The SAGA histone deubiquitinase module controls yeast replicative lifespan via Sir2 interaction.

We have analyzed the yeast replicative lifespan of a large number of open reading frame (ORF) deletions. Here, we report that strains lacking genes SGF73, SGF11, and UBP8 encoding SAGA/SLIK complex histone deubiquitinase module (DUBm) components are exceptionally long lived. Strains lacking other SAGA/SALSA components, including the acetyltransferase encoded by GCN5, are not long lived; however, these genes are required for the lifespan extension observed in DUBm deletions. Moreover, the SIR2-encoded histone deacetylase is required, and we document both a genetic and physical interaction between DUBm and Sir2. A series of studies assessing Sir2-dependent functions lead us to propose that DUBm strains are exceptionally long lived because they promote multiple prolongevity events, including reduced rDNA recombination and altered silencing of telomere-proximal genes. Given that ataxin-7, the human Sgf73 ortholog, causes the neurodegenerative disease spinocerebellar ataxia type 7, our findings indicate that the genetic and epigenetic interactions between DUBm and SIR2 will be relevant to neurodegeneration and aging.

[1]  John R Yates,et al.  Deubiquitination of Histone H2B by a Yeast Acetyltransferase Complex Regulates Transcription* , 2004, Journal of Biological Chemistry.

[2]  J. Workman,et al.  Yeast Sgf73/Ataxin-7 serves to anchor the deubiquitination module into both SAGA and Slik(SALSA) HAT complexes , 2009, Epigenetics & Chromatin.

[3]  E. Hurt,et al.  Yeast Ataxin-7 links histone deubiquitination with gene gating and mRNA export , 2008, Nature Cell Biology.

[4]  D. Sterner,et al.  Inhibition of TATA-Binding Protein Function by SAGA Subunits Spt3 and Spt8 at Gcn4-Activated Promoters , 2000, Molecular and Cellular Biology.

[5]  L. Guarente,et al.  Extrachromosomal rDNA Circles— A Cause of Aging in Yeast , 1997, Cell.

[6]  J. Boeke,et al.  An unusual form of transcriptional silencing in yeast ribosomal DNA. , 1997, Genes & development.

[7]  T. Chiba,et al.  Barrier Proteins Remodel and Modify Chromatin To Restrict Silenced Domains , 2004, Molecular and Cellular Biology.

[8]  A. Shilatifard,et al.  Histone H4 lysine-16 acetylation regulates cellular lifespan , 2009, Nature.

[9]  Matt Kaeberlein,et al.  Regulation of Yeast Replicative Life Span by TOR and Sch9 in Response to Nutrients , 2005, Science.

[10]  Ali Shilatifard,et al.  Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. , 2003, Genes & development.

[11]  S. Jazwinski Rtg2 protein: at the nexus of yeast longevity and aging. , 2005, FEMS yeast research.

[12]  B. Chait,et al.  Polyglutamine-expanded ataxin-7 inhibits STAGA histone acetyltransferase activity to produce retinal degeneration. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. Taylor,et al.  Repeat expansion disease: progress and puzzles in disease pathogenesis , 2010, Nature Reviews Genetics.

[14]  B. Kennedy,et al.  Genome-wide analysis of yeast aging. , 2012, Sub-cellular biochemistry.

[15]  F. Wilcoxon,et al.  Individual comparisons of grouped data by ranking methods. , 1946, Journal of economic entomology.

[16]  M. Osley,et al.  A role for H2B ubiquitylation in DNA replication. , 2012, Molecular cell.

[17]  B. Chait,et al.  Human STAGA Complex Is a Chromatin-Acetylating Transcription Coactivator That Interacts with Pre-mRNA Splicing and DNA Damage-Binding Factors In Vivo , 2001, Molecular and Cellular Biology.

[18]  L. Guarente Sirtuins, aging, and metabolism. , 2011, Cold Spring Harbor symposia on quantitative biology.

[19]  M. A. Vega-Palas,et al.  Telomeric transcriptional silencing in a natural context , 1997, Nature Genetics.

[20]  Matt Kaeberlein,et al.  Quantitative evidence for conserved longevity pathways between divergent eukaryotic species. , 2008, Genome research.

[21]  H. Orr,et al.  Nuclear localization of the spinocerebellar ataxia type 7 protein, ataxin-7. , 1999, Human molecular genetics.

[22]  E. Kaplan,et al.  Nonparametric Estimation from Incomplete Observations , 1958 .

[23]  L. Kruglyak,et al.  A Natural Polymorphism in rDNA Replication Origins Links Origin Activation with Calorie Restriction and Lifespan , 2013, PLoS genetics.

[24]  B. Kennedy,et al.  Measuring Replicative Life Span in the Budding Yeast , 2009, Journal of visualized experiments : JoVE.

[25]  B. Stillman,et al.  A common telomeric gene silencing assay is affected by nucleotide metabolism. , 2011, Molecules and Cells.

[26]  John J. Wyrick,et al.  Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast , 1999, Nature.

[27]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[28]  Làszlò Tora,et al.  Ataxin-7 is a subunit of GCN5 histone acetyltransferase-containing complexes. , 2004, Human molecular genetics.

[29]  J. Workman,et al.  Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange , 2012, Nature Structural &Molecular Biology.

[30]  A. Brice,et al.  Spinocerebellar ataxia 7 (SCA7) , 2003, Cytogenetic and Genome Research.

[31]  M. A. Vega-Palas,et al.  Telomeric silencing of a natural subtelomeric gene , 2000, Molecular and General Genetics MGG.

[32]  S. Fields,et al.  Genes determining yeast replicative life span in a long-lived genetic background , 2005, Mechanisms of Ageing and Development.

[33]  N. Krogan,et al.  Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. , 2005, Molecular cell.

[34]  B. Kennedy,et al.  Replicative aging in yeast: the means to the end. , 2008, Annual review of cell and developmental biology.

[35]  R. E. Esposito,et al.  A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA , 1989, Cell.

[36]  Michael Grunstein,et al.  Sir2 deacetylates histone H3 lysine 56 to regulate telomeric heterochromatin structure in yeast. , 2007, Molecular cell.

[37]  B. Kennedy,et al.  Mutation in the silencing gene S/R4 can delay aging in S. cerevisiae , 1995, Cell.

[38]  C. Ware,et al.  Polyglutamine-Expanded Ataxin-7 Antagonizes CRX Function and Induces Cone-Rod Dystrophy in a Mouse Model of SCA7 , 2001, Neuron.

[39]  Y. Agid,et al.  Cloning of the SCA7 gene reveals a highly unstable CAG repeat expansion , 1997, Nature Genetics.

[40]  R. Mortimer,et al.  Life Span of Individual Yeast Cells , 1959, Nature.

[41]  M. Hatashita,et al.  C‐terminus of the Sgf73 subunit of SAGA and SLIK is important for retention in the larger complex and for heterochromatin boundary function , 2013, Genes to cells : devoted to molecular & cellular mechanisms.

[42]  S. Gygi,et al.  A High-Confidence Interaction Map Identifies SIRT1 as a Mediator of Acetylation of USP22 and the SAGA Coactivator Complex , 2013, Molecular and Cellular Biology.

[43]  L. Pillus,et al.  A unique class of conditional sir2 mutants displays distinct silencing defects in Saccharomyces cerevisiae. , 2002, Genetics.

[44]  A Dürr,et al.  Spinocerebellar ataxia type 7 (SCA7): a neurodegenerative disorder with neuronal intranuclear inclusions. , 1998, Human molecular genetics.

[45]  Matt Kaeberlein,et al.  Sir2-Independent Life Span Extension by Calorie Restriction in Yeast , 2004, PLoS biology.

[46]  Bing Li,et al.  Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. , 2011, Molecular cell.

[47]  Christopher J. Murakami,et al.  Sir2 deletion prevents lifespan extension in 32 long‐lived mutants , 2011, Aging cell.

[48]  Julia M. Schulze,et al.  Splitting the task: Ubp8 and Ubp10 deubiquitinate different cellular pools of H2BK123. , 2011, Genes & development.

[49]  A. Heck,et al.  Identification of Pep4p as the Protease Responsible for Formation of the SAGA-related SLIK Protein Complex* , 2010, The Journal of Biological Chemistry.

[50]  L. Pillus,et al.  The SAGA Subunit Ada2 Functions in Transcriptional Silencing , 2009, Molecular and Cellular Biology.

[51]  F. Pryde,et al.  Limitations of silencing at native yeast telomeres , 1999, The EMBO journal.

[52]  Jianxun Song,et al.  USP22 antagonizes p53 transcriptional activation by deubiquitinating Sirt1 to suppress cell apoptosis and is required for mouse embryonic development. , 2012, Molecular cell.

[53]  Oscar M. Aparicio,et al.  Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae , 1991, Cell.

[54]  D. Shore,et al.  Gcn5 and Sirtuins Regulate Acetylation of the Ribosomal Protein Transcription Factor Ifh1 , 2013, Current Biology.

[55]  M. Kaeberlein,et al.  Regulation of mRNA translation as a conserved mechanism of longevity control. , 2010, Advances in experimental medicine and biology.

[56]  A. Mal Histone methyltransferase Suv39h1 represses MyoD‐stimulated myogenic differentiation , 2006, The EMBO journal.

[57]  K. Hofmann,et al.  Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. , 2003, Human molecular genetics.

[58]  G. Fourel,et al.  Cohabitation of insulators and silencing elements in yeast subtelomeric regions , 1999, The EMBO journal.

[59]  A. Mushegian,et al.  Conserved phosphoprotein interaction motif is functionally interchangeable between ataxin-7 and arrestins. , 2000, Biochemistry.

[60]  B. Kennedy,et al.  The TOR pathway comes of age. , 2009, Biochimica et biophysica acta.

[61]  P. Silver,et al.  Elimination of replication block protein Fob1 extends the life span of yeast mother cells. , 1999, Molecular cell.

[62]  Harry T Orr,et al.  Pathogenic Mechanisms of a Polyglutamine-mediated Neurodegenerative Disease, Spinocerebellar Ataxia Type 1* , 2009, Journal of Biological Chemistry.

[63]  Claude C. Warzecha,et al.  The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression. , 2008, Molecular cell.

[64]  Mark A. McCormick,et al.  Integration of multiple nutrient cues and regulation of lifespan by ribosomal transcription factor Ifh1. , 2013, Cell reports.

[65]  Matt Kaeberlein,et al.  Yeast Life Span Extension by Depletion of 60S Ribosomal Subunits Is Mediated by Gcn4 , 2008, Cell.

[66]  M. McVey,et al.  The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. , 1999, Genes & development.

[67]  H. Stunnenberg,et al.  A TFTC/STAGA module mediates histone H2A and H2B deubiquitination, coactivates nuclear receptors, and counteracts heterochromatin silencing. , 2008, Molecular cell.