Swapping the Gene-Specific and Regional Silencing Specificities of the Hst1 and Sir2 Histone Deacetylases

REFERENCES

• Ai, W., P. G. Bertram, C. K. Tsang, T. F. Chan, and X. F. Zheng. 2002. Regulation of subtelomeric silencing during stress response. Mol. Cell. 10:1295–1305.
   PubMedGoogle Scholar
• Avalos, J. L., I. Celic, S. Muhammad, M. S. Cosgrove, J. D. Boeke, and C. Wolberger. 2002. Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Mol. Cell 10:523–535.
   PubMed Web of Science ®Google Scholar
• Brachmann, C. B., J. M. Sherman, S. E. Devine, E. E. Cameron, L. Pillus, and J. D. Boeke. 1995. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev. 9:2888–2902.
   PubMed Web of Science ®Google Scholar
• Chang, J. H., H. C. Kim, K. Y. Hwang, J. W. Lee, S. P. Jackson, S. D. Bell, and Y. Cho. 2002. Structural basis for the NAD-dependent deacetylase mechanism of Sir2. J. Biol. Chem. 277:34489–34498.
   PubMedGoogle Scholar
• Cockell, M. M., S. Perrod, and S. M. Gasser. 2000. Analysis of Sir2p domains required for rDNA and telomeric silencing in Saccharomyces cerevisiae. Genetics 154:1069–1083.
   PubMedGoogle Scholar
• Cubizolles, F., F. Martino, S. Perrod, and S. M. Gasser. 2006. A homotrimer-heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. Mol. Cell 21:825–836.
   PubMedGoogle Scholar
• Cuperus, G., R. Shafaatian, and D. Shore. 2000. Locus specificity determinants in the multifunctional yeast silencing protein Sir2. EMBO J. 19:2641–2651.
   PubMedGoogle Scholar
• Cuperus, G., and D. Shore. 2002. Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics 162:633–645.
   PubMedGoogle Scholar
• Denu, J. M. 2003. Linking chromatin function with metabolic networks: Sir2 family of NAD+-dependent deacetylases. Trends Biochem. Sci. 28:41–48.
   PubMed Web of Science ®Google Scholar
• Derbyshire, M. K., K. G. Weinstock, and J. N. Strathern. 1996. HST1, a new member of the SIR2 family of genes. Yeast 12:631–640.
   PubMed Web of Science ®Google Scholar
• Dryden, S. C., F. A. Nahhas, J. E. Nowak, A. S. Goustin, and M. A. Tainsky. 2003. Role for human SIRT2 NAD-dependent deacetylase activity in control of mitotic exit in the cell cycle. Mol. Cell. Biol. 23:3173–3185.
   PubMed Web of Science ®Google Scholar
• Finnin, M. S., J. R. Donigian, and N. P. Pavletich. 2001. Structure of the histone deacetylase SIRT2. Nat. Struct. Biol. 8:621–625.
   PubMedGoogle Scholar
• Frye, R. A. 2000. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res. Commun. 273:793–798.
   PubMed Web of Science ®Google Scholar
• Gailus-Durner, V., J. Xie, C. Chintamaneni, and A. K. Vershon. 1996. Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene. Mol. Cell. Biol. 16:2777–2786.
   PubMedGoogle Scholar
• Gotta, M., S. Strahl-Bolsinger, H. Renauld, T. Laroche, B. K. Kennedy, M. Grunstein, and S. M. Gasser. 1997. Localization of Sir2p: the nucleolus as a compartment for silent information regulators. EMBO J. 16:3243–3255.
   PubMedGoogle Scholar
• Hallows, W. C., S. Lee, and J. M. Denu. 2006. Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases. Proc. Natl. Acad. Sci. USA 103:10230–10235.
   PubMed Web of Science ®Google Scholar
• Hoppe, G. J., J. C. Tanny, A. D. Rudner, S. A. Gerber, S. Danaie, S. P. Gygi, and D. Moazed. 2002. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol. 22:4167–4180.
   PubMed Web of Science ®Google Scholar
• Huang, J., and D. Moazed. 2003. Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes Dev. 17:2162–2176.
   PubMed Web of Science ®Google Scholar
• Imai, S., C. M. Armstrong, M. Kaeberlein, and L. Guarente. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795–800.
   PubMed Web of Science ®Google Scholar
• Irlbacher, H., J. Franke, T. Manke, M. Vingron, and A. E. Ehrenhofer-Murray. 2005. Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression. Genes Dev. 19:1811–1822.
   PubMed Web of Science ®Google Scholar
• Landry, J., J. T. Slama, and R. Sternglanz. 2000. Role of NAD+ in the deacetylase activity of the SIR2-like proteins. Biochem. Biophys. Res. Commun. 278:685–690.
   PubMed Web of Science ®Google Scholar
• Landry, J., A. Sutton, S. T. Tafrov, R. C. Heller, J. Stebbins, L. Pillus, and R. Sternglanz. 2000. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl. Acad. Sci. USA 97:5807–5811.
   PubMed Web of Science ®Google Scholar
• Luo, J., A. Y. Nikolaev, S. Imai, D. Chen, F. Su, A. Shiloh, L. Guarente, and W. Gu. 2001. Negative control of p53 by Sir2α promotes cell survival under stress. Cell 107:137–148.
   PubMed Web of Science ®Google Scholar
• Lynch, P. J., H. B. Fraser, E. Sevastopoulos, J. Rine, and L. N. Rusche. 2005. Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae. Mol. Cell. Biol. 25:5920–5932.
   PubMed Web of Science ®Google Scholar
• Marmorstein, R. 2004. Structure and chemistry of the Sir2 family of NAD+-dependent histone/protein deactylases. Biochem. Soc. Trans. 32:904–909.
   PubMed Web of Science ®Google Scholar
• McCord, R., M. Pierce, J. Xie, S. Wonkatal, C. Mickel, and A. K. Vershon. 2003. Rfm1, a novel tethering factor required to recruit the Hst1 histone deacetylase for repression of middle sporulation genes. Mol. Cell. Biol. 23:2009–2016.
   PubMedGoogle Scholar
• Min, J., J. Landry, R. Sternglanz, and R. M. Xu. 2001. Crystal structure of a SIR2 homolog-NAD complex. Cell 105:269–279.
   PubMed Web of Science ®Google Scholar
• Moazed, D., A. Kistler, A. Axelrod, J. Rine, and A. D. Johnson. 1997. Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc. Natl. Acad. Sci. USA 94:2186–2191.
   PubMedGoogle Scholar
• Muhlrad, D., R. Hunter, and R. Parker. 1992. A rapid method for localized mutagenesis of yeast genes. Yeast 8:79–82.
   PubMed Web of Science ®Google Scholar
• North, B. J., B. L. Marshall, M. T. Borra, J. M. Denu, and E. Verdin. 2003. The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase. Mol. Cell 11:437–444.
   PubMed Web of Science ®Google Scholar
• Pagans, S., A. Pedal, B. J. North, K. Kaehlcke, B. L. Marshall, A. Dorr, C. Hetzer-Egger, P. Henklein, R. Frye, M. W. McBurney, H. Hruby, M. Jung, E. Verdin, and M. Ott. 2005. SIRT1 regulates HIV transcription via Tat deacetylation. PloS Biol. 3:e41.
   PubMed Web of Science ®Google Scholar
• Perrod, S., M. M. Cockell, T. Laroche, H. Renauld, A. L. Ducrest, C. Bonnard, and S. M. Gasser. 2001. A cytosolic NAD-dependent deacetylase, Hst2p, can modulate nucleolar and telomeric silencing in yeast. EMBO J. 20:197–209.
   PubMed Web of Science ®Google Scholar
• Pierce, M., M. Wagner, J. Xie, V. Gailus-Durner, J. Six, A. K. Vershon, and E. Winter. 1998. Transcriptional regulation of the SMK1 mitogen-activated protein kinase gene during meiotic development in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:5970–5980.
   PubMedGoogle Scholar
• Pijnappel, W. W., D. Schaft, A. Roguev, A. Shevchenko, H. Tekotte, M. Wilm, G. Rigaut, B. Seraphin, R. Aasland, and A. F. Stewart. 2001. The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. Genes Dev. 15:2991–3004.
   PubMedGoogle Scholar
• Rusche, L. N., and J. Rine. 2001. Conversion of a gene-specific repressor to a regional silencer. Genes Dev. 15:955–967.
   PubMed Web of Science ®Google Scholar
• Schwer, B., B. J. North, R. A. Frye, M. Ott, and E. Verdin. 2002. The human silent information regulator (Sir)2 homologue hSIRT3 is a mitochondrial nicotinamide adenine dinucleotide-dependent deacetylase. J. Cell Biol. 158:647–657.
   PubMed Web of Science ®Google Scholar
• Sherman, J. M., E. M. Stone, L. L. Freeman-Cook, C. B. Brachmann, J. D. Boeke, and L. Pillus. 1999. The conserved core of a human SIR2 homologue functions in yeast silencing. Mol. Biol. Cell 10:3045–3059.
   PubMedGoogle Scholar
• Shou, W., J. H. Seol, A. Shevchenko, C. Baskerville, D. Moazed, Z. W. Chen, J. Jang, H. Charbonneau, and R. J. Deshaies. 1999. Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97:233–244.
   PubMed Web of Science ®Google Scholar
• Smith, J. S., and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241–254.
   PubMed Web of Science ®Google Scholar
• Starai, V. J., H. Takahashi, J. D. Boeke, and J. C. Escalante-Semerena. 2003. Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae. Genetics 163:545–555.
   PubMedGoogle Scholar
• Straight, A. F., W. Shou, G. J. Dowd, C. W. Turck, R. J. Deshaies, A. D. Johnson, and D. Moazed. 1999. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97:245–256.
   PubMed Web of Science ®Google Scholar
• Sutton, A., R. C. Heller, J. Landry, J. S. Choy, A. Sirko, and R. Sternglanz. 2001. A novel form of transcriptional silencing by sum1-1 requires hst1 and the origin recognition complex. Mol. Cell. Biol. 21:3514–3522.
   PubMed Web of Science ®Google Scholar
• Tanny, J. C., G. J. Dowd, J. Huang, H. Hilz, and D. Moazed. 1999. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99:735–745.
   PubMedGoogle Scholar
• Tanny, J. C., D. S. Kirkpatrick, S. A. Gerber, S. P. Gygi, and D. Moazed. 2004. Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions. Mol. Cell. Biol. 24:6931–6946.
   PubMedGoogle Scholar
• van der Horst, A., L. G. Tertoolen, L. M. de Vries-Smits, R. A. Frye, R. H. Medema, and B. M. Burgering. 2004. FOXO4 is acetylated upon peroxide stress and deacetylated by the longevity protein hSir2(SIRT1). J. Biol. Chem. 279:28873–28879.
   PubMed Web of Science ®Google Scholar
• Vaquero, A., M. B. Scher, D. H. Lee, A. Sutton, H. L. Cheng, F. W. Alt, L. Serrano, R. Sternglanz, and D. Reinberg. 2006. SirT2 is a histone deacetylase with preference for histone H4 Lys 16 during mitosis. Genes Dev. 20:1256–1261.
   PubMed Web of Science ®Google Scholar
• Vaziri, H., S. K. Dessain, E. Ng Eaton, S. I. Imai, R. A. Frye, T. K. Pandita, L. Guarente, and R. A. Weinberg. 2001. hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell 107:149–159.
   PubMed Web of Science ®Google Scholar
• Verdin, E., F. Dequiedt, and H. G. Kasler. 2003. Class II histone deacetylases: versatile regulators. Trends Genet. 19:286–293.
   PubMed Web of Science ®Google Scholar
• Xie, J., M. Pierce, V. Gailus-Durner, M. Wagner, E. Winter, and A. K. Vershon. 1999. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J. 18:6448–6454.
   PubMed Web of Science ®Google Scholar
• Zhao, K., X. Chai, A. Clements, and R. Marmorstein. 2003. Structure and autoregulation of the yeast Hst2 homolog of Sir2. Nat. Struct. Biol. 10:864–871.
   PubMedGoogle Scholar
• Zhao, K., X. Chai, and R. Marmorstein. 2003. Structure of the yeast Hst2 protein deacetylase in ternary complex with 2′-O-acetyl ADP ribose and histone peptide. Structure 11:1403–1411.
   PubMedGoogle Scholar
• Zhao, K., R. Harshaw, X. Chai, and R. Marmorstein. 2004. Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases. Proc. Natl. Acad. Sci. USA 101:8563–8568.
   PubMed Web of Science ®Google Scholar