Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state

Genome Biology

Volumn 4, Issue 1, 2002, Pages

  Lascaris, Romeo ^a,c   Bussemaker, Harmen J ^a,d   Boorsma, André ^a   Piper, Matt ^b   van der Spek, Hans ^a   Grivell, Les ^a,e   Blom, Jolanda ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^c NETHERLANDS CANCER INSTITUTE   (Netherlands)

^d Columbia University ^*  (United States)

^e EMBO   (Germany)

Author keywords

Additional Data File; Diauxic Shift; Mitochondrial Biogenesis; Upstream Activation Sequence; Zinc Metabolism

Indexed keywords

CCAAT BINDING FACTOR; GLUCOSE; HAP4 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR; ZINC;

ARTICLE; CELL DIVISION; DRUG EFFECT; FUNGAL GENE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MITOCHONDRION; SACCHAROMYCES CEREVISIAE; UPREGULATION;

CCAAT-BINDING FACTOR; CELL DIVISION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GLUCOSE; MITOCHONDRIA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; UP-REGULATION; ZINC;

EID: 0037263985     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2002-4-1-r3     Document Type: Article

References (28)

1. DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997, 278: 680-686. 10.1126/science.278.5338.680. DOI: 10.1126/science.278.5338.680
2. Blom J, De Mattos MJ, Grivell LA: Redirection of the respiro-fermentative flux distribution in Saccharomyces cerevisiae by overexpression of the transcription factor Hap4p. Appl Environ Microbiol. 2000, 66: 1970-1973. 10.1128/AEM.66.5.1970-1973.2000. DOI: 10.1128/AEM.66.5.1970-1973.2000
3. Wagner A: Robustness against mutations in genetic networks of yeast. Nat Genet. 2000, 24: 355-361. 10.1038/74174. DOI: 10.1038/74174
4. Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet. 2001, 27: 167-171. 10.1038/84792. DOI: 10.1038/84792
5. Bereiter-Hahn J: Dimethylaminostyrylmethylpyridiniumiodine (DASPMI) as a fluorescent probe for mitochondria in situ. Biochim Biophys Acta. 1976, 423: 1-14. 10.1016/0005-2728(76)90096-7. DOI: 10.1016/0005-2728(76)90096-7
6. Pringle JR: Staining of bud scars and other cell wall chitin with calcofluor. Methods Enzymol. 1991, 194: 732-735. DOI: 10.1016/0076-6879(91)94055-H
7. Mewes HW, Rafael J: The 2-(dimethylaminostyryl)-1-methylpyridinium cation as indicator of the mitochondrial membrane potential. FEBS Lett. 1981, 131: 7-10. 10.1016/0014-5793(81)80875-7. DOI: 10.1016/0014-5793(81)80875-7
8. Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F: MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res. 1997, 25: 28-30. 10.1093/nar/25.1.28. DOI: 10.1093/nar/25.1.28
9. Lyons TJ, Gasch AP, Gaither LA, Botstein D, Brown PO, Eide DJ: Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc Natl Acad Sci USA. 2000, 97: 7957-7962. 10.1073/pnas.97.14.7957. DOI: 10.1073/pnas.97.14.7957
10. Zhao H, Butler E, Rodgers J, Spizzo T, Duesterhoeft S, Eide D: Regulation of zinc homeostasis in yeast by binding of the ZAP1 transcriptional activator to zinc-responsive promoter elements. J Biol Chem. 1998, 273: 28713-28720. 10.1074/jbc.273.44.28713. DOI: 10.1074/jbc.273.44.28713
11. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257. DOI: 10.1091/mbc.11.12.4241
12. Shamji AF, Kuruvilla FG, Schreiber SL: Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr Biol. 2000, 10: 1574-1581. 10.1016/S0960-9822(00)00866-6. DOI: 10.1016/S0960-9822(00)00866-6
13. Kang W, Matsushita Y, Grohmann L, Graack HR, Kitakawa M, Isono K: Cloning and analysis of the nuclear gene for YmL33, a protein of the large subunit of the mitochondrial ribosome in Saccharomyces cerevisiae. J Bacteriol. 1991, 173: 4013-4020.
14. Partaledis JA, Mason TL: Structure and regulation of a nuclear gene in Saccharomyces cerevisiae that specifies MRP13, a protein of the small subunit of the mitochondrial ribosome. Mol Cell Biol. 1988, 8: 3647-3660. DOI: 10.1128/MCB.8.9.3647
15. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, et al: Functional discovery via a compendium of expression profiles. Cell. 2000, 102: 109-126. DOI: 10.1016/S0092-8674(00)00015-5
16. van Maris AJA, Bakker BM, Brandt M, Boorsma A, De Mattos MJ, Grivell LA, Pronk JT, Blom J: Modulating the distribution of fluxes among respiration and fermentation by overexpression of HAP4 in Saccharomyces cerevisiae. FEMS Yeast Res. 2001, 1: 139-149. 10.1016/S1567-1356(01)00022-8. DOI: 10.1016/S1567-1356(01)00022-8
17. Nijtmans LG, de Jong L, Artal Sanz M, Coates PJ, Berden JA, Back JW, Muijsers AO, van der Spek H, Grivell LA: Prohibitins act as a membrane-bound chaperone for the stabilization of mitochondrial proteins. EMBO J. 2000, 19: 2444-2451. 10.1093/emboj/19.11.2444. DOI: 10.1093/emboj/19.11.2444
18. Schagger H, von Jagow G: Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal Biochem. 1991, 199: 223-231. DOI: 10.1016/0003-2697(91)90094-A
19. out reaction domain. Eur J Biochem. 1993, 215: 601-609. DOI: 10.1111/j.1432-1033.1993.tb18071.x
20. Lascaris RF, Groot E, Hoen PB, Mager WH, Planta RJ: Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res. 2000, 28: 1390-1396. 10.1093/nar/28.6.1390. DOI: 10.1093/nar/28.6.1390
21. Stanford: functional genomics facility. [http://www.microarray.org]
22. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863. DOI: 10.1073/pnas.95.25.14863
23. Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F: TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 2000, 28: 316-319. 10.1093/nar/28.1.316. DOI: 10.1093/nar/28.1.316
24. Quandt K, Frech K, Karas H, Wingender E, Werner T: MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 1995, 23: 4878-4884. DOI: 10.1093/nar/23.23.4878
25. van Helden J, Andre B, Collado-Vides J: A web site for the computational analysis of yeast regulatory sequences. Yeast. 2000, 16: 177-187. 10.1002/(SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO;2-9. DOI: 10.1002/(SICI)1097-0061(20000130)16:2<177::AID-YEA516>3.0.CO;2-9
26. Pavlidis P, Lewis DP, Noble WS: Exploring gene expression data with class scores. Pac Symp Biocomput. 2002, 474-485.
27. 2+-ATPases. Nature. 1986, 319: 689-693. DOI: 10.1038/319689a0
28. Ferea TL, Botstein D, Brown PO, Rosenzweig RF: Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci USA. 1999, 96: 9721-9726. 10.1073/pnas.96.17.9721. DOI: 10.1073/pnas.96.17.9721