Sirtuin/Sir2 Phylogeny, Evolutionary Considerations and Structural Conservation

Ahuja, 2007, Regulation of insulin secretion by SIRT4, a mitochondrial ADP-ribo-syltransferase, J. Biol. Chem, 282, 33583, 10.1074/jbc.M705488200

Aparicio, 1991, Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae, Cell, 66, 1279, 10.1016/0092-8674(91)90049-5

Astrom, 2003, The Drosophila melanogaster sir2+ gene is nonessential and has only minor effects on position-effect variegation, Genetics, 163, 931, 10.1093/genetics/163.3.931

Avalos, 2002, Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Mol, Cell, 10, 523

Baldauf, 2003, The deep roots of eukaryotes, Science, 300, 1703, 10.1126/science.1085544

Blander, 2005, SIRT1 shows no substrate specificity in vitro, J. Biol. Chem, 280, 9780, 10.1074/jbc.M414080200

Bowler, 2008, The Phaeodactylum genome reveals the evolutionary history of diatom genomes, Nature, 456, 239, 10.1038/nature07410

Braunstein, 1993, Transcriptional silencing in yeast is associated with reduced nucleosome acetylation, Genes Dev, 7, 592, 10.1101/gad.7.4.592

Braunstein, 1996, Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol, Cell Biol, 16, 4349

Brunet, 2004, Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase, Science, 303, 2011, 10.1126/science.1094637

Bryk, 1997, Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast, Genes Dev, 11, 255, 10.1101/gad.11.2.255

Chang, 2002, Structural basis for the NAD-dependent deacetylase mechanism of Sir2, J. Biol. Chem, 277, 34489, 10.1074/jbc.M205460200

Cohen, 2004, Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase, Science, 305, 390, 10.1126/science.1099196

Dai, 2007, SIRT1 interacts with p73 and suppresses p73-dependent transcriptional activity, J. Cell Physiol, 210, 161, 10.1002/jcp.20831

Dali-Youcef, 2007, Sirtuins: The ‘magnificent seven’, function, metabolism and longevity, Ann. Med, 39, 335, 10.1080/07853890701408194

der Ou, 2007, Structural evolution of C-terminal domains in the p53 family, EMBO J, 26, 3463, 10.1038/sj.emboj.7601764

Du, 2009, Investigating the ADP- ribosyltransferase activity of sirtuins with NAD analogs and 32P- NAD, Biochemistry, 48, 2878, 10.1021/bi802093g

Dryden, 2003, Role for human SIRT2 NAD-dependent deacetylase activity in control of mitotic exit in the cell cycle. Mol, Cell Biol, 23, 3173

Eichinger, 2005, The genome of the social amoeba Dictyostelium discoideum, Nature, 435, 43, 10.1038/nature03481

Finnin, 2001, Structure of the histone deacetylase SIRT2. Nat. Struct, Biol, 8, 621

Ford, 2006, Mammalian Sir2 homolog SIRT7 is an activator of RNA polymerase I transcription, Genes Dev, 20, 1075, 10.1101/gad.1399706

Fritze, 1997, Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA, EMBO J, 16, 6495, 10.1093/emboj/16.21.6495

Frye, 2000, Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res, Commun, 273, 793

Gardner, 2002, Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, 419, 498, 10.1038/nature01097

Ghedin, 2007, Draft genome of the filarial nematode parasite Brugia malayi, Science, 317, 1756, 10.1126/science.1145406

Gottlieb, 1989, A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA, Cell, 56, 771, 10.1016/0092-8674(89)90681-8

Greiss, 2008, C. elegans SIR-2. 1 translocation is linked to a proapoptotic pathway parallel to cep-1/p53 during DNA damage-induced apoptosis, Genes Dev., 22, 2831, 10.1101/gad.482608

Haigis, 2006, Mammalian sirtuins - emerging roles in physiology, aging, and calorie restriction, Genes Dev, 20, 2913, 10.1101/gad.1467506

Haigis, 2006, SIRT4 inhibits glutamate dehydrogenase and opposes the effects of calorie restriction in pancreatic beta cells, Cell, 126, 941, 10.1016/j.cell.2006.06.057

Hallows, 2006, Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases, Proc. Natl. Acad. Sci. USA, 103, 10230, 10.1073/pnas.0604392103

Hiratsuka, 2003, Proteomics-based identification of differentially expressed genes in human gliomas: Down-regulation of SIRT2 gene. Biochem. Biophys. Res, Commun, 309, 558

Holbert, 2005, Structure and activity of enzymes that remove histone modifications, Curr. Opin. Struct. Biol, 15, 673, 10.1016/j.sbi.2005.10.006

Hu, 2008, Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by Ab Initio QM/MM molecular dynamics simulations, J. Am. Chem. Soc, 130, 16721, 10.1021/ja807269j

Huson, 2006, Application of phylogenetic networks in evolutionary studies. Mol. Biol, Evol, 23, 254

Imai, 2000, Transcriptional silencing and longevity protein Sir2 is an NAD- dependent histone deacetylase, Nature, 403, 795, 10.1038/35001622

Inoue, 2006, SIRT2, a tubulin deacetylase, acts to block the entry to chromosome condensation in response to mitotic stress, Oncogene, 26, 945, 10.1038/sj.onc.1209857

Ivy, 1985, Map positions of yeast genes SIR1, SIR3 and SIR4, Genetics, 111, 735, 10.1093/genetics/111.4.735

Ivy, 1986, Cloning and characterization of four SIR genes of Saccharomyces cerevisiae. Mol. Cell, Biol, 6, 688

Jin, 2007, Cytoplasm-localized SIRT1 enhances apoptosis, J. Cell Physiol, 213, 88, 10.1002/jcp.21091

Kaeberlein, 1999, The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms, Genes Dev, 13, 2570, 10.1101/gad.13.19.2570

Katinka, 2001, Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi, Nature, 414, 450, 10.1038/35106579

Kawahara, 2009, SIRT6 links histone h3 lysine 9 deacetylation to NF-kappaB-dependent gene expression and organismal life span, Cell, 136, 62, 10.1016/j.cell.2008.10.052

Khan, 2005, Unstructured conformations are a substrate requirement for the Sir2 family of NAD- dependent protein deacetylases, J. Biol. Chem, 280, 36073, 10.1074/jbc.M508247200

King, 2008, The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans, Nature, 451, 783, 10.1038/nature06617

Klar, 1979, MAR1 - a Regulator of the HMa and HMa Loci in Saccharomyces cerevisiae, Genetics, 93, 37, 10.1093/genetics/93.1.37

Kowieski, 2008, Acetylationdependent ADP-ribosylation by Trypanosoma brucei Sir2, J. Biol. Chem, 283, 5317, 10.1074/jbc.M707613200

Landry, 2000, The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases, Proc. Natl. Acad. Sci. USA, 97, 5807, 10.1073/pnas.110148297

Liszt, 2005, Mouse Sir2 homolog SirT6 is a nuclear ADP-ribosyltransferase, J. Biol. Chem, 280, 21313, 10.1074/jbc.M413296200

Lombard, 2008, SIRT6 in DNA repair, metabolism and ageing, J. Intern. Med, 263, 128, 10.1111/j.1365-2796.2007.01902.x

Longo, 2006, Sirtuins in aging and age- related disease, Cell, 126, 257, 10.1016/j.cell.2006.07.002

Luo, 2001, Negative control of p53 by Sir2alpha promotes cell survival under stress, Cell, 107, 137, 10.1016/S0092-8674(01)00524-4

Mead, 2007, Swapping the gene-specific and regional silencing specificities of the Hst1 and Sir2 histone deacetylases. Mol. Cell, Biol, 27, 2466

Meng, 2006, Tools for integrated sequence-structure analysis with UCSF Chimera, Bmcbioinformatics, 7, 339

Michishita, 2005, Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Mol. Biol, Cell, 16, 4623

Michishita, 2008, SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin, Nature, 452, 492, 10.1038/nature06736

Min, 2001, Crystal structure of a SIR2 homolog-NAD complex, Cell, 105, 269, 10.1016/S0092-8674(01)00317-8

Motta, 2004, Mammalian SIRT1 represses forkhead transcription factors, Cell, 116, 551, 10.1016/S0092-8674(04)00126-6

Newman, 2002, A Drosophila homologue of Sir2 modifies position-effect variegation but does not affect life span, Genetics, 162, 1675, 10.1093/genetics/162.4.1675

North, 2004, Sirtuins: Sir2-related NAD- dependent protein deacetylases, Genomebiol, 5, 224

Oberdoerffer, 2008, SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging, Cell, 135, 907, 10.1016/j.cell.2008.10.025

Pankow, 2007, The p53 tumor suppressorlike protein nvp63 mediates selective germ cell death in the sea anemone Nematostella vectensis, Plos ONE, 2, e782, 10.1371/journal.pone.0000782

Pettersen, 2004, UCSF Chimera - a visualization system for exploratory research and analysis, J. Comput. Chem, 25, 1605, 10.1002/jcc.20084

Picard, 2004, Sirt1 promotes fat mobilization in white adipocytes by repressing PPAR-gamma, Nature, 429, 771, 10.1038/nature02583

Potente, 2007, SIRT1 controls endothelial angiogenic functions during vascular growth, Genes Dev, 21, 2644, 10.1101/gad.435107

Pruitt, 2006, Inhibition of SIRT1 reactivates silenced cancer genes without loss of promoter DNA hypermethylation, Plos Genet, 2, e40, 10.1371/journal.pgen.0020040

Rensing, 2008, The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants, Science, 319, 64, 10.1126/science.1150646

Richards, 2008, The genome of the model beetle and pest Tribolium castaneum, Nature, 452, 949, 10.1038/nature06784

Rodgers, 2005, Nutrient control of glucose homeostasis through a complex of PGC-1alpha and SIRT1, Nature, 434, 113, 10.1038/nature03354

Rogina, 2004, Sir2 mediates longevity in the fly through a pathway related to calorie restriction, Proc. Natl. Acad. Sci. USA, 101, 15998, 10.1073/pnas.0404184101

Rosenberg, 2002, Drosophila Sir2 is required for heterochromatic silencing and by euchromatic Hairy/E(Spl). bHLH repressors in segmentation and sex determination, Cell, 109, 447, 10.1016/S0092-8674(02)00732-8

Sauve, 2001, Chemistry of gene silencing: The mechanism of NAD+-dependent deacetylation reactions, Biochemistry, 40, 15456, 10.1021/bi011858j

Schlicker, 2008, Substrates and regulation mechanisms for the human mitochondrial sirtuins Sirt3 and Sirt5, J. Mol. Biol, 382, 790, 10.1016/j.jmb.2008.07.048

Schwer, 2008, Conserved metabolic regulatory functions of sirtuins, Cell Metab, 7, 104, 10.1016/j.cmet.2007.11.006

Schwer, 2006, Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2, Proc. Natl. Acad. Sci. USA, 103, 10224, 10.1073/pnas.0603968103

Shou, 1999, Exit from mitosis is triggered by Tem1- dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex, Cell, 97, 233, 10.1016/S0092-8674(00)80733-3

Sinclair, 1997, Extrachromosomal rDNA circles - a cause of aging in yeast, Cell, 91, 1033, 10.1016/S0092-8674(00)80493-6

Smith, 2000, A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family, Proc. Natl. Acad. Sci USA, 97, 6658, 10.1073/pnas.97.12.6658

Solignac, 2007, The genome of Apis mellifera: Dialog between linkage mapping and sequence assembly, Genome Biol, 8, 403, 10.1186/gb-2007-8-3-403

Srivastava, 2008, The Trichoplax genome and the nature of placozoans, Nature, 454, 955, 10.1038/nature07191

Stein, 2003, The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics, Plos Biol, 1, E45, 10.1371/journal.pbio.0000045

Straight, 1999, Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity, Cell, 97, 245, 10.1016/S0092-8674(00)80734-5

Tanner, 2000, Silent information regulator 2 family of NAD- dependent his- tone/protein deacetylases generates a unique product, 1-O- acetyl-ADP-ribose, Proc. Natl. Acad. Sci. USA, 97, 14178, 10.1073/pnas.250422697

Tanno, 2007, Nucleocytoplasmic shuttling of the NAD+-dependent histone deacetylase SIRT1, J. Biol. Chem, 282, 6823, 10.1074/jbc.M609554200

Tanny, 2001, Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: Evidence for acetyl transfer from substrate to an NAD breakdown product, Proc. Natl. Acad. Sci. USA, 98, 415, 10.1073/pnas.98.2.415

Tanny, 1999, An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing, Cell, 99, 735, 10.1016/S0092-8674(00)81671-2

Tissenbaum, 2001, Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans, Nature, 410, 227, 10.1038/35065638

Tsang, 1998, J.Biol. Chem, 273, 31788, 10.1074/jbc.273.48.31788

van der Horst, 2004, FOXO4 is acetylated upon peroxide stress and deacetylated by the longevity protein hSir2SIRT1, J. Biol. Chem, 279, 28873, 10.1074/jbc.M401138200

Vaquero, 2004, Human SirT1 interacts with histone H1 and promotes formation of facultative heterochromatin. Mol, Cell, 16, 93

Vaquero, 2006, SirT2 is a histone deacetylase with preference for histone H4 Lys 16 during mitosis, Genes Dev, 20, 1256, 10.1101/gad.1412706

Vaquero, 2007, SIRT1 regulates the histone methyltransferase SUV39H1 during heterochromatin formation, Nature, 450, 440, 10.1038/nature06268

Vaziri, 2001, hSIR2(SIRT1). functions as an NAD-dependent p53 deacetylase, Cell, 107, 149, 10.1016/S0092-8674(01)00527-X

Wang, 2006, Interactions between E2F1 and SirT1 regulate apoptotic response to DNA damage. Nat, Cell Biol, 8, 1025

Waterhouse, 2009, Jalview Version 2 - a multiple sequence alignment editor and analysis workbench, Bioinformatics, 25, 1189, 10.1093/bioinformatics/btp033

Wood, 2004, Sirtuin activators mimic caloric restriction and delay ageing in metazoans, Nature, 430, 686, 10.1038/nature02789

Yamamoto, 2007, Sirtuin functions in health and disease. Mol, Endocrinol, 21, 1745

Yeung, 2004, Modulation of NF-kappaB- dependent transcription and cell survival by the SIRT1 deacetylase, EMBO J, 23, 2369, 10.1038/sj.emboj.7600244

Zhao, 2003, Structure and autoregulation of the yeast Hst2 homolog of Sir2. Nat. Struct, Biol, 10, 864

Zhao, 2003, Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O- acetyl ADP ribose and histone peptide, Structure, 11, 1403, 10.1016/j.str.2003.09.016

Zhao, 2004, Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases, Proc. Natl. Acad. Sci. USA, 101, 8563, 10.1073/pnas.0401057101