae. Curr. Genet. 40:91-109
39. Forsburg SL, Guarente L. 1989. Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev. 3:1166-78
40. Foury F, Roganti T, Lecrenier N, Purnelle B. 1998. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 440:325-31
41. +-dependent isocitrate dehydrogenase can be suppressed by mutations in the CIT1 gene encoding citrate synthase and other genes of oxidative metabolism. Arch. Biochem. Biophys. 344:139-49
42. Gangloff SP, Marguet D, Lauquin GJ. 1990. Molecular cloning of the yeast mitochondrial aconitase gene (ACO1) and evidence of a synergistic regulation of expression by glucose plus glutamate. Mol. Cell Biol. 10:3551-61
43. Gelperin D, Weigle J, Nelson K, Roseboom P, Irie K, et al. 1995. 14-3-3 proteins: potential roles in vesicular transport and Ras signaling in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 92:11539-43
44. Giannattasio S, Liu Z, Thornton J, Butow RA. 2005. Retrograde response to mitochondrial dysfunction is separable from TOR1/2 regulation of retrograde gene expression. J. Biol. Chem. 280:42528-35
45. Grant PA, Sterner DE, Duggan LJ, Workman JL, Berger SL. 1998. The SAGA unfolds: convergence of transcription regulators in chromatin-modifying complexes. Trends Cell Biol. 8:193-97
46. Guaragnella N, Butow RA. 2003. ATO3 encoding a putative outward ammonium transporter is an RTG-independent retrograde responsive gene regulated by GCN4 and the Ssy1-Ptr3-Ssy5 amino acid sensor system. J. Biol. Chem. 278:45882-87
47. Hallstrom TC, Moye-Rowley WS. 2000. Multiple signals from dysfunctional mitochondria activate the pleiotropic drug resistance pathway in Saccharomyces cerevisiae. J. Biol. Chem. 275:37347-56
48. Hamilton B, Dong Y, Shindo M, Liu W, Odell I, et al. 2005. A systematic RNAi screen for longevity genes in C. elegans. Genes Dev. 19:1544-55
49. Hampsey M. 1997. A SAGA of histone acetylation and gene expression. Trends Genet. 13:427-29
50. Hao B, Zheng N, Schulman BA, Wu G, Miller JJ, et al. 2005. Structural basis of the Cks1-dependent recognition of p27(Kip1) by the SCF(Skp2) ubiquitin ligase. Mol. Cell 20:9-19
51. Hara K, Manila Y, Long X, Yoshino K, Oshiro N, et al. 2002. Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110:177-89
52. Haselbeck RJ, McAlister-Henn L. 1993. Function and expression of yeast mitochondrial NAD- and NADP-specific isocitrate dehydrogenases. J. Biol. Chem. 268:12116-22
53. Haviernik P, Laquin GJ. 1996. ACO1 expression in Saccharomyces cerevisiae is regulated by the HAP complex. Folia Microbiol. 41:96-98
54. Hekimi S, Guarente L. 2003. Genetics and the specificity of the aging process. Science 299:1351-54
55. Hentze MW, Muckenthaler MU, Andrews NC. 2004. Balancing acts: molecular control of mammalian iron metabolism. Cell 117:285-97
56. Hershko A. 2005. The ubiquitin system for protein degradation and some of its roles in the control of the cell division cycle. Cell Death Differ. 12:1191-97
57. Hsiung YG, Chang HC, Pellequer JL, La Valle R, Lanker S, Wittenberg C. 2001. F-box protein Grr1 interacts with phosphorylated targets via the cationic surface of its leucine-rich repeat. Mol. Cell Biol. 21:2506-20
58. Hurley JH. 1996. The sugar kinase/heat shock protein 70/actin superfamily: implications of conserved structure for mechanism. Annu. Rev. Biophys. Biomol. Struct. 25:137-62
59. Hwang WW, Venkatasubrahmanyam S, Ianculescu AG, Tong A, Boone C, Madhani HD. 2003. A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Mol. Cell 11:261-66
60. Jazwinski SM. 2005. The retrograde response links metabolism with stress responses, chromatin-dependent gene activation, and genome stability in yeast aging. Gene 354:22-27
61. Jazwinski SM, Chen JB, Sun J. 1993. A single gene change can extend yeast life span: the role of Ras in cellular senescence. Adv. Exp. Med. Biol. 330:45-53
62. Jia Y, Rothermel B, Thornton J, Butow RA. 1997. A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol. Cell Biol. 17:1110-17
63. Jiang JC, Jaruga E, Repnevskaya MV, Jazwinski SM. 2000. An intervention resembling caloric restriction prolongs life span and retards aging in yeast. FASEB J. 14:2135-37
64. Kaplan RS, Mayor JA, Kakhniashvili D, Gremse DA, Wood DO, Nelson DR. 1996. Deletion of the nuclear gene encoding the mitochondrial citrate transport protein from Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 226:657-62
65. Katzmann DJ, Burnett PE, Golin J, Mahe Y, Moye-Rowley WS. 1994. Transcriptional control of the yeast PDR5 gene by the PDR3 gene product. Mol. Cell Biol. 14:4653-61
66. Kaufman BA, Newman SM, Hallberg RL, Slaughter CA, Perlman PS, Butow RA. 2000. In organello formaldehyde crosslinking of proteins to mtDNA: identification of bifunctional proteins. Proc. Natl. Acad. Sci. USA 97:7772-77
67. Kennedy ET. 2006. Evidence for nutritional benefits in prolonging wellness. Am. J. Clin. Nutr. 83:410S-14S
68. Kim DH, Sarbassov DD, Ali SM, King JE, Latek RR, et al. 2002. mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110:163-75
69. Kim DH, Sarbassov DD, Ali SM, Latek RR, Guntur KV, et al. 2003. GbetaL, a positive regulator of the rapamycin-sensitive pathway required for the nutrient-sensitive interaction between raptor and mTOR. Mol. Cell 11:895-904
70. Kim JH, Brachet V, Moriya H, Johnston M. 2006. Integration of transcriptional and posttranslational regulation in a glucose signal transduction pathway in Saccharomyces cerevisiae. Eukaryot. Cell 5:167-73
71. Kim KS, Rosenkrantz MS, Guarente L. 1986. Saccharomyces cerevisiae contains two functional citrate synthase genes. Mol. Cell Biol. 6:1936-42
72. Kim SJ, Swanson MJ, Qiu H, Govind CK, Hinnebusch AG. 2005. Activator Gcn4p and Cyc8p/Tup1p are interdependent for promoter occupancy at ARG1 in vivo. Mol. Cell Biol. 25:11171-83
73. Kirchman PA, Kim S, Lai CY, Jazwinski SM. 1999. Interorganelle signaling is a determinant of longevity in Saccharomyces cerevisiae. Genetics 152:179-90
74. Kobe B, Deisenhofer J. 1995. A structural basis of the interactions between leucine-rich repeats and protein ligands. Nature 374:183-86
75. 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. 151:863-78
76. Koonin EV. 1994. Yeast protein controlling interorganelle communication is related to bacterial phosphatases containing the Hsp 70-type ATP-binding domain. Trends Biochem. Sci. 19:156-57
77. Kristensen O, Laurberg M, Liljas A, Kastrup JS, Gajhede M. 2004. Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry 43:8894-900
78. Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J, Ruvkun G. 2003. A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat. Genet. 33:40-48
79. Liao X, Butow RA. 1993. RTG1 and RTG2: two yeast genes required for a novel path of communication from mitochondria to the nucleus. Cell 72:61-71
80. Liao XS, Small WC, Srere PA, Butow RA. 1991. Intramitochondrial functions regulate nonmitochondrial citrate synthase (CIT2) expression in Saccharomyces cerevisiae. Mol. Cell Biol. 11:38-46
81. Lin SJ, Defossez PA, Guarente L. 2000. Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae. Science 289:2126-28
82. Liu X, Jiang N, Hughes B, Bigras E, Shoubridge E, Hekimi S. 2005. Evolutionary conservation of the clk-1-dependent mechanism of longevity: loss of mclk1 increases cellular fitness and lifespan in mice. Genes Dev. 19:2424-34
83. Liu Z, Butow RA. 1999. A transcriptional switch in the expression of yeast tricarboxylic acid cycle genes in response to a reduction or loss of respiratory function. Mol. Cell Biol. 19:6720-28
84. Liu Z, Sekito T, Epstein CB, Butow RA. 2001. RTG-dependent mitochondria to nucleus signaling is negatively regulated by the seven WD-repeat protein Lst8p. EMBO J. 20:7209-19
85. 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 12:401-11
86. Grr1. Mol. Biol. Cell 16:4893-904
87. Loewith R, Jacinto E, Wullschleger S, Lorberg A, Crespo JL, et al. 2002. Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control. Mol. Cell 10:457-68
88. Luo Y, Bond JD, Ingrain VM. 1997. Compromised mitochondrial function leads to increased cytosolic calcium and to activation of MAP kinases. Proc. Natl. Acad. Sci. USA 94:9705-10
89. Magasanik B, Kaiser CA. 2002. Nitrogen regulation in Saccharomyces cerevisiae. Gene 290:1-18
90. Massari ME, Grant PA, Pray-Grant MG, Berger SL, Workman JL, Murre C. 1999. A conserved motif present in a class of helix-loop-helix proteins activates transcription by direct recruitment of the SAGA complex. Mol. Cell 4:63-73
91. Massari ME, Jennings PA, Murre C. 1996. The AD1 transactivation domain of E2A contains a highly conserved helix which is required for its activity in both Saccharomyces cerevisiae and mammalian cells. Mol. Cell Biol. 16:121-29
92. Massari ME, Murre C. 2000. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell Biol. 20:429-40
93. Matsuura A, Anraku Y. 1993. Characterization of the MKS1 gene, a new negative regulator of the Ras-cyclic AMP pathway in Saccharomyces cerevisiae. Mol. Gen. Genet. 238:6-16
94. Mayer RJ. 2000. The meteoric rise of regulated intracellular proteolysis. Nat. Rev. Mol. Cell Biol. 1:145-48
95. McCammon MT, Epstein CB, Przybyla-Zawislak B, McAlister-Henn L, Butow RA. 2003. Global transcription analysis of Krebs tricarboxylic acid cycle mutants reveals an alternating pattern of gene expression and effects on hypoxic and oxidative genes. Mol. Biol. Cell 14:958-72
96. Mortimer RK, Johnston JR. 1959. Life span of individual yeast cells. Nature 183:1751-52
97. Moye-Rowley WS. 2005. Retrograde regulation of multidrug resistance in Saccharomyces cerevisiae. Gene 354:15-21
98. Nash P, Tang X, Orlicky S, Chen Q, Gertler FB, et al. 2001. Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication. Nature 414:514-21
99. Neer EJ, Schmidt CJ, Nambudripad R, Smith TF. 1994. The ancient regulatory-protein family of WD-repeat proteins. Nature 371:297-300
100. Nissen TL, Schulze U, Nielsen J, Villadsen J. 1997. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 143(Part 1):203-18
101. Olesen JT, Guarente L. 1990. The HAP2 subunit of yeast CCAAT transcriptional activator contains adjacent domains for subunit association and DNA recognition: model for the HAP2/3/4 complex. Genes Dev. 4:1714-29
102. Orlicky S, Tang X, Willems A, Tyers M, Sicheri F. 2003. Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase. Cell 112:243-56
103. Palkova Z, Devaux F, Icicova M, Minarikova L, Le Crom S, Jacq C. 2002. Ammonia pulses and metabolic oscillations guide yeast colony development. Mol. Biol. Cell 13:3901-14
104. Palkova Z, Janderova B, Gabriel J, Zikanova B, Pospisek M, Forstova J. 1997. Ammonia mediates communication between yeast colonies. Nature 390:532-36
105. Palmieri L, Lasorsa FM, Vozza A, Agrimi G, Fiermonte G, et al. 2000. Identification and functions of new transporters in yeast mitochondria. Biochim. Biophys. Acta 1459:363-69
106. Parikh VS, Morgan MM, Scott R, Clements LS, Butow RA. 1987. The mitochondrial genotype can influence nuclear gene expression in yeast. Science 235:576-80
107. Pray-Grant MG, Schieltz D, McMahon SJ, Wood JM, Kennedy EL, et al. 2002. The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol. Cell Biol. 22:8774-86
108. Przybyla-Zawislak B, Gadde DM, Ducharme K, McCammon MT. 1999. Genetic and biochemical interactions involving tricarboxylic acid cycle (TCA) function using a collection of mutants defective in all TCA cycle genes. Genetics 152:153-66
109. Quong MW, Massari ME, Zwart R, Murre C. 1993. A new transcriptional- activation motif restricted to a class of helix-loop-helix proteins is functionally conserved in both yeast and mammalian cells. Mol. Cell Biol. 13:792-800
110. Ramos F, Dubois E, Pierard A. 1988. Control of enzyme synthesis in the lysine biosynthetic pathway of Saccharomyces cerevisiae. Evidence for a regulatory role of gene LYS14. Eur. J. Biochem. 171:171-76
111. Ramos F, Wiame JM. 1985. Mutation affecting the specific regulatory control of lysine biosynthetic enzymes in Saccharomyces cerevisiae. Mol. Gen. Genet. 200:291-94
112. Regenberg B, Holmberg S, Olsen LD, Kielland-Brandt MC. 1998. Dip5p mediates high-affinity and high-capacity transport of L-glutamate and L-aspartate in Saccharomyces cerevisiae. Curr. Genet. 33:171-77
113. Reinke A, Anderson S, McCaffery JM, Yates J, Aronova S, et al. 2004. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae. J. Biol. Chem. 279:14752-62
114. Roberg KJ, Bickel S, Rowley N, Kaiser CA. 1997. Control of amino acid permease sorting in the late secretory pathway of Saccharomyces cerevisine by SEC13, LST4, LST7 and LST8. Genetics 147:1569-84
115. Roberg KJ, Rowley N, Kaiser CA. 1997. Physiological regulation of membrane protein sorting late in the secretory pathway of Saccharomyces cerevisiae. J. Cell Biol. 137:1469-82
116. Roberts RL, Mosch HU, Fink GR. 1997. 14-3-3 proteins are essential for RAS/MAPK cascade signaling during pseudohyphal development in S. cerevisiae. Cell 89:1055-65
117. Rodal AA, Tetreault JW, Lappalainen P, Drubin DG, Amberg DC. 1999. Aip1p interacts with cofilin to disassemble actin filaments. J. Cell Biol. 145:1251-64
118. Rosenkrantz M, Kell CS, Pennell EA, Devenish LJ. 1994. The HAP2,3,4 transcriptional activator is required for derepression of the yeast citrate synthase gene, CIT1. Mol. Microbiol. 13:119-31
119. Rosenkrantz M, Kell CS, Pennell EA, Webster M, Devenish LJ. 1994. Distinct upstream activation regions for glucose-repressed and derepressed expression of the yeast citrate synthase gene CIT1. Curr. Genet. 25:185-95
120. Rothermel BA, Thornton JL, Butow RA. 1997. Rtg3p, a basic helix-loop-helix/leucine zipper protein that functions in mitochondrial-induced changes in gene expression, contains independent activation domains. J. Biol. Chem. 272:19801-7
121. Sekito T, Liu Z, Thornton J, Butow RA. 2002. RTG-dependent mitochondria-to-nucleus signaling is regulated by MKS1 and is linked to formation of yeast priori [URE3]. Mol. Biol. Cell 13:795-804
122. Sekito T, Thornton J, Butow RA. 2000. Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p. Mol. Biol. Cell 11:2103-15
123. Shamji AF, Kuruvilla FG, Schreiber SL. 2000. Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr. Biol. 10:1574-81
124. Sinclair DA. 2005. Toward a unified theory of caloric restriction and longevity regulation. Mech. Ageing Oev. 126:987-1002
125. Sinclair DA, Guarente L. 1997. Extrachromosomal rDNA circles-a cause of aging in yeast. Cell 91:1033-42
126. Smith TF, Gaitatzes C, Saxena K, Neer EJ. 1999. The WD repeat: a common architecture for diverse functions. Trends Biochem. Sci. 24:181-85
127. Grr1 targets in the glucose and amino acid signaling pathways. Mol. Cell Biol. 24:8994-9005
128. Sun J, Kale SP, Childress AM, Pinswasdi C, Jazwinski SM. 1994. Divergent roles of RAS1 and RAS2 in yeast longevity. J. Biol. Chem. 269:18638-45
129. Swiegers JH, Dippenaar N, Pretorius IS, Bauer FF. 2001. Carnitine-dependent metabolic activities in Saccharomyces cerevisiae: three carnitine acetyltransferases are essential in a carnitine-dependent strain. Yeast. 18:585-95
130. Tate JJ, Cooper TG. 2003. Tor1/2 regulation of retrograde gene expression in Saccharomyces cerevisiae derives indirectly as a consequence of alterations in ammonia metabolism. J. Biol. Chem. 278:36924-33
131. 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. 277:20477-82
132. Traven A, Wong JM, Xu D, Sopta M, Ingles CJ. 2001. Interorganellar communication. Altered nuclear gene expression profiles in a yeast mitochondrial DNA mutant. J. Biol. Chem. 276:4020-27
133. Tzivion G, Avruch J. 2002. 14-3-3 proteins; active cofactors in cellular regulation by serine/threonine phosphorylation. J. Biol. Chem. 277:3061-64
134. van Heusden GP, Griffiths DJ, Ford JC, Chin AWTF, Schrader PA, et al. 1995. The 14-3-3 proteins encoded by the BMH1 and BMH2 genes are essential in the yeast Saccharomyces cerevisiae and can be replaced by a plant homologue. Eur. J. Biochem. 229:45-53
135. van Heusden GP, Steensma HY. 2001. 14-3-3 Proteins are essential for regulation of RTG3-dependent transcription in Saccharomyces cerevisiae. Yeast 18:1479-91
136. van Roermund CW, Elgersma Y, Singh N, Wanders RJ, Tabak HF. 1995. The membrane of peroxisomes in Saccharomyces cerevisiae is impermeable to NAD(H) and acetyl-CoA under in vivo conditions. EMBO J. 14:3480-86
137. van Roermund CW, Hettema EH, van den Berg M, Tabak HF, Wanders RJ. 1999. Molecular characterization of carnitine-dependent transport of acetyl-CoA from peroxisomes to mitochondria in Saccharomyces cerevisiae and identification of a plasma membrane carnitine transporter, Agp2p. EMBO J. 18:5843-52
138. Varshavsky A. 2006. The early history of the ubiquitin field. Protein Sci. 15:647-54
139. Velot C, Haviernik P, Lauquin GJ. 1996. The Saccharomyces cerevisiae RTG2 gene is a regulator of aconitase expression under catabolite repression conditions. Genetics 144:893-903
140. Verma R, Annan RS, Huddleston MJ, Carr SA, Reynard G, Deshaies RJ. 1997. Phosphorylation of Sic1p by G1 Cdk required for its degradation and entry into S phase. Science 278:455-60
141. Wedaman KP, Reinke A, Anderson S, Yates J, McCaffery JM, Powers T. 2003. Tor kinases are in distinct membrane-associated protein complexes in Saccharomyces cerevisiae. Mol. Biol. Cell 14:1204-20
142. Willems AR, Goh T, Taylor L, Chernushevich I, Shevchenko A, Tyers M. 1999. SCF ubiquitin protein ligases and phosphorylation-dependentproteolysis. Philos. Trans. R. Soc. London Ser. B 354:1533-50
143. Wu G, Xu G, Schulman BA, Jeffrey PD, Harper JW, Pavletich NP. 2003. Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase. Mol. Cell 11:1445-56
144. Wullschleger S, Loewith R, Hall MN. 2006. TOR signaling in growth and metabolism. Cell 124:471-84
145. Wullschleger S, Loewith R, Oppliger W, Hall MN. 2005. Molecular organization of target of rapamycin complex 2. J. Biol. Chem. 280:30697-704
146. Yaffe MB, Rittinger K, Volinia S, Caron PR, Aitken A, et al. 1997. The structural basis for 14-3-3:phosphopeptide binding specificity. Cell 91:961-71
147. Zhang L, Hach A. 1999. Molecular mechanism of heme signaling in yeast: the transcriptional activator Hap1 serves as the key mediator. Cell Mol. Life Sci. 56:415-26
148. Zhang X, Kolaczkowska A, Devaux F, Panwar SL, Hallstrom TC, et al. 2005. Transcriptional regulation by Lge1p requires a function independent of its role in histone H2B ubiquitination. J. Biol. Chem. 280:2759-70
149. Zhang X, Moye-Rowley WS. 2001. Saccharomyces cerevisiae multidrug resistance gene expression inversely correlates with the status of the F(0) component of the mitochondrial ATPase. J. Biol. Chem. 276:47844-52
150. Zikanova B, Kuthan M, Ricicova M, Forstova J, Palkova Z. 2002. Amino acids control ammonia pulses in yeast colonies. Biochem. Biophys. Res. Commun. 294:962-67