Nutritional homeostasis in batch and steady-state culture of yeast

Molecular Biology of the Cell

Volumn 15, Issue 9, 2004, Pages 4089-4104

  Saldanha, Alok J ^a,b   Brauer, Matthew J ^a,c   Botstein, David ^a,c  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE; PHOSPHATE; SULFATE; URACIL;

ARTICLE; BACTERIUM CULTURE; CELL CYCLE; CHEMOSTAT; CULTURE MEDIUM; FUNGUS CULTURE; GENE EXPRESSION REGULATION; GROWTH RATE; HOMEOSTASIS; NONHUMAN; NUTRIENT; NUTRITION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; STEADY STATE; STRESS;

AMINO ACIDS; CELL CYCLE; CULTURE MEDIA; GENE EXPRESSION PROFILING; GENES, FUNGAL; GENOMICS; HOMEOSTASIS; LEUCINE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOSPHATES; RIBOSOMAL PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SULFATES; URACIL;

BACTERIA (MICROORGANISMS); FUNGI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 4344685444     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E04-04-0306     Document Type: Article

References (47)

1. Ashburner, M., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29.
2. Boer, V.M., de Winde, J.H., Pronk, J.T., and Piper, M.D. (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.
3. Carroll, A.S., and O'Shea, E.K. (2002). Pho85 and signaling environmental conditions. Trends Biochem. Sci. 27, 87-93.
4. Chen, P.S., Toribara, T., and Warner, H. (1956). Microdetermination of phosphorus. Anal. Chem. 28, 1756-1758.
5. Denis-Duphil, M. (1989). Pyrimidine biosynthesis in Saccharomyces cerevisiae: the ura2 cluster gene, its multifunctional enzyme product, and other structural or regulatory genes involved in de novo UMP synthesis. Biochem. Cell Biol. 67, 612-631.
6. DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
7. Dobbin, K., and Simon, R. (2002). Comparison of microarray designs for class comparison and class discovery. Bioinformatics 18, 1438-1445.
8. Dwight, S.S., et al. (2002). Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30, 69-72.
9. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868.
10. Entian, K.D., and Koetter, P. (1998). Yeast mutant and plasmid collections. In: Yeast Gene Analysis, vol. 26, ed. A.J.P. Brown and M.F. Tuite, London: Academic Press, United Kingdom, 431-449.
11. Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D., and Brown, P.O. (2000). Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241-4257.
12. Gasch, A.P., and Werner-Washburne, M. (2002). The genomics of yeast responses to environmental stress and starvation. Funct. Integr. Genomics 2, 181-192.
13. Gollub, J., et al. (2003). The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 31, 94-96.
14. Harris, M.A., et al. (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. Database issue 32, D258-261.
15. Hartwell, L.H. (1974). Saccharomyces cerevisiae cell cycle. Bacteriol. Rev. 38, 164-198.
16. Hayes, A., Zhang, N., Wu, J., Butler, P.R., Hauser, N.C., Hoheisel, J.D., Lim, F.L., Sharrocks, A.D., and Oliver, S.G. (2002). Hybridization array technology coupled with chemostat culture: tools to interrogate gene expression in Saccharomyces cerevisiae. Methods 26, 281-290.
17. Kal, A.J., et al. (1999). Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol. Biol. Cell 10, 1859-1872.
18. Kohlhaw, G.B. (2003). Leucine biosynthesis in fungi: entering metabolism through the back door. Microbiol. Mol. Biol. Rev. 67, 1-15, table of contents.
19. Lange, H.C., and Heijnen, J.J. (2001). Statistical reconciliation of the elemental and molecular biomass composition of Saccharomyces cerevisiae. Biotechnol. Bioeng. 75, 334-344.
20. Liu, X., and Clarke, N.D. (2002). Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol. 323, 1-8.
21. Losson, R., Fuchs, R.P., and Lacroute, F. (1985). Yeast promoters URA1 and URA3. Examples of positive control. J. Mol. Biol. 185, 65-81.
22. Lyons, T.J., Gasch, A.P., Gaither, L.A., Botstein, D., Brown, P.O., and Eide, D.J. (2000). Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast. Proc. Natl. Acad. Sci. USA 97, 7957-7962.
23. Monod, J. (1942). Recherches sure la croissance des cultures bacteriennes. Paris: Herman & Cie.
24. Monod, J. (1950). La Technique de culture continue. Theorie et applications. Ann. Inst. Pasteur 79, 390-410.
25. Novick, A., and Szilard, L. (1950). Description of the chemostat. Science 715-716.
26. Oestreicher, N., and Scazzocchio, C. (1995). A single amino acid change in a pathway-specific transcription factor results in differing degrees of constitutivity, hyperinducibility and derepression of several structural genes. J. Mol. Biol. 249, 693-699.
27. Ogawa, N., DeRisi, J., and Brown, P.O. (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.
28. Oppenheim, D.S., and Yanofsky, C. (1980). Translational coupling during expression of the tryptophan operon of Escherichia coli. Genetics 95, 785-795.
29. Patton, E.E., Peyraud, C., Rouillon, A., Surdin-Kerjan, Y., Tyers, M., and Thomas, D. (2000). SCF(Met30)-mediated control of the transcriptional activator Met4 is required for the G(1)-S transition. EMBO J. 19, 1613-1624.
30. Persson, B.L., Petersson, J., Fristedt, U., Weinander, R., Berhe, A., and Pattison, J. (1999). Phosphate permeases of Saccharomyces cerevisiae: structure, function and regulation. Biochim. Biophys. Acta 1422, 255-272.
31. Piper, M.D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J., and Pronk, J.T. (2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008.
32. Reichard, P. (2002). Ribonucleotide reductases: the evolution of allosteric regulation. Arch. Biochem. Biophys. 397, 149-155.
33. Schneider, K.R., Smith, R.L., and O'Shea, E.K. (1994). Phosphate-regulated inactivation of the kinase PHO80-PHO85 by the CDK inhibitor PHO81. Science 266, 122-126.
34. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D., and Futcher, B. (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297.
35. Springer, M., Wykoff, D.D., Miller, N., and O'Shea, E.K. (2003). Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes. PLoS Biol. 1, E28.
36. ter Linde, J.J., Liang, H., Davis, R.W., Steensma, H.Y., van Dijken, J.P., and Pronk, J.T. (1999). Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J. Bacteriol. 181, 7409-7413.
37. Thomas, D., Rothstein, R., Rosenberg, N., and Surdin-Kerjan, Y. (1988). SAM2 encodes the second methionine S-adenosyl transferase in Saccharomyces cerevisiae: physiology and regulation of both enzymes. Mol. Cell. Biol. 8, 5132-5139.
38. Thomas, D., and Surdin-Kerjan, Y. (1997). Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 61, 503-532.
39. Townsend, J.P. (2003). Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 4, 41.
40. van Dijken, J.P., et al. (2000). An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microbiol. Technol. 26, 706-714.
41. Verma, R., Annan, R.S., Huddleston, M.J., Carr, S.A., Reynard, G., and Deshaies, R.J. (1997). Phosphorylation of Sic1p by G1 Cdk required for its degradation and entry into S phase. Science 278, 455-460.
42. Volland, C., Urban-Grimal, D., Geraud, G., and Haguenauer-Tsapis, R. (1994). Endocytosis and degradation of the yeast uracil permease under adverse conditions. J. Biol. Chem. 269, 9833-9841.
43. Wang, D., Zheng, F., Holmberg, S., and Kohlhaw, G.B. (1999). Yeast transcriptional regulator Leu3p. Self-masking, specificity of masking, and evidence for regulation by the intracellular level of Leu3p. J. Biol. Chem. 274, 19017-19024.
44. Warner, J.R. (1999). The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437-440.
45. Wu, J., Zhang, N., Hayes, A., Panoutsopoulou, K., and Oliver, S.G. (2004). Global analysis of nutrient control of gene expression in Saccharomyces cerevisiae during growth and starvation. Proc. Natl. Acad. Sci. USA 101, 3148-3153.
46. Yang, Y.H., and Speed, T. (2002). Design issues for cDNA microarray experiments. Nat. Rev. Genet. 3, 579-588.
47. Zhao, Y., Sohn, J.H., and Warner, J.R. (2003). Autoregulation in the biosynthesis of ribosomes. Mol. Cell. Biol. 23, 699-707.