The structural plasticity of SCA7 domains defines their differential nucleosome‐binding properties

SAGA (Spt–Ada–Gcn5 acetyltransferase), a coactivator complex involved in chromatin remodelling, harbours both histone acetylation and deubiquitination activities. ATXN7/Sgf73 and ATXN7L3, two subunits of the SAGA deubiquitination module, contain an SCA7 domain characterized by an atypical zinc‐finger. We show that the yeast Sgf73–SCA7 domain is not required to recruit Sgf73 into SAGA. Instead, it binds to nucleosomes, a property that is conserved in the human ATXN7–SCA7 domain but is lost in the ATXN7L3 domain. The solution structures of the SCA7 domain of both ATXN7 and ATXN7L3 reveal a new, common zinc‐finger motif at the heart of two distinct folds, providing a molecular basis for the observed functional differences.     

Histone deacetylase-3 interacts with ataxin-7 and is altered in a spinocerebellar ataxia type 7 mouse model

Spinocerebellar ataxia type 7 (SCA7) is caused by a toxic polyglutamine (polyQ) expansion in the N-terminus of the protein ataxin-7. Ataxin-7 has a known function in the histone acetylase complex, Spt/Ada/Gcn5 acetylase (STAGA) chromatin-remodeling complex. We hypothesized that some histone deacetylase (HDAC) family members would impact the posttranslational modification of normal and expanded ataxin-7 and possibly modulate ataxin-7 function or neurotoxicity associated with the polyQ expansion. Interestingly, when we coexpressed each HDAC family member in the presence of ataxin-7 we found that HDAC3 increased the posttranslational modification of normal and expanded ataxin-7. Specifically, HDAC3 stabilized ataxin-7 and increased modification of the protein. Further, HDAC3 physically interacts with ataxin-7. The physical interaction of HDAC3 with normal and polyQ-expanded ataxin-7 affects the toxicity in a polyQ-dependent manner. We detect robust HDAC3 expression in neurons and glia in the cerebellum and an increase in the levels of HDAC3 in SCA7 mice. Consistent with this we found altered lysine acetylation levels and deacetylase activity in the brains of SCA7 transgenic mice. This study implicates HDAC3 and ataxin-7 interaction as a target for therapeutic intervention in SCA7, adding to a growing list of neurodegenerative diseases that may be treated by HDAC inhibitors.     

裂殖酵母SAGA各亚基亚细胞荧光定位分析

SAGA(Spt-Ada-Gcn5 Acetyltransferase complex)是一个多亚基保守的转录复合物, 在裂殖酵母(Schizosaccharomyces pombe)里由19个亚基组成, 调控体内10%基因的转录。文章通过构建原位整合荧光菌株, 完整地分析了SAGA所有亚基的亚细胞荧光定位。荧光数据显示这些亚基的定位可分为4种类型, 提示SAGA亚基除共同参与转录调控之外, 可能还有其他功能。SAGA亚基Sgf73是联系去泛素化模块与SAGA其他模块的桥梁, 它的缺失不仅明显减少了去泛素化亚基Ubp8、Sgf11、Sus1核内的定位, 同时也影响了乙酰化亚基Gcn5、Sgf29、Ngg1以及核心结构亚基Spt7在细胞核内的定位, 这提示Sgf73对维持SAGA的酶学功能和稳定性至关重要。另外, sgf73+的缺失还造成了胞质分裂的缺陷, 导致细胞出现多核多膈膜表型。在△sgf73里过量表达膈膜降解途径中的关键基因ace2+和mid2+的回补结果表明, ace2+不能回补sgf73+缺失造成的缺陷, 而mid2+也仅能部分回补, 提示Sgf73可能还通过其他途径影响了胞质分裂。     

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

Despite the availability of several large‐scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild‐type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well‐studied complexes, Spt–Ada–Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high‐resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.     

Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation

The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an important chromatin modifying complex that can both acetylate and deubiquitinate histones. Sgf29 is a novel component of the SAGA complex. Here, we report the crystal structures of the tandem Tudor domains of Saccharomyces cerevisiae and human Sgf29 and their complexes with H3K4me2 and H3K4me3 peptides, respectively, and show that Sgf29 selectively binds H3K4me2/3 marks. Our crystal structures reveal that Sgf29 harbours unique tandem Tudor domains in its C-terminus. The tandem Tudor domains in Sgf29 tightly pack against each other face-to-face with each Tudor domain harbouring a negatively charged pocket accommodating the first residue alanine and methylated K4 residue of histone H3, respectively. The H3A1 and K4me3 binding pockets and the limited binding cleft length between these two binding pockets are the structural determinants in conferring the ability of Sgf29 to selectively recognize H3K4me2/3. Our in vitro and in vivo functional assays show that Sgf29 recognizes methylated H3K4 to recruit the SAGA complex to its targets sites and mediates histone H3 acetylation, underscoring the importance of Sgf29 in gene regulation.