Polyphosphate Loss Promotes SNF/SWI- and Gcn5-Dependent Mitotic Induction of PHO5

REFERENCES

• Barbaric, S., J. Walker, A. Schmid, J. Q. Svejstrup, and W. Hürz. 2001. Increasing the rate of chromatin remodeling and gene activation—a novel role for the histone acetyltransferase Gcn5. EMBO J. 20: 4944–4951.
   PubMedGoogle Scholar
• Brachmann, C. B., A. Davies, G. J. Cost, E. Caputo, J. Li, P. Hieter, and J. D. Boeke. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115–132.
   PubMed Web of Science ®Google Scholar
• Brownell, J. E., J. X. Zhou, T. Ranalli, R. Kobayashi, D. G. Edmondson, S. Y. Roth, and C. D. Allis. 1996. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84: 843–851.
   PubMed Web of Science ®Google Scholar
• Cho, R. J., M. J. Campbell, E. A. Winzeler, L. Steinmetz, A. Conway, L. Wodicka, T. G. Wolfsberg, A. E. Gabrielian, D. Landsman, D. J. Lockhart, and R. W. Davis. 1998. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2: 65–73.
   PubMed Web of Science ®Google Scholar
• Clark, J. E., H. Beegen, and H. G. Wood. 1986. Isolation of intact chains of polyphosphate from “Propionibacterium shermanii” grown on glucose or lactate. J. Bacteriol. 168: 1212–1219.
   PubMed Web of Science ®Google Scholar
• Cohen, A., N. Perzov, H. Nelson, and N. Nelson. 1999. A novel family of yeast chaperons involved in the distribution of V-ATPase and other membrane proteins. J. Biol. Chem. 274: 26885–26893.
   PubMed Web of Science ®Google Scholar
• Cross, F. R., and A. H. Tinkelenberg. 1991. A potential positive feedback loop controlling CLN1 and CLN2 gene expression at the start of the yeast cell cycle. Cell 65: 875–883.
   PubMedGoogle Scholar
• Dunn, T., K. Gable, and T. Beeler. 1994. Regulation of cellular Ca2+ by yeast vacuoles. J. Biol. Chem. 269: 7273–7278.
   PubMed Web of Science ®Google Scholar
• Elledge, S. J., and R. W. Davis. 1989. DNA damage induction of ribonucleotide reductase. Mol. Cell. Biol. 9: 4932–4940.
   PubMed Web of Science ®Google Scholar
• Gaudreau, L., A. Schmid, D. Blaschke, M. Ptashne, and W. Hürz. 1997. RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter. Cell 89: 55–62.
   PubMedGoogle Scholar
• Gillies, R. J., K. Ugurbil, J. A. den Hollander, and R. G. Shulman. 1981. 31P NMR studies of intracellular pH and phosphate metabolism during cell division cycle of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 78: 2125–2129.
   PubMed Web of Science ®Google Scholar
• Grant, P. A., L. Duggan, J. Côté, S. M. Roberts, J. E. Brownell, R. Candau, R. Ohba, T. Owen-Hughes, C. D. Allis, F. Winston, S. L. Berger, and J. L. Workman. 1997. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11: 1640–1650.
   PubMed Web of Science ®Google Scholar
• Gregory, P. D., A. Schmid, M. Zavari, L. Lui, S. L. Berger, and W. Hürz. 1998. Absence of Gcn5 HAT activity defines a novel state in the opening of chromatin at the PHO5 promoter in yeast. Mol. Cell 1: 495–505.
   PubMedGoogle Scholar
• Gregory, P. D., A. Schmid, M. Zavari, M. Munsterkotter, and W. Hürz. 1999. Chromatin remodelling at the PHO8 promoter requires SWI-SNF and SAGA at a step subsequent to activator binding. EMBO J. 18: 6407–6414.
   PubMedGoogle Scholar
• Han, M., U. J. Kim, P. Kayne, and M. Grunstein. 1988. Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J. 7: 2221–2228.
   PubMedGoogle Scholar
• Hereford, L. M., M. A. Osley, T. R. Ludwig, and C. S. McLaughlin. 1981. Cell-cycle regulation of yeast histone mRNA. Cell 24: 367–375.
   PubMed Web of Science ®Google Scholar
• Hess, K. R., W. Zhang, K. A. Baggerly, D. N. Stivers, and K. R. Coombes. 2001. Microarrays: handling the deluge of data and extracting reliable information. Trends Biotechnol. 19: 463–468.
   PubMed Web of Science ®Google Scholar
• Holstege, F. C. P., E. G. Jennings, J. J. Wyrick, T. I. Lee, C. J. Hengartner, M. R. Green, T. Golub, E. S. Lander, and R. A. Young. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717–728.
   PubMed Web of Science ®Google Scholar
• Huang, D., J. Moffat, and B. Andrews. 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: 5076–5088.
   PubMed Web of Science ®Google Scholar
• Iyer, V. R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, and P. O. Brown. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533–538.
   PubMed Web of Science ®Google Scholar
• Kladde, M. P., M. Xu, and R. T. Simpson. 1996. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J. 15: 6290–6300.
   PubMedGoogle Scholar
• Komeili, A., and E. K. O'Shea. 1999. Roles of phosphorylation sites in regulating activity of the transcription factor Pho4. Science 284: 977–980.
   PubMedGoogle Scholar
• Kornberg, A., N. N. Rao, and D. Ault-Riché. 1999. Inorganic polyphosphate: a molecule of many functions. Annu. Rev. Biochem. 68: 89–125.
   PubMed Web of Science ®Google Scholar
• Krebs, J. E., C. J. Fry, M. L. Samuels, and C. L. Peterson. 2000. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102: 587–598.
   PubMed Web of Science ®Google Scholar
• Kumble, K. D., and A. Kornberg. 1996. Endopolyphosphatases for long chain inorganic polyphosphate in yeast and mammals. J. Biol. Chem. 271: 27146–27151.
   PubMed Web of Science ®Google Scholar
• Lau, W. W., K. R. Schneider, and E. K. O'Shea. 1998. A genetic study of signaling processes for repression of PHO5 transcription in Saccharomyces cerevisiae. Genetics 150: 1349–1359.
   PubMedGoogle Scholar
• Laurent, B. C., I. Treich, and M. Carlson. 1993. The yeast SNF2/SWI2-protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev. 7: 583–591.
   PubMedGoogle Scholar
• Lenburg, M. E., and E. K. O'Shea. 1996. Signaling phosphate starvation. Trends Biochem. Sci. 21: 383–387.
   PubMedGoogle Scholar
• Lew, D. J., T. Weinert, and J. R. Pringle. 1997. Cell cycle control in Saccharomyces cerevisiae, p. 607–695. In J. R. Pringle, J. R. Broach, and E. W. Jones (ed.), The molecular and cellular biology of the yeast Saccharomyces. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
   Google Scholar
• Lillie, S. H., and J. R. Pringle. 1980. Reserve carbohydrate metabolism in Saccharomyces cerevisiae: responses to nutrient limitation. J. Bacteriol. 143: 1384–1394.
   PubMed Web of Science ®Google Scholar
• Müller, O., M. J. Bayer, C. Peters, J. S. Andersen, M. Mann, and A. Mayer. 2002. The Vtc proteins in vacuole fusion: coupling NSF activity to V0 trans-complex formation. EMBO J. 21: 259–269.
   PubMed Web of Science ®Google Scholar
• Nicolay, K., W. A. Scheffers, P. M. Bruinenberg, and R. Kaptein. 1983. In vivo 31P NMR studies on the role of the vacuole in phosphate metabolism in yeasts. Arch. Microbiol. 134: 270–275.
   PubMedGoogle 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
• O'Neill, E. M., A. Kaffman, E. R. Jolly, and E. K. O'Shea. 1996. Regulation of PHO4 nuclear localization by the PHO80-PHO85 cyclin-CDK complex. Science 271: 209–212.
   PubMed Web of Science ®Google Scholar
• Oshima, Y., N. Ogawa, and S. Harashima. 1996. Regulation of phosphatase synthesis in Saccharomyces cerevisiae—a review. Gene 179: 171–177.
   PubMed Web of Science ®Google Scholar
• Pringle, J. R., and L. H. Hartwell. 1981. The Saccharomyces cerevisiae cell cycle, p. 97–142. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces: life cycle and inheritance. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
   Google Scholar
• Rose, M. D., F. Winston, and P. Hieter. 1990. Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor Laboratory Press, Plainview, N.Y.
   Google Scholar
• Schmid, A., K. D. Fascher, and W. Hürz. 1992. Nucleosome disruption at the yeast PHO5 promoter upon PHO5 induction occurs in the absence of DNA replication. Cell 71: 853–864.
   PubMedGoogle Scholar
• Schneider, K. R., R. L. Smith, and E. K. O'Shea. 1994. Phosphate-regulated inactivation of the kinase PHO80-PHO85 by the CDK inhibitor PHO81. Science 266: 122–126.
   PubMedGoogle Scholar
• Sethuraman, A., N. N. Rao, and A. Kornberg. 2001. The endopolyphosphatase gene: essential in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 98: 8542–8547.
   PubMed Web of Science ®Google Scholar
• Shirahama, K., Y. Yazaki, K. Sakano, Y. Wada, and Y. Ohsumi. 1996. Vacuolar function in the phosphate homeostasis of the yeast Saccharomyces cerevisiae. Plant Cell Physiol. 37: 1090–1093.
   PubMedGoogle Scholar
• Spellman, P. T., G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9: 3273–3297.
   PubMed Web of Science ®Google Scholar
• Sudarsanam, P., V. R. Iyer, P. O. Brown, and F. Winston. 2000. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97: 3364–3369.
   PubMed Web of Science ®Google Scholar
• Urech, K., M. Durr, T. Boller, A. Wiemken, and J. Schwencke. 1978. Localization of polyphosphate in vacuoles of Saccharomyces cerevisiae. Arch. Microbiol. 116: 275–278.
   PubMed Web of Science ®Google Scholar
• Veinot-Drebot, L. M., G. C. Johnston, and R. A. Singer. 1991. A cyclin protein modulates mitosis in the budding yeast Saccharomyces cerevisiae. Curr. Genet. 19: 15–19.
   PubMedGoogle Scholar
• Wang, Y., C. L. Liu, J. D. Storey, R. J. Tibshirani, D. Herschlag, and P. O. Brown. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99: 5860–5865.
   PubMed Web of Science ®Google Scholar
• Wurst, H., T. Shiba, and A. Kornberg. 1995. The gene for a major exopolyphosphatase of Saccharomyces cerevisiae. J. Bacteriol. 177: 898–906.
   PubMed Web of Science ®Google Scholar
• Wykoff, D. D., and E. K. O'Shea. 2001. Phosphate transport and sensing in Saccharomyces cerevisiae. Genetics 159: 1491–1499.
   PubMedGoogle Scholar