Deciphering NAD-Dependent Deacetylases

Structural comparisons between other Sir2p family members, especially of the zinc binding and helical domains, should reveal further clues to the sources of substrate specificity. This first structure of Sir2-Af1 represents a road map to guide construction of hybrid proteins aimed at deciphering the function of different family members. For example, the structure identifies more precise locations at which the zinc binding domains and/or helical domains may be exchanged between different family members, and identifies surfaces and sites that may tested for their roles in specifying interacting partners and substrates. Each new structure solved, particularly those with bound substrates or reaction intermediates will aid understanding of the unusual, emerging mechanism of NAD-dependent deacetylation.Beyond the structural information, exciting data from other fronts add to the range of potential substrates and biological roles Sir2p and its homologs may have. Already, the recognition of TAFI68 as a substrate of mammalian Sir2p suggests an in vivo role in PolI-directed transcription (Muth et al., 2001xMuth, V., Nadaud, S., Grummt, I., and Voit, R. EMBO J. 2001; 20: 1353–1362Crossref | Scopus (151)See all References(Muth et al., 2001). The discovery that modestly increased SIR2 gene dosage influences lifespan of both yeast and the metazoan Caenorhabditis elegans points to conserved, organismally significant roles for the enzymes (Tissenbaum and Guarente, 2001xTissenbaum, H.A. and Guarente, L. Nature. 2001; 410: 227–230Crossref | PubMed | Scopus (1205)See all References(Tissenbaum and Guarente, 2001). That a major HST-encoded activity in yeast is cytoplasmic and can disrupt gene regulation when imported into the nucleus underscores the importance of regulation of distinct family members, even within the same cell (Perrod et al., 2001xPerrod, S., Cockell, M.M., Laroche, T., Renauld, H., Ducrest, A.L., Bonnard, C., and Gasser, S.M. EMBO J. 2001; 20: 197–209Crossref | Scopus (110)See all References(Perrod et al., 2001). Finally, accumulating microarray surveys for transcriptional effects of Sir2p and other deacetylases in yeast (Wyrick et al. 1999xWyrick, J.J., Holstege, F.C., Jennings, E.G., Causton, H.C., Shore, D., Grunstein, M., Lander, E.S., and Young, R.A. Nature. 1999; 402: 418–421Crossref | PubMed | Scopus (295)See all References, Bernstein et al. 2000xBernstein, B.E., Tong, J.K., and Schreiber, S.L. Proc. Natl. Acad. Sci. USA. 2000; 97: 13708–13713Crossref | PubMed | Scopus (283)See all References), and recent mapping of genomic targets of a Drosophila Sir2p (van Steensel et al., 2001xvan Steensel, B., Delrow, J., and Henikoff, S. Nat. Genet. 2001; 27: 304–308Crossref | PubMed | Scopus (173)See all References(van Steensel et al., 2001) all raise the possibility that Sir2p and its partners function to both activate and repress transcription.Thus, it seems likely that Sir2p and its homologs can function to fine-tune genomic regulation in several ways. There may be both positive or negative effects on transcription. There may be direct effects suppressing recombination. There may be effects modulating, or responding to, intracellular energetics and physiology via NAD. Understanding the structures, mechanisms, and substrates of the Sir2p/Hstp family of enzymes should ultimately reveal much about modifying and modulating activities of ancient enzymes and their evolving effects on chromatin, genomic control, and beyond.