Yeast Ataxin-7 links histone deubiquitination with gene gating and mRNA export

Article · July 2008with42 Reads
DOI: 10.1038/ncb1733 · Source: PubMed
Abstract
Targeting of a gene to the nuclear pore complexes (NPCs), known as gene gating, can affect its transcriptional state. However, the mechanism underlying gene gating is poorly understood. Here, we have identified SAGA-associated Sgf73 (ref. 10), the yeast orthologue of human Ataxin-7 (ref. 11), as a regulator of histone H2B ubiquitin levels, a modification linked to both transcription initiation and elongation. Sgf73 is a key component of a minimal histone-deubiquitinating complex. Activation of the H2B deubiquitinating protease, Ubp8, is cooperative and requires complex formation with the amino-terminal zinc-finger-containing domain of Sgf73 and Sgf11-Sus1. Through a separate domain, Sgf73 mediates recruitment of the TREX-2 mRNA export factors Sac3 and Thp1 to SAGA and their stable interaction with Sus1-Cdc31. This latter step is crucial to target TREX-2 to the NPC. Loss of Sgf73 from SAGA abrogates gene gating of GAL1 and causes a GAL1 mRNA export defect. Thus, Sgf73 provides a molecular scaffold to integrate the regulation of H2B ubiquitin levels, tethering of a gene to the NPC and export of mRNA.
5 Figures
    • The deubiquitinating enzyme USP22 (Ubp8 in yeast) closely associates with two adaptor proteins, ATXN7L3 and ENY2 (Sgf11 and Sus1 in yeast, respectively) (Lan et al., 2015; Zhang et al., 2008b; Zhao et al., 2008), and a fourth protein, ATXN7 (Sgf73), anchors the DUB module to the larger SAGA complex. Proper structural organization of the entire module is crucial for DUB activity (Kö hler et al., 2008 Lan et al., 2015; Lang et al., 2011; Samara et al., 2010). USP22 was originally described as part of an 11 gene ''death from cancer signature'' that defines tumors with a cancer stem cell phenotype including aggressive growth, metastasis, and resistance to therapy (Glinsky, 2006).
    [Show abstract] [Hide abstract] ABSTRACT: Histone H2B monoubiquitination (H2Bub1) is centrally involved in gene regulation. The deubiquitination module (DUBm) of the SAGA complex is a major regulator of global H2Bub1 levels, and components of this DUBm are linked to both neurodegenerative diseases and cancer. Unexpectedly, we find that ablation of USP22, the enzymatic center of the DUBm, leads to a reduction, rather than an increase, in global H2bub1 levels. In contrast, depletion of non-enzymatic components, ATXN7L3 or ENY2, results in increased H2Bub1. These observations led us to discover two H2Bub1 DUBs, USP27X and USP51, which function independently of SAGA and compete with USP22 for ATXN7L3 and ENY2 for activity. Like USP22, USP51 and USP27X are required for normal cell proliferation, and their depletion suppresses tumor growth. Our results reveal that ATXN7L3 and ENY2 orchestrate activities of multiple deubiquitinating enzymes and that imbalances in these activities likely potentiate human diseases including cancer. Atanassov et al. identify two deubiquitinating enzymes (DUBs) that act on the histone H2B, independent of the SAGA complex. They demonstrate that two adaptor proteins, ATXN7L3 and ENY2, orchestrate the functions of multiple DUBs and that imbalances in these activities likely potentiate different pathologies.
    Article · Apr 2016
    • Possibly, TREX-2 can contact both SAGA and Mediator given that SAGA modulates the TREX-2 C-terminal domain (Kö hler et al., 2008), whereas Mediator interacts with the PCI domain (Fig- ure 7 ). Yeast TREX-2 localizes mainly to the NPC basket, however , this interaction is regulated (Fischer et al., 2004; Kö hler et al., 2008). Conceivably, a fraction of TREX-2 can shuttle between NPCs and the nuclear interior, thereby expanding its operating range.
    [Show abstract] [Hide abstract] ABSTRACT: Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with the Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent at specific genes. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing. Our data provide mechanistic insight into how an NPC-associated adaptor complex accesses the core transcription machinery. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · Aug 2015
    • Interestingly, the SAGA complex is engaged in several transcription regulatory processes, for instance, facilitating recruitment of the RNA polymerase II, transcription elongation, promoting nucleosome eviction and replication-coupled nucleosome assembly [15,192021. In addition, the SAGA complex is associated with nuclear export of transcribed mRNA, co-transcriptional spliceosome assembly and transcriptional silencing at telomere region22232425. Albeit, extensive evidences about the SAGA complex coding proteins in human, S. cerevisiae and other metazoan species are present, the knowledge about plants SAGA complex still needs to be elucidated. However, functions of few individual proteins of the SAGA complex are reported in plants, which have been shown to be involved in light signaling, stress response and histone modification262728293031.
    [Show abstract] [Hide abstract] ABSTRACT: The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA sub-units in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.
    Full-text · Article · Aug 2015
    • Previous work has indicated that Mex67:Mtr2 binds primarily to the N-terminal region of Sac3 (Fischer et al., 2002). In yeast, TREX-2 also facilitates the localization of many actively transcribing genes, such as GAL1, to NPCs, which in turn facilitates the removal of repression mediated by de-ubiquitinylation by Ulp1 (Texari et al., 2013) and, through interactions between TREX-2 and the SAGA complex, can couple transcription, processing, and polyadenylation with the export of mature mRNAs to the cytoplasm (Rodriguez-Navarro et al., 2004; Kö hler et al., 2008). Although crystal structures have been obtained for parts of the Saccharomyces TREX-2 complex, such as Sac3 CID bound to Sus1 and Cdc31 (Jani et al., 2009Jani et al., , 2014) or Sac3 M bound to Thp1 and Sem1 (), it has been more difficult to obtain structural information about the complete complex and its interactions with Mex67:Mtr2.
    [Show abstract] [Hide abstract] ABSTRACT: The TREX-2 complex integrates mRNA nuclear export into the gene expression pathway and is based on a Sac3 scaffold to which Thp1, Sem1, Sus1, and Cdc31 bind. TREX-2 also binds the mRNA nuclear export factor, Mex67:Mtr2, through the Sac3 N-terminal region (Sac3N). Here, we characterize Chaetomium thermophilum TREX-2, show that the in vitro reconstituted complex has an annular structure, and define the structural basis for interactions between Sac3, Sus1, Cdc31, and Mex67:Mtr2. Crystal structures show that the binding of C. thermophilum Sac3N to the Mex67 NTF2-like domain (Mex67(NTF2L)) is mediated primarily through phenylalanine residues present in a series of repeating sequence motifs that resemble those seen in many nucleoporins, and Mlp1 also binds Mex67:Mtr2 using a similar motif. Deletion of Sac3N generated growth and mRNA export defects in Saccharomyces cerevisiae, and we propose TREX-2 and Mlp1 function to facilitate export by concentrating mature messenger ribonucleoparticles at the nuclear pore entrance. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
    Full-text · Article · Jun 2015
    • Sus1 has other functions in addition to its activity in SAGA, which may make its role in yeast RLS unpredictable. Strains lacking both SGF73 and UBP8 have lifespans identical to the SGF73 single deletion, consistent with the prediction that both deletions enhance lifespan by a similar mechanism and cause increased levels of ubiquitinated H2B (Figure S1B) (Kö hler et al., 2008).
    [Show abstract] [Hide abstract] ABSTRACT: 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.
    Full-text · Article · Jul 2014
    • CG-1521 exhibits an increased growth inhibitory effect on the sgf73Δ strain compared to the wild-type. Sgf73 tethers the DUB module to the SAGA complex [45] and recruits the complex to its substrate to stimulate the formation of the pre-initiation complex [46]. It is probable that the sensitivity of the sgf73Δ strain to CG-1521 is due to its latter role in the formation of the pre-initiation complex.
    [Show abstract] [Hide abstract] ABSTRACT: Background Previous studies from our laboratory and others have demonstrated that in addition to altering chromatin acetylation and conformation, histone deacetylase inhibitors (HDACi) disrupt the acetylation status of numerous transcription factors and other proteins. A whole genome yeast deletion library screen was used to identify components of the transcriptional apparatus that modulate the sensitivity to the hydroxamic acid-based HDACi, CG-1521. Results Screening 4852 haploid Saccharomyces cerevisiae deletion strains for sensitivity to CG-1521 identifies 407 sensitive and 80 resistant strains. Gene ontology (GO) enrichment analysis shows that strains sensitive to CG-1521 are highly enriched in processes regulating chromatin remodeling and transcription as well as other ontologies, including vacuolar acidification and vesicle-mediated transport. CG-1521-resistant strains include those deficient in the regulation of transcription and tRNA modification. Components of the SAGA histone acetyltransferase (HAT) complex are overrepresented in the sensitive strains, including the catalytic subunit, Gcn5. Cell cycle analysis indicates that both the wild-type and gcn5Δ strains show a G1 delay after CG-1521 treatment, however the gcn5Δ strain displays increased sensitivity to CG-1521-induced cell death compared to the wild-type strain. To test whether the enzymatic activity of Gcn5 is necessary in the response to CG-1521, growth assays with a yeast strain expressing a catalytically inactive variant of the Gcn5 protein were performed and the results show that this strain is less sensitive to CG-1521 than the gcn5Δ strain. Conclusion Genome-wide deletion mutant screening identifies biological processes that affect the sensitivity to the HDAC inhibitor CG-1521, including transcription and chromatin remodeling. This study illuminates the pathways involved in the response to CG-1521 in yeast and provides incentives to understand the mechanisms of HDAC inhibitors in cancer cells. The data presented here demonstrate that components of the SAGA complex are involved in mediating the response to CG-1521. Additional experiments suggest that functions other than the acetyltransferase activity of Gcn5 may be sufficient to attenuate the effects of CG-1521 on cell growth. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-528) contains supplementary material, which is available to authorized users.
    Full-text · Article · Jun 2014
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