Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae

REFERENCES

• Abdel-Sater, F., I. Iraqui, A. Urrestarazu, and B. Andre. 2004. The external amino acid signaling pathway promotes activation of Stp1 and Uga35/Dal81 transcription factors for induction of the AGP1 gene in Saccharomyces cerevisiae. Genetics 166:1727–1739.
   PubMedGoogle Scholar
• Andre, B. 1990. The UGA3 gene regulating the GABA catabolic pathway in Saccharomyces cerevisiae codes for a putative zinc-finger protein acting on RNA amount. Mol. Gen. Genet. 220:269–276.
   PubMedGoogle Scholar
• Andre, B., C. Hein, M. Grenson, and J. C. Jauniaux. 1993. Cloning and expression of the UGA4 gene coding for the inducible GABA-specific transport protein of Saccharomyces cerevisiae. Mol. Gen. Genet. 237:17–25.
   PubMedGoogle Scholar
• Andre, B., D. Talibi, S. Soussi Boudekou, C. Hein, S. Vissers, and D. Coornaert. 1995. Two mutually exclusive regulatory systems inhibit UASGATA, a cluster of 5′-GAT(A/T)A-3′ upstream from the UGA4 gene of Saccharomyces cerevisiae. Nucleic Acids Res. 23:558–564.
   PubMedGoogle Scholar
• Andreasson, C., and P. O. Ljungdahl. 2002. Receptor-mediated endoproteolytic activation of two transcription factors in yeast. Genes Dev. 16:3158–3172.
   PubMed Web of Science ®Google Scholar
• Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25–29.
   PubMed Web of Science ®Google Scholar
• Bar-Joseph, Z., G. K. Gerber, T. I. Lee, N. J. Rinaldi, J. Y. Yoo, F. Robert, D. B. Gordon, E. Fraenkel, T. S. Jaakkola, R. A. Young, and D. K. Gifford. 2003. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21:1337–1342.
   PubMed Web of Science ®Google Scholar
• Béchet, J., M. Grenson, and J. M. Wiame. 1970. Mutations affecting the repressibility of arginine biosynthetic enzymes in Saccharomyces cerevisiae. Eur. J. Biochem. 12:31–39.
   PubMedGoogle Scholar
• Beck, T., and M. N. Hall. 1999. The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature 402:689–692.
   PubMed Web of Science ®Google Scholar
• Becker, B., A. Feller, M. el Alami, E. Dubois, and A. Pierard. 1998. A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p-mediated activation and apparent repression by lysine. Mol. Microbiol. 29:151–163.
   PubMedGoogle Scholar
• Bernard, F., and B. Andre. 2001. Genetic analysis of the signalling pathway activated by external amino acids in Saccharomyces cerevisiae. Mol. Microbiol. 41:489–502.
   PubMed Web of Science ®Google Scholar
• Boczko, E. M., T. G. Cooper, T. Gedeon, K. Mischaikow, D. G. Murdock, S. Pratap, and K. S. Wells. 2005. Structure theorems and the dynamics of nitrogen catabolite repression in yeast. Proc. Natl. Acad. Sci. USA. 102:5647–5652.
   PubMed Web of Science ®Google Scholar
• Boer, V. M., J. M. Daran, M. J. Almering, J. H. Winde, and J. T. Pronk. 2005. Contribution of the Saccharomyces cerevisiae transcriptional regulator Leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures. FEMS Yeast Res. 5:885–897.
   PubMed Web of Science ®Google Scholar
• Boer, V. M., J. H. Winde, J. T. Pronk, and M. D. Piper. 2003. The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J. Biol. Chem. 278:3265–3274.
   PubMed Web of Science ®Google Scholar
• Boles, E., and B. Andre. 2004. Role of transporter-like sensors in glucose and amino acid signalling in yeast, p. 121–153. In E. Boles and K. Reinhard (ed.), Molecular mechanisms controlling transmembrane transport. Springer, Berlin, Germany.
   Google Scholar
• Boles, E., P. D. Jong-Gubbels, and J. T. Pronk. 1998. Identification and characterization of MAE1, the Saccharomyces cerevisiae structural gene encoding mitochondrial malic enzyme. J. Bacteriol. 180:2875–2882.
   PubMedGoogle Scholar
• Bossinger, J., R. P. Lawther, and T. G. Cooper. 1974. Nitrogen repression of the allantoin degradative enzymes in Saccharomyces cerevisiae. J. Bacteriol. 118:821–829.
   PubMedGoogle Scholar
• Brandriss, M. C. 1987. Evidence for positive regulation of the proline utilization pathway in Saccharomyces cerevisiae. Genetics 117:429–435.
   PubMedGoogle Scholar
• Brandriss, M. C., and B. Magasanik. 1980. Proline: an essential intermediate in arginine degradation in Saccharomyces cerevisiae. J. Bacteriol. 143:1403–1410.
   PubMedGoogle Scholar
• Causton, H. C., B. Ren, S. S. Koh, C. T. Harbison, E. Kanin, E. G. Jennings, T. I. Lee, H. L. True, E. S. Lander, and R. A. Young. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12:323–337.
   PubMed Web of Science ®Google Scholar
• Chang, T. H., and J. Abelson. 1990. Identification of a putative amidase gene in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 18:7180.
   PubMedGoogle Scholar
• Chelstowska, A., Z. Liu, Y. Jia, D. Amberg, and R. A. Butow. 1999. Signalling between mitochondria and the nucleus regulates the expression of a new d-lactate dehydrogenase activity in yeast. Yeast 15:1377–1391.
   PubMed Web of Science ®Google Scholar
• Coffman, J. A., R. Rai, D. M. Loprete, T. Cunningham, V. Svetlov, and T. G. Cooper. 1997. Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J. Bacteriol. 179:3416–3429.
   PubMed Web of Science ®Google Scholar
• Cooper, T. G. 1982. Nitrogen metabolism in Saccharomyces cerevisiae, p. 39–99. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces cerevisiae: metabolism and gene expression, vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Cooper, T. G. 1996. Allantoin degradative system—an integrated transcriptional response to multiple signals, p. 139–169. In G. Marzluf and R. Bambrl (ed.), Mycota, vol. III. Springer-Verlag, Berlin, Germany.
   Google Scholar
• Cooper, T. G. 2002. Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol. Rev. 26:223–238.
   PubMed Web of Science ®Google Scholar
• Coornaert, D., S. Vissers, B. Andre, and M. Grenson. 1992. The UGA43 negative regulatory gene of Saccharomyces cerevisiae contains both a GATA-1 type zinc finger and a putative leucine zipper. Curr. Genet. 21:301–307.
   PubMedGoogle Scholar
• Coschigano, P. W., and B. Magasanik. 1991. The URE2 gene product of Saccharomyces cerevisiae plays an important role in the cellular response to the nitrogen source and has homology to glutathione S-transferases. Mol. Cell. Biol. 11:822–832.
   PubMed Web of Science ®Google Scholar
• Cox, K. H., A. B. Pinchak, and T. G. Cooper. 1999. Genome-wide transcriptional analysis in S. cerevisiae by mini-array membrane hybridization. Yeast 15:703–713.
   PubMedGoogle Scholar
• Cui, X., and G. A. Churchill. 2003. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4:210.
   PubMed Web of Science ®Google Scholar
• Cunningham, T. S., and T. G. Cooper. 1991. Expression of the DAL80 gene, whose product is homologous to the GATA factors and is a negative regulator of multiple nitrogen catabolic genes in Saccharomyces cerevisiae, is sensitive to nitrogen catabolite repression. Mol. Cell. Biol. 11:6205–6215.
   PubMed Web of Science ®Google Scholar
• Cunningham, T. S., V. V. Svetlov, R. Rai, W. Smart, and T. G. Cooper. 1996. G1n3p is capable of binding to UAS(NTR) elements and activating transcription in Saccharomyces cerevisiae. J. Bacteriol. 178:3470–3479.
   PubMedGoogle Scholar
• De Boer, M., J. P. Bebelman, P. M. Goncalves, J. Maat, H. Van Heerikhuizen, and R. J. Planta. 1998. Regulation of expression of the amino acid transporter gene BAP3 in Saccharomyces cerevisiae. Mol. Microbiol. 30:603–613.
   PubMed Web of Science ®Google Scholar
• DeRisi, J., B. van den Hazel, P. Marc, E. Balzi, P. Brown, C. Jacq, and A. Goffeau. 2000. Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett. 470:156–160.
   PubMed Web of Science ®Google Scholar
• Des Etages, S. A., D. A. Falvey, R. J. Reece, and M. C. Brandriss. 1996. Functional analysis of the PUT3 transcriptional activator of the proline utilization pathway in Saccharomyces cerevisiae. Genetics 142:1069–1082.
   PubMedGoogle Scholar
• Des Etages, S. A., D. Saxena, H. L. Huang, D. A. Falvey, D. Barber, and M. C. Brandriss. 2001. Conformational changes play a role in regulating the activity of the proline utilization pathway-specific regulator in Saccharomyces cerevisiae. Mol. Microbiol. 40:890–899.
   PubMedGoogle Scholar
• Didion, T., M. Grausland, C. Kielland-Brandt, and H. A. Andersen. 1996. Amino acids induce expression of BAP2, a branched-chain amino acid permease gene in Saccharomyces cerevisiae. J. Bacteriol. 178:2025–2029.
   PubMed Web of Science ®Google Scholar
• Didion, T., B. Regenberg, M. U. Jorgensen, M. C. Kielland-Brandt, and H. A. Andersen. 1998. The permease homologue Ssy1p controls the expression of amino acid and peptide transporter genes in Saccharomyces cerevisiae. Mol. Microbiol. 27:643–650.
   PubMed Web of Science ®Google Scholar
• Dubois, E., D. Hiernaux, M. Grenson, and J. M. Wiame. 1978. Specific induction of catabolism and its relation to repression of biosynthesis in arginine metabolism of Saccharomyces cerevisiae. J. Mol. Biol. 122:383–406.
   PubMedGoogle Scholar
• Dubois, E., and F. Messenguy. 1997. Integration of the multiple controls regulating the expression of the arginase gene CAR1 of Saccharomyces cerevisiae in response to different nitrogen signals: role of Gln3p, ArgRp-Mcm1p, and Ume6p. Mol. Gen. Genet. 253:568–580.
   PubMedGoogle Scholar
• Dubois, E. L., and J. M. Wiame. 1976. Non specific induction of arginase in Saccharomyces cerevisiae. Biochimie 58:207–211.
   PubMed Web of Science ®Google Scholar
• Dwight, S. S., M. A. Harris, K. Dolinski, C. A. Ball, G. Binkley, K. R. Christie, D. G. Fisk, L. Issel-Tarver, M. Schroeder, G. Sherlock, A. Sethuraman, S. Weng, D. Botstein, and J. M. Cherry. 2002. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30:69–72.
   PubMedGoogle Scholar
• Eckert-Boulet, N., P. S. Nielsen, C. Friis, M. M. Dos Santos, J. Nielsen, M. C. Kielland-Brandt, and B. Regenberg. 2004. Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p. Yeast 21:635–648.
   PubMedGoogle Scholar
• Eide, D. J. 2001. Functional genomics and metal metabolism. Genome Biol. 2:REVIEWS1028.
   PubMedGoogle Scholar
• Forsberg, H., C. F. Gilstring, A. Zargari, P. Martinez, and P. O. Ljungdahl. 2001. The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids. Mol. Microbiol. 42:215–228.
   PubMed Web of Science ®Google Scholar
• Forsberg, H., and P. O. Ljungdahl. 2001. Sensors of extracellular nutrients in Saccharomyces cerevisiae. Curr. Genet. 40:91–109.
   PubMed Web of Science ®Google Scholar
• Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241–4257.
   PubMed Web of Science ®Google Scholar
• Gentleman, R. C., V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. Yang, and J. Zhang. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80.
   PubMed Web of Science ®Google Scholar
• Gietz, D., A. St. Jean, R. A. Woods, and R. H. Schiestl. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20:1425.
   PubMed Web of Science ®Google Scholar
• Gimeno, C. J., P. O. Ljungdahl, C. A. Styles, and G. R. Fink. 1992. Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS. Cell 68:1077–1090.
   PubMed Web of Science ®Google Scholar
• Grenson, M. 1992. Amino acid transporters in yeast: structure, function and regulation, p. 219–245. In J. J. L. L. M. De Pont (ed.), Molecular aspects of transport proteins. Elsevier Science, New York, NY.
   Google Scholar
• Hansen, J., S. V. Bruun, L. M. Bech, and C. Gjermansen. 2002. The level of MXR1 gene expression in brewing yeast during beer fermentation is a major determinant for the concentration of dimethyl sulfide in beer. FEMS Yeast Res. 2:137–149.
   PubMed Web of Science ®Google Scholar
• Harbison, C. T., D. B. Gordon, T. I. Lee, N. J. Rinaldi, K. D. Macisaac, T. W. Danford, N. M. Hannett, J. B. Tagne, D. B. Reynolds, J. Yoo, E. G. Jennings, J. Zeitlinger, D. K. Pokholok, M. Kellis, P. A. Rolfe, K. T. Takusagawa, E. S. Lander, D. K. Gifford, E. Fraenkel, and R. A. Young. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431:99–104.
   PubMed Web of Science ®Google Scholar
• Hesslinger, C., and G. Sawers. 1998. The tdcE gene in Escherichia coli strain W3110 is separated from the rest of the tdc operon by insertion of IS5 elements. DNA Seq. 9:183–188.
   PubMed Web of Science ®Google Scholar
• Hikkel, I., A. Lucau-Danila, T. Delaveau, P. Marc, F. Devaux, and C. Jacq. 2003. A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast. J. Biol. Chem. 278:11427–11432.
   PubMedGoogle Scholar
• Hinnebusch, A. 1996. Translational control of GCN4: gene-specific regulation by phosphorylation of eIF2, p. 199–244. In W. B. Hershey, M. B. Mathews, and N. Soneberg (ed.), Translational control. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Hinnebusch, A. G. 1992. General and pathway-specific regulatory mechanisms controlling the synthesis of amino acid biosynthetic enzymes in Saccharomyces cerevisiae, p. 319–414. In E. W. Jones, J. R. Pringle, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces—gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Hinnebusch, A. G. 2005. Translational regulation of GCN4 and the general amino acid control of yeast. Annu. Rev. Microbiol. 59:407–450.
   PubMed Web of Science ®Google Scholar
• Holmberg, S., and P. Schjerling. 1996. Cha4p of Saccharomyces cerevisiae activates transcription via serine/threonine response elements. Genetics 144:467–478.
   PubMedGoogle Scholar
• Huang, H. L., and M. C. Brandriss. 2000. The regulator of the yeast proline utilization pathway is differentially phosphorylated in response to the quality of the nitrogen source. Mol. Cell. Biol. 20:892–899.
   PubMed Web of Science ®Google Scholar
• Huh, W. K., J. V. Falvo, L. C. Gerke, A. S. Carroll, R. W. Howson, J. S. Weissman, and E. K. O'Shea. 2003. Global analysis of protein localization in budding yeast. Nature 425:686–691.
   PubMed Web of Science ®Google Scholar
• Iraqui, I., S. Vissers, B. Andre, and A. Urrestarazu. 1999. Transcriptional induction by aromatic amino acids in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:3360–3371.
   PubMed Web of Science ®Google Scholar
• Iraqui, I., S. Vissers, F. Bernard, J. O. Craene, E. Boles, A. Urrestarazu, and B. Andre. 1999. Amino acid signaling in Saccharomyces cerevisiae: a permease-like sensor of external amino acids and F-box protein Grr1p are required for transcriptional induction of the AGP1 gene, which encodes a broad-specificity amino acid permease. Mol. Cell. Biol. 19:989–1001.
   PubMed Web of Science ®Google Scholar
• Iraqui, I., S. Vissers, M. Cartiaux, and A. Urrestarazu. 1998. Characterisation of Saccharomyces cerevisiae ARO8 and ARO9 genes encoding aromatic aminotransferases I and II reveals a new aminotransferase subfamily. Mol. Gen. Genet. 257:238–248.
   PubMedGoogle Scholar
• Ishida, C., C. Aranda, L. Valenzuela, L. Riego, A. DeLuna, F. Recillas-Targa, P. Filetici, R. Lopez-Revilla, and A. Gonzalez. 2006. The UGA3-GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae. Mol. Microbiol. 59:1790–1806.
   PubMedGoogle Scholar
• Jacobs, P., J. C. Jauniaux, and M. Grenson. 1980. A cis-dominant regulatory mutation linked to the argB-argC gene cluster in Saccharomyces cerevisiae. J. Mol. Biol. 139:691–704.
   PubMed Web of Science ®Google Scholar
• Jauniaux, J. C., and M. Grenson. 1990. GAP1, the general amino acid permease gene of Saccharomyces cerevisiae. Nucleotide sequence, protein similarity with the other bakers yeast amino acid permeases, and nitrogen catabolite repression. Eur. J. Biochem. 190:39–44.
   PubMedGoogle Scholar
• Jia, M. H., R. A. Larossa, J. M. Lee, A. Rafalski, E. Derose, G. Gonye, and Z. Xue. 2000. Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol. Genomics 3:83–92.
   PubMedGoogle Scholar
• Jones, E. W., and G. R. Fink. 1982. Regulation of amino acid and nucleotide biosynthesis in yeast, p. 181–299. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces—metabolism and gene expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
   Google Scholar
• Kellis, M., N. Patterson, M. Endrizzi, B. Birren, and E. S. Lander. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241–254.
   PubMed Web of Science ®Google Scholar
• Kim, J. M., H. Yoshikawa, and K. Shirahige. 2001. A member of the YER057c/yjgf/Uk114 family links isoleucine biosynthesis and intact mitochondria maintenance in Saccharomyces cerevisiae. Genes Cells 6:507–517.
   PubMedGoogle Scholar
• Klasson, H., G. R. Fink, and P. O. Ljungdahl. 1999. Ssy1p and Ptr3p are plasma membrane components of a yeast system that senses extracellular amino acids. Mol. Cell. Biol. 19:5405–5416.
   PubMed Web of Science ®Google Scholar
• Kodama, Y., F. Omura, K. Takahashi, K. Shirahige, and T. Ashikari. 2002. Genome-wide expression analysis of genes affected by amino acid sensor Ssy1p in Saccharomyces cerevisiae. Curr. Genet. 41:63–72.
   PubMedGoogle Scholar
• Kohlhaw, G. B. 2003. Leucine biosynthesis in fungi: entering metabolism through the back door. Microbiol. Mol. Biol. Rev. 67:1–15.
   PubMed Web of Science ®Google Scholar
• Kohrer, K., and H. Domdey. 1991. Preparation of high molecular weight RNA. Methods Enzymol. 194:398–405.
   PubMed Web of Science ®Google Scholar
• Kradolfer, P., P. Niederberger, and R. Hutter. 1982. Tryptophan degradation in Saccharomyces cerevisiae: characterization of two aromatic aminotransferases. Arch. Microbiol. 133:242–248.
   PubMed Web of Science ®Google Scholar
• Le Crom, S., F. Devaux, C. Jacq, and P. Marc. 2002. yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res. 30:76–79.
   PubMedGoogle Scholar
• Le Crom, S., F. Devaux, P. Marc, X. Zhang, W. S. Moye-Rowley, and C. Jacq. 2002. New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system. Mol. Cell. Biol. 22:2642–2649.
   PubMedGoogle Scholar
• Liao, X., and R. A. Butow. 1993. RTG1 and RTG2: two yeast genes required for a novel path of communication from mitochondria to the nucleus. Cell 72:61–71.
   PubMed Web of Science ®Google Scholar
• Linnen, J. M., C. P. Bailey, and D. L. Weeks. 1993. Two related localized mRNAs from Xenopus laevis encode ubiquitin-like fusion proteins. Gene 128:181–188.
   PubMedGoogle Scholar
• Longtine, M. S., A. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953–961.
   PubMed Web of Science ®Google Scholar
• Lyons, T. J., A. P. Gasch, L. A. Gaither, D. Botstein, P. O. Brown, and D. J. Eide. 2000. Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc. Natl. Acad. Sci. USA 97:7957–7962.
   PubMed Web of Science ®Google Scholar
• Ma, Y., and L. M. Hendershot. 2001. The unfolding tale of the unfolded protein response. Cell 107:827–830.
   PubMed Web of Science ®Google Scholar
• Magasanik, B. 1992. Regulation of nitrogen utilization, p. 238–317. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces—metabolism and gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• Magasanik, B., and C. A. Kaiser. 2002. Nitrogen regulation in Saccharomyces cerevisiae. Gene 290:1–18.
   PubMed Web of Science ®Google Scholar
• Magasanik, B., and F. C. Neidhardt. 1987. Regulation of carbon and nitrogen utilization, p. 1318–1325. In F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium, vol. 2. American Society for Microbiology, Washington, DC.
   Google Scholar
• Makuc, J., S. Paiva, M. Schauen, R. Kramer, B. Andre, M. Casal, C. Leao, and E. Boles. 2001. The putative monocarboxylate permeases of the yeast Saccharomyces cerevisiae do not transport monocarboxylic acids across the plasma membrane. Yeast 18:1131–1143.
   PubMed Web of Science ®Google Scholar
• Malpertuy, A., F. Tekaia, S. Casaregola, M. Aigle, F. Artiguenave, G. Blandin, M. Bolotin-Fukuhara, E. Bon, P. Brottier, J. de Montiqny, P. Durrens, C. Gaillardin, A. Lepingle, B. Llorente, C. Neuveglise, O. Ozier-Kalogeropoulos, S. Potier, W. Saurin, C. Toffano-Nioche, M. Wesolowski-Louvel, P. Wincker, J. Weissenbach, J. Souciet, and B. Dujon. 2000. Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Lett. 487:113–121.
   PubMedGoogle Scholar
• Marc, P., F. Devaux, and C. Jacq. 2001. yMGV: a database for visualization and data mining of published genome-wide yeast expression data. Nucleic Acids Res. 29:E63.
   PubMedGoogle Scholar
• Natarajan, K., M. R. Meyer, B. M. Jackson, D. Slade, C. Roberts, A. G. Hinnebusch, and M. J. Marton. 2001. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21:4347–4368.
   PubMed Web of Science ®Google Scholar
• Nelissen, B., W. R. De, and A. Goffeau. 1997. Classification of all putative permeases and other membrane plurispanners of the major facilitator superfamily encoded by the complete genome of Saccharomyces cerevisiae. FEMS Microbiol. Rev. 21:113–134.
   PubMed Web of Science ®Google Scholar
• Niederberger, P., G. Miozzari, and R. Hutter. 1981. Biological role of the general control of amino acid biosynthesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 1:584–593.
   PubMed Web of Science ®Google Scholar
• Normington, K., K. Kohno, Y. Kozutsumi, M. J. Gething, and J. Sambrook. 1989. S. cerevisiae encodes an essential protein homologous in sequence and function to mammalian BiP. Cell 57:1223–1236.
   PubMed Web of Science ®Google Scholar
• Ogawa, N., J. DeRisi, and P. O. Brown. 2000. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol. Biol. Cell 11:4309–4321.
   PubMed Web of Science ®Google Scholar
• Oliphant, A. R., C. J. Brandl, and K. Struhl. 1989. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 9:2944–2949.
   PubMed Web of Science ®Google Scholar
• Onda, M., K. Ota, T. Chiba, Y. Sakaki, and T. Ito. 2004. Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt tolerance. Gene 332:51–59.
   PubMedGoogle Scholar
• Oxelmark, E., A. Marchini, I. Malanchi, F. Magherini, L. Jaquet, M. A. Hajibagheri, K. J. Blight, J. C. Jauniaux, and M. Tommasino. 2000. Mmf1p, a novel yeast mitochondrial protein conserved throughout evolution and involved in maintenance of the mitochondrial genome. Mol. Cell. Biol. 20:7784–7797.
   PubMedGoogle Scholar
• Pace, H. C., and C. Brenner. 2001. The nitrilase superfamily: classification, structure and function. Genome Biol. 2:REVIEWS0001.1–REVIEWS0001.9.
   Web of Science ®Google Scholar
• Patil, C., and P. Walter. 2001. Intracellular signaling from the endoplasmic reticulum to the nucleus: the unfolded protein response in yeast and mammals. Curr. Opin. Cell Biol. 13:349–355.
   PubMed Web of Science ®Google Scholar
• Perpete, P., O. Duthoit, M. S. De, L. Imray, A. I. Lawton, K. E. Stavropoulos, V. W. Gitonga, M. J. Hewlins, and J. R. Dickinson. 2006. Methionine catabolism in Saccharomyces cerevisiae. FEMS Yeast Res. 6:48–56.
   PubMed Web of Science ®Google Scholar
• Petersen, J. G., M. C. Kielland-Brandt, T. Nilsson-Tillgren, C. Bornaes, and S. Holmberg. 1988. Molecular genetics of serine and threonine catabolism in Saccharomyces cerevisiae. Genetics 119:527–534.
   PubMed Web of Science ®Google Scholar
• Puig, S., E. Askeland, and D. J. Thiele. 2005. Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. Cell 120:99–110.
   PubMed Web of Science ®Google Scholar
• Ramos, F., E. Dubois, and A. Pierard. 1988. Control of enzyme synthesis in the lysine biosynthetic pathway of Saccharomyces cerevisiae. Evidence for a regulatory role of gene LYS14. Eur. J. Biochem. 171:171–176.
   PubMedGoogle Scholar
• Ramos, F., M. E. Guezzar, M. Grenson, and J. M. Wiame. 1985. Mutations affecting the enzymes involved in the utilization of 4-aminobutyric acid as nitrogen source by the yeast Saccharomyces cerevisiae. Eur. J. Biochem. 149:401–404.
   PubMedGoogle Scholar
• Reihl, P., and J. Stolz. 2005. The monocarboxylate transporter homolog Mch5p catalyzes riboflavin (vitamin B2) uptake in Saccharomyces cerevisiae. J. Biol. Chem. 280:39809–39817.
   PubMed Web of Science ®Google Scholar
• Roberg, K. J., N. Rowley, and C. A. Kaiser. 1997. Physiological regulation of membrane protein sorting late in the secretory pathway of Saccharomyces cerevisiae. J. Cell Biol. 137:1469–1482.
   PubMed Web of Science ®Google Scholar
• Rogers, B., A. Decottignies, M. Kolaczkowski, E. Carvajal, E. Balzi, and A. Goffeau. 2001. The pleiotropic drug ABC transporters from Saccharomyces cerevisiae. J. Mol. Microbiol. Biotechnol. 3:207–214.
   PubMed Web of Science ®Google Scholar
• Rose, M. D., L. M. Misra, and J. P. Vogel. 1989. KAR2, a karyogamy gene, is the yeast homolog of the mammalian BiP/GRP78 gene. Cell 57:1211–1221.
   PubMed Web of Science ®Google Scholar
• Rowen, D. W., N. Esiobu, and B. Magasanik. 1997. Role of GATA factor Nil2p in nitrogen regulation of gene expression in Saccharomyces cerevisiae. J. Bacteriol. 179:3761–3766.
   PubMed Web of Science ®Google Scholar
• Ruepp, A., A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Guldener, G. Mannhaupt, M. Munsterkotter, and H. W. Mewes. 2004. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32:5539–5545.
   PubMed Web of Science ®Google Scholar
• Saeed, A. I., V. Sharov, J. White, J. Li, W. Liang, N. Bhagabati, J. Braisted, M. Klapa, T. Currier, M. Thiagarajan, A. Sturn, M. Snuffin, A. Rezantsev, D. Popov, A. Ryltsov, E. Kostukovich, I. Borisovsky, Z. Liu, A. Vinsavich, V. Trush, and J. Quackenbush. 2003. TM4: a free, open-source system for microarray data management and analysis. BioTechniques 34:374–378.
   PubMed Web of Science ®Google Scholar
• Scherens, B., A. Feller, F. Vierendeels, F. Messenguy, and E. Dubois. 2006. Identification of direct and indirect targets of the Gln3 and Gat1 activators by transcriptional profiling in response to nitrogen availability at short and long term. FEMS Yeast Res. 6:777–791.
   PubMed Web of Science ®Google Scholar
• Schroder, M., J. S. Chang, and R. J. Kaufman. 2000. The unfolded protein response represses nitrogen-starvation induced developmental differentiation in yeast. Genes Dev. 14:2962–2975.
   PubMedGoogle Scholar
• Schroder, M., R. Clark, C. Y. Liu, and R. J. Kaufman. 2004. The unfolded protein response represses differentiation through the RPD3-SIN3 histone deacetylase. EMBO J. 23:2281–2292.
   PubMedGoogle Scholar
• Sentheshanuganathan, S. 1960. The mechanism of the formation of higher alcohols from amino acids by Saccharomyces cerevisiae. Biochem. J. 74:568–576.
   PubMedGoogle Scholar
• Shamji, A. F., F. G. Kuruvilla, and S. L. Schreiber. 2000. Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr. Biol. 10:1574–1581.
   PubMed Web of Science ®Google Scholar
• Simonis, N., S. J. Wodak, G. N. Cohen, and J. van Helden. 2004. Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics 20:2370–2379.
   PubMedGoogle Scholar
• Sosa, E., C. Aranda, L. Riego, L. Valenzuela, A. DeLuna, J. M. Cantu, and A. Gonzalez. 2003. Gcn4 negatively regulates expression of genes subjected to nitrogen catabolite repression. Biochem. Biophys. Res. Commun. 310:1175–1180.
   PubMedGoogle Scholar
• Soussi-Boudekou, S., S. Vissers, A. Urrestarazu, J. C. Jauniaux, and B. Andre. 1997. Gzf3p, a fourth GATA factor involved in nitrogen-regulated transcription in Saccharomyces cerevisiae. Mol. Microbiol. 23:1157–1168.
   PubMedGoogle Scholar
• Spear, E., and D. T. Ng. 2001. The unfolded protein response: no longer just a special teams player. Traffic 2:515–523.
   PubMed Web of Science ®Google Scholar
• Talibi, D., M. Grenson, and B. Andre. 1995. Cis- and trans-acting elements determining induction of the genes of the gamma-aminobutyrate (GABA) utilization pathway in Saccharomyces cerevisiae. Nucleic Acids Res. 23:550–557.
   PubMedGoogle Scholar
• Talla, E., F. Tekaia, L. Brino, and B. Dujon. 2003. A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization. BMC Genomics 4:38.
   PubMedGoogle Scholar
• Thomas, D., A. Becker, and Y. Surdin-Kerjan. 2000. Reverse methionine biosynthesis from S-adenosylmethionine in eukaryotic cells. J. Biol. Chem. 275:40718–40724.
   PubMedGoogle Scholar
• Thomas, D., and Y. Surdin-Kerjan. 1997. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 61:503–532.
   PubMed Web of Science ®Google Scholar
• Travers, K. J., C. K. Patil, L. Wodicka, D. J. Lockhart, J. S. Weissman, and P. Walter. 2000. Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101:249–258.
   PubMed Web of Science ®Google Scholar
• Turner, G. C., F. Du, and A. Varshavsky. 2000. Peptides accelerate their uptake by activating a ubiquitin-dependent proteolytic pathway. Nature 405:579–583.
   PubMedGoogle Scholar
• Urrestarazu, A., S. Vissers, I. Iraqui, and M. Grenson. 1998. Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination. Mol. Gen. Genet. 257:230–237.
   PubMedGoogle Scholar
• Valenzuela, L., C. Aranda, and A. Gonzalez. 2001. TOR modulates GCN4-dependent expression of genes turned on by nitrogen limitation. J. Bacteriol. 183:2331–2334.
   PubMedGoogle Scholar
• Valenzuela, L., P. Ballario, C. Aranda, P. Filetici, and A. Gonzalez. 1998. Regulation of expression of GLT1, the gene encoding glutamate synthase in Saccharomyces cerevisiae. J. Bacteriol. 180:3533–3540.
   PubMedGoogle Scholar
• Van Helden, J. 2003. Regulatory sequence analysis tools. Nucleic Acids Res. 31:3593–3596.
   PubMed Web of Science ®Google Scholar
• Van Helden, J., B. Andre, and J. Collado-Vides. 1998. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281:827–842.
   PubMed Web of Science ®Google Scholar
• Vuralhan, Z., M. A. Luttik, S. L. Tai, V. M. Boer, M. A. Morais, D. Schipper, M. J. Almering, P. Kotter, J. R. Dickinson, J. M. Daran, and J. T. Pronk. 2005. Physiological characterization of the ARO10-dependent, broad-substrate-specificity 2-oxo acid decarboxylase activity of Saccharomyces cerevisiae. Appl. Environ. Microbiol. 71:3276–3284.
   PubMedGoogle Scholar
• Vuralhan, Z., M. A. Morais, S. L. Tai, M. D. Piper, and J. T. Pronk. 2003. Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 69:4534–4541.
   PubMed Web of Science ®Google Scholar
• Wach, A. 1996. PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12:259–265.
   PubMed Web of Science ®Google Scholar
• Webb, A. D., and J. L. Ingraham. 1963. Fusel oil. Adv. Appl. Microbiol. 5:317–353.
   Google Scholar
• Wiame, J. M., M. Grenson, and H. N. Arst, Jr. 1985. Nitrogen catabolite repression in yeasts and filamentous fungi. Adv. Microb. Physiol. 26:1–88.
   PubMed Web of Science ®Google Scholar
• Wong, D. T., H. A. Davis, K. Kuplent, S. Doares, J. A. Sorge, and R. Mullinax. 2000. Fairplay™ microarray labeling kit for preparing uniformly labeled cDNA. Strategies 13:131–132.
   Google Scholar
• Wu, J., N. Zhang, A. Hayes, K. Panoutsopoulou, and S. G. Oliver. 2004. Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation. Proc. Natl. Acad. Sci. USA 101:3148–3153.
   PubMedGoogle Scholar
• Yang, R., S. A. Wek, and R. C. Wek. 2000. Glucose limitation induces GCN4 translation by activation of Gcn2 protein kinase. Mol. Cell. Biol. 20:2706–2717.
   PubMedGoogle Scholar
• Yang, Y. H., S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed. 2002. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:e15.
   PubMed Web of Science ®Google Scholar