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

Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
Nature Cell Biology (Impact Factor: 19.68). 07/2008; 10(6):707-15. DOI: 10.1038/ncb1733
Source: PubMed


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.

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Available from: Ed Hurt, Jul 09, 2015
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    • "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., 2009, 2014 "
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    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.
    Structure 06/2015; 23(7). DOI:10.1016/j.str.2015.05.002 · 5.62 Impact Factor
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    • "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). "
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    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.
    Cell Reports 07/2014; 8(2). DOI:10.1016/j.celrep.2014.06.037 · 8.36 Impact Factor
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    • "In addition to serving as an anchor to keep the deubiquitinase module tethered to SAGA, Sgf73 plays a critical role in ensuring the proper conformation of Nonstop for full enzymatic function of the deubiquitinase (Kohler et al. 2010; Samara et al. 2010). Consequently, disruption of Sgf73 reduces SAGA-mediated H2Bub deubiquitination , resulting in global increases in this critical histone modification (Kohler et al. 2008; Lee et al. 2009). To determine the effect of Ataxin-7 loss on H2Bub levels in Drosophila, we collected mutant wandering third instar larvae and acid-extracted histones for immunoblotting with histone modification-specific antibodies. "
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    ABSTRACT: The Spt-Ada-Gcn5-acetyltransferase (SAGA) chromatin-modifying complex possesses acetyltransferase and deubiquitinase activities. Within this modular complex, Ataxin-7 anchors the deubiquitinase activity to the larger complex. Here we identified and characterized Drosophila Ataxin-7 and found that reduction of Ataxin-7 protein results in loss of components from the SAGA complex. In contrast to yeast, where loss of Ataxin-7 inactivates the deubiquitinase and results in increased H2B ubiquitination, loss of Ataxin-7 results in decreased H2B ubiquitination and H3K9 acetylation without affecting other histone marks. Interestingly, the effect on ubiquitination was conserved in human cells, suggesting a novel mechanism regulating histone deubiquitination in higher organisms. Consistent with this mechanism in vivo, we found that a recombinant deubiquitinase module is active in the absence of Ataxin-7 in vitro. When we examined the consequences of reduced Ataxin-7 in vivo, we found that flies exhibited pronounced neural and retinal degeneration, impaired movement, and early lethality.
    Genes & development 02/2014; 28(3):259-72. DOI:10.1101/gad.225151.113 · 10.80 Impact Factor
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