H2B Ubiquitin Protease Ubp8 and Sgf11 Constitute a Discrete Functional Module within the Saccharomyces cerevisiae SAGA Complex

ABSTRACT The SAGA complex is a multisubunit protein complex involved in transcriptional regulation in Saccharomyces cerevisiae. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation (Gcn5) and histone deubiquitylation (Ubp8). We recently showed that H2B ubiquitylation and Ubp8-mediated deubiquitylation are both required for transcriptional activation. For this study, we investigated the interaction of Ubp8 with SAGA. Using mutagenesis, we identified a putative zinc (Zn) binding domain within Ubp8 as being critical for the association with SAGA. The Zn binding domain is required for H2B deubiquitylation and for growth on media requiring Ubp8's function in gene activation. Furthermore, we identified an 11-kDa subunit of SAGA, Sgf11, and showed that it is required for the Ubp8 association with SAGA and for H2B deubiquitylation. Different approaches indicated that the functions of Ubp8 and Sgf11 are related and separable from those of other components of SAGA. In particular, the profiles of Ubp8 and Sgf11 deletions were remarkably similar in microarray analyses and synthetic genetic interactions and were distinct from those of the Spt3 and Spt8 subunits of SAGA, which are involved in TBP regulation. These data indicate that Ubp8 and Sgf11 likely represent a new functional module within SAGA that is involved in gene regulation through H2B deubiquitylation.

[1]  A. Link,et al.  Cluster Analysis of Mass Spectrometry Data Reveals a Novel Component of SAGA , 2004, Molecular and Cellular Biology.

[2]  A. Buchberger,et al.  Shp1 and Ubx2 are adaptors of Cdc48 involved in ubiquitin‐dependent protein degradation , 2004, EMBO reports.

[3]  Patrick Schultz,et al.  Molecular architecture of the S. cerevisiae SAGA complex. , 2004, Molecular cell.

[4]  E. Ezhkova,et al.  Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. , 2004, Molecular cell.

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

[6]  Wei-Hua Wu,et al.  ATP-Driven Exchange of Histone H2AZ Variant Catalyzed by SWR1 Chromatin Remodeling Complex , 2004, Science.

[7]  Oreto Antúnez,et al.  Sus1, a Functional Component of the SAGA Histone Acetylase Complex and the Nuclear Pore-Associated mRNA Export Machinery , 2004, Cell.

[8]  Huiming Ding,et al.  A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. , 2003, Molecular cell.

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

[10]  Ronen Marmorstein,et al.  Structural basis for histone and phosphohistone binding by the GCN5 histone acetyltransferase. , 2003, Molecular cell.

[11]  Brendan J. Frey,et al.  A Panoramic View of Yeast Noncoding RNA Processing , 2003, Cell.

[12]  R. Gaynor,et al.  Histone H3 phosphorylation by IKK-α is critical for cytokine-induced gene expression , 2003, Nature.

[13]  D. Stillman,et al.  Regulation of TATA-Binding Protein Binding by the SAGA Complex and the Nhp6 High-Mobility Group Protein , 2003, Molecular and Cellular Biology.

[14]  M. Johnston,et al.  The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. , 2003, Molecular cell.

[15]  Kevin Struhl,et al.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. , 2003, Molecular cell.

[16]  Muyang Li,et al.  Crystal Structure of a UBP-Family Deubiquitinating Enzyme in Isolation and in Complex with Ubiquitin Aldehyde , 2002, Cell.

[17]  John R. Yates,et al.  The Novel SLIK Histone Acetyltransferase Complex Functions in the Yeast Retrograde Response Pathway , 2002, Molecular and Cellular Biology.

[18]  Tamás Fischer,et al.  The mRNA export machinery requires the novel Sac3p–Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores , 2002, The EMBO journal.

[19]  G. Cagney,et al.  RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach , 2002, Molecular and Cellular Biology.

[20]  R. Eisenman,et al.  Histone deacetylase 6 binds polyubiquitin through its zinc finger (PAZ domain) and copurifies with deubiquitinating enzymes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[21]  D. Sterner,et al.  SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcription , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Mark Johnston,et al.  Methylation of Histone H3 by COMPASS Requires Ubiquitination of Histone H2B by Rad6* , 2002, The Journal of Biological Chemistry.

[23]  F. Winston,et al.  Analysis of Spt7 Function in the Saccharomyces cerevisiae SAGA Coactivator Complex , 2002, Molecular and Cellular Biology.

[24]  Brian D. Strahl,et al.  Gene silencing: Trans-histone regulatory pathway in chromatin , 2002, Nature.

[25]  Zu-Wen Sun,et al.  Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast , 2002, Nature.

[26]  Andrew J. Link,et al.  Proteomics of the Eukaryotic Transcription Machinery: Identification of Proteins Associated with Components of Yeast TFIID by Multidimensional Mass Spectrometry , 2002, Molecular and Cellular Biology.

[27]  Andrew J. Bannister,et al.  Histone Methylation Dynamic or Static? , 2002, Cell.

[28]  Ioannis Xenarios,et al.  Microarray Deacetylation Maps Determine Genome-Wide Functions for Yeast Histone Deacetylases , 2002, Cell.

[29]  Thomas Kodadek,et al.  Recruitment of a 19S Proteasome Subcomplex to an Activated Promoter , 2002, Science.

[30]  J. Jaehning,et al.  Ctr9, Rtf1, and Leo1 Are Components of the Paf1/RNA Polymerase II Complex , 2002, Molecular and Cellular Biology.

[31]  S. Squazzo,et al.  The Paf1 complex physically and functionally associates with transcription elongation factors in vivo , 2002, The EMBO journal.

[32]  Nevan J. Krogan,et al.  COMPASS, a Histone H3 (Lysine 4) Methyltransferase Required for Telomeric Silencing of Gene Expression* , 2002, The Journal of Biological Chemistry.

[33]  P. Grant,et al.  Role of the Ada2 and Ada3 Transcriptional Coactivators in Histone Acetylation* , 2002, The Journal of Biological Chemistry.

[34]  D. Sterner,et al.  The SANT Domain of Ada2 Is Required for Normal Acetylation of Histones by the Yeast SAGA Complex* , 2002, The Journal of Biological Chemistry.

[35]  P. Grant,et al.  Set2 Is a Nucleosomal Histone H3-Selective Methyltransferase That Mediates Transcriptional Repression , 2002, Molecular and Cellular Biology.

[36]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[37]  R. Kornberg,et al.  A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3 , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Rein Aasland,et al.  The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4 , 2001, The EMBO journal.

[39]  J. Davie,et al.  Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. , 2001, Genes & development.

[40]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[41]  Nevan J. Krogan,et al.  Characterization of a Six-Subunit Holo-Elongator Complex Required for the Regulated Expression of a Group of Genes in Saccharomyces cerevisiae , 2001, Molecular and Cellular Biology.

[42]  J. Garin,et al.  Identification of Components of the Murine Histone Deacetylase 6 Complex: Link between Acetylation and Ubiquitination Signaling Pathways , 2001, Molecular and Cellular Biology.

[43]  M Wilm,et al.  The S. cerevisiae SET3 complex includes two histone deacetylases, Hos2 and Hst1, and is a meiotic-specific repressor of the sporulation gene program. , 2001, Genes & development.

[44]  Nevan J. Krogan,et al.  COMPASS: A complex of proteins associated with a trithorax-related SET domain protein , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[45]  L. Tora,et al.  Histone Folds Mediate Selective Heterodimerization of Yeast TAFII25 with TFIID Components yTAFII47 and yTAFII65 and with SAGA Component ySPT7 , 2001, Molecular and Cellular Biology.

[46]  K. Ozato,et al.  Distinct but overlapping roles of histone acetylase PCAF and of the closely related PCAF-B/GCN5 in mouse embryogenesis. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Yvonne A. Evrard,et al.  Loss of Gcn5l2 leads to increased apoptosis and mesodermal defects during mouse development , 2000, Nature Genetics.

[48]  A. Amerik,et al.  Analysis of the Deubiquitinating Enzymes of the Yeast Saccharomyces cerevisiae , 2000, Biological chemistry.

[49]  S. Berger,et al.  Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. , 2000, Molecular cell.

[50]  M. Osley,et al.  Rad6-dependent ubiquitination of histone H2B in yeast. , 2000, Science.

[51]  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.

[52]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[53]  M. Brand,et al.  Three-dimensional structures of the TAFII-containing complexes TFIID and TFTC. , 1999, Science.

[54]  A. Dudley,et al.  The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. , 1999, Genes & development.

[55]  Ronen Marmorstein,et al.  Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide , 1999, Nature.

[56]  D. Sterner,et al.  Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Fred Winston,et al.  Functional Organization of the Yeast SAGA Complex: Distinct Components Involved in Structural Integrity, Nucleosome Acetylation, and TATA-Binding Protein Interaction , 1999, Molecular and Cellular Biology.

[58]  J R Yates,et al.  The ATM-related cofactor Tra1 is a component of the purified SAGA complex. , 1998, Molecular cell.

[59]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[60]  P. Philippsen,et al.  Additional modules for versatile and economical PCR‐based gene deletion and modification in Saccharomyces cerevisiae , 1998, Yeast.

[61]  J Schultz,et al.  SMART, a simple modular architecture research tool: identification of signaling domains. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[62]  F. Winston,et al.  Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. , 1997, Genetics.

[63]  R Ohba,et al.  Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. , 1997, Genes & development.

[64]  S. Berger,et al.  Histone acetyltransferase activity and interaction with ADA2 are critical for GCN5 function in vivo , 1997, The EMBO journal.

[65]  S. Berger,et al.  Characterization of Physical Interactions of the Putative Transcriptional Adaptor, ADA2, with Acidic Activation Domains and TATA-binding Protein (*) , 1995, The Journal of Biological Chemistry.

[66]  Charles Boone,et al.  A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. , 2003, Molecular cell.

[67]  Yi Zhang,et al.  Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. , 2003, Molecular cell.

[68]  R. Gaynor,et al.  Histone H3 phosphorylation by IKK-alpha is critical for cytokine-induced gene expression. , 2003, Nature.

[69]  B. Strahl,et al.  A nucleosomal function for IkappaB kinase-alpha in NF-kappaB-dependent gene expression. , 2003, Nature.

[70]  W. Baumeister,et al.  The 26S proteasome: a molecular machine designed for controlled proteolysis. , 1999, Annual review of biochemistry.

[71]  H. Erdjument-Bromage,et al.  Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. , 1999, Molecular cell.

[72]  S. Berger,et al.  Structural and Functional Analysis of Yeast Putative Adaptors EVIDENCE FOR AN ADAPTOR COMPLEX IN VIVO * , 1996 .