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Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase

Abstract

Yeast Sir2 is a heterochromatin component that silences transcription at silent mating loci1, telomeres2 and the ribosomal DNA3,4, and that also suppresses recombination in the rDNA5 and extends replicative life span6. Mutational studies indicate that lysine 16 in the amino-terminal tail of histone H4 and lysines 9, 14 and 18 in H3 are critically important in silencing, whereas lysines 5, 8 and 12 of H4 have more redundant functions7,8,9. Lysines 9 and 14 of histone H3 and lysines 5, 8 and 16 of H4 are acetylated in active chromatin and hypoacetylated in silenced chromatin, and overexpression of Sir2 promotes global deacetylation of histones9,10, indicating that Sir2 may be a histone deacetylase. Deacetylation of lysine 16 of H4 is necessary for binding the silencing protein, Sir3 (ref. 8). Here we show that yeast and mouse Sir2 proteins are nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylases, which deacetylate lysines 9 and 14 of H3 and specifically lysine 16 of H4. Our analysis of two SIR2 mutations supports the idea that this deacetylase activity accounts for silencing, recombination suppression and extension of life span in vivo. These findings provide a molecular framework of NAD-dependent histone deacetylation that connects metabolism, genomic silencing and ageing in yeast and, perhaps, in higher eukaryotes.

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Figure 1: In vitro deacetylation assays of the H3 peptide (residues 1–20) di-acetylated at lysines 9 and 14 by recombinant yeast Sir2.
Figure 2: Amino-terminal sequencing of peaks 4 and 5 of the Sir2 deacetylase reaction at 1 mM NAD as determined by Edman degradation.
Figure 3: The deacetylation activity of yeast Sir2 on the H4 peptide (residues 2–19) tetra-acetylated at lysines 5, 8, 12 and 16.
Figure 4: Effects of inhibitors on the deacetylase and ADP-ribosyltransferase activities of recombinant Sir2 (rSir2).
Figure 5: Deacetylation activity of Sir2 is essential for silencing, recombination suppression and life-span extension in vivo.

References

  1. Rine, J. & Herskowitz, I. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae . Genetics 116, 9–22 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Gottschling, D. E., Aparicio, O. M., Billington, B. L. & Zakian, V. A. Position effect at S. cerevisiae telomeres: reversible repression of Pol ll transcription. Cell 63, 751– 762 (1990).

    Article  CAS  PubMed  Google Scholar 

  3. Bryk, M. et al. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11, 255–269 (1997).

    Article  CAS  PubMed  Google Scholar 

  4. Smith, J. S. & Boeke, J. D. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11, 241–254 (1997).

    Article  CAS  PubMed  Google Scholar 

  5. Gottlieb, S. & Esposito, R. E. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56, 771–776 (1989).

    Article  CAS  PubMed  Google Scholar 

  6. Kaeberlein, M., McVey, M. & Guarente, L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 13, 2570–2580 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Thompson, J. S., Ling, X. & Grunstein, M. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature 369 , 245–247 (1994).

    Article  ADS  CAS  PubMed  Google Scholar 

  8. Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S. M. & Grunstein, M. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: A molecular model for the formation of heterochromatin in yeast. Cell 80, 583– 592 (1995).

    Article  CAS  PubMed  Google Scholar 

  9. Braunstein, M., Sobel, R. E., Allis, C. D., Turner, B. M. & Broach, J. R. Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol. 16, 4349–4356 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Braunstein, M., Rose, A. B., Holmes, S. G., Allis, C. D. & Broach, J. R. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7, 592–604 (1993).

    Article  CAS  PubMed  Google Scholar 

  11. Sinclair, D. A. & Guarente, L. Extrachromosomal rDNA circles—a cause of aging in yeast. Cell 91, 1–20 (1997).

    Article  Google Scholar 

  12. Brachmann, C. B. et al. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability. Genes Dev. 9, 2888–2902 (1995).

    Article  CAS  PubMed  Google Scholar 

  13. Tsang, A. W. & Escalante-Semerena, J. C. CobB, a new member of the SIR2 family of eucaryotic regulatory proteins, is required to compensate for the lack of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase activity in cobT mutants during cobalamin biosynthesis in Salmonella typhimurium LT2. J. Biol. Chem. 273, 31788–31794 (1998).

    Article  CAS  PubMed  Google Scholar 

  14. Frye, R. A. Characterization of five human cDNAs with homology to yeast SIR2 gene: Sir2-like proteins (Sirtuins) metabolize NAD and may have protein ADP-ribosyltransferase activity. Biochem. Biophys. Res. Commun. 260, 273–279 (1999).

    Article  CAS  PubMed  Google Scholar 

  15. Tanny, J. C., Dowd, G. J., Huang, J., Hilz, H. & Moazed, D. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99, 735– 745 (1999).

    Article  CAS  PubMed  Google Scholar 

  16. Yoshida, M., Kijima, M. & Akita, M. & Beppu, T. Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by Trichostatin A. J. Biol. Chem. 265, 17174–17179 (1990).

    CAS  PubMed  Google Scholar 

  17. Taunton, J., Hassig, C. A. & Schreiber, S. L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408–411 (1996).

    Article  ADS  CAS  PubMed  Google Scholar 

  18. Banasik, M. & Ueda, K. Inhibitors and activators of ADP-ribosylation reactions. Mol. Cel. Biochem. 138, 185– 197 (1994).

    Article  CAS  Google Scholar 

  19. Mills, K. D., Sinclair, D. A. & Guarente, L. MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks. Cell 97, 609–620 (1999).

    Article  CAS  PubMed  Google Scholar 

  20. Martin, S. G., Laroche, T., Suka, N., Grunstein, M. & Gasser, S. M. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97, 621–633 (1999).

    Article  CAS  PubMed  Google Scholar 

  21. Boulton, S. J. & Jackson, S. P. Identification of a Saccharomyces cerevisiae Ku80 homolog: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 24 , 4639–4648 (1998).

    Article  Google Scholar 

  22. Tsukamoto, Y., Kato, J. & Ikeda, H. Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature 388, 900– 903 (1997).

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Adamietz, P. & Rudolph, A. ADP-ribosylation of nuclear proteins in vivo: identification of histone H2B as a major acceptor for mono- and poly(ADP-ribose) in dimethyl sulfate-treated hepatoma AH7974 cells. J. Biol. Chem. 259, 6841–6846 (1984).

    CAS  PubMed  Google Scholar 

  24. Kreimeyer, A., Wielckens, K., Adamietz, P. & Hilz, H. DNA repair-associated ADP-ribosylation in vivo: modification of histone H1 differs from that of the principal acceptor proteins. J. Biol. Chem. 259, 890–896 ( 1984).

    CAS  PubMed  Google Scholar 

  25. Pero, R. W., Holmgren, K. & Persson, L. Gamma-radiation induced ADP-ribosyltransferase activity and mammalian longevity. Mutat. Res. 142, 69–73 (1985).

    Article  CAS  PubMed  Google Scholar 

  26. Meyer, T. & Hilz, H. Production of anti-(ADP-ribose) antibodies with the aid of a dinucleotide-pyrophosphatase-resident hapten and their application for the detection of mono(ADP-ribosyl)ated polypeptides. Eur. J. Biochem 155, 157–165 ( 1986).

    Article  CAS  PubMed  Google Scholar 

  27. Muller, I., Zimmermann, M., Becker, D. & Flomer, M. Calendar life span versus budding life span of Saccharomyces cerevisiae. Mech. Ageing Dev. 12, 47–52 ( 1980).

    Article  CAS  PubMed  Google Scholar 

  28. Lakowski, B. & Hekimi, S. The genetics of caloric restriction in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 95, 13091–13096 (1998).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Weindruch, R. H., Walford, R. L., Fligiel, S. & Guthrie, D. The retardation of aging in mice by dietary restriction: Longevity, cancer, immunity, and lifetime energy intake. J. Nutr. 116, 641–654 (1986).

    Article  CAS  PubMed  Google Scholar 

  30. Roth, G. S. Calorie restriction in primates: will it work and how will we know? J. Am. Geriatr. Soc. 47, 896–903 (1999).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank R. Cook, A. Park, and H. Amoroso at the MIT Biopolymers lab for the HPLC and electron-spray mass spectroscopy, and P. Matsudaira for the MALDI mass spectroscopy. We also thank S. Inamoto for bacterial strains, and H. Tissenbaum and E. Ford for comments on the paper. This work was funded by The Human Frontier Science Program Organization Long-Term Fellowship to S. I., a NIH predoctoral grant to C.A. and M.K., and grants from the NIH, Seaver Foundation, Ellison Medical Foundation, and Howard and Linda Stern Fund to L.G.

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Imai, Si., Armstrong, C., Kaeberlein, M. et al. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403, 795–800 (2000). https://doi.org/10.1038/35001622

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