组蛋白甲基化位点结合结构域的结构与功能研究
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摘要
组蛋白的翻译后修饰是表观遗传调控的重要手段之一,一般发生在组蛋白柔性的N端尾巴上,包括甲基化、乙酰化、磷酸化和泛素化等。组蛋白的这些翻译后修饰位点往往包含特定的生物学信息,被称为“组蛋白密码”。“组蛋白密码”可以被一些含有特定结构域的蛋白和蛋白复合物识别,启动下游的生物学过程。过去几十年来,人们通过生物化学及生物物理学等方法鉴定出许多可以特异性地结合组蛋白翻译后修饰位点的结构域。人们根据这些结构域氨基酸序列的同源性以及与组蛋白翻译后修饰位点的结合方式,将它们分为Bromo结构域、PHD结构域、WD40repeat结构域及Royal超家族结构域等一些结构域超家族。基于组蛋白翻译后修饰的多样性,这些结构域涉及到细胞内大部分生物学过程,而且目前发现许多疾病的发生与组蛋白翻译后修饰位点结合结构域的功能异常有关。相比较其他的翻译后修饰方式,组蛋白的甲基化具有更为复杂的修饰模式和调控方式,其结合结构域也相应地更为多样。本论文主要针对Royal超家族中特异性结合组蛋白甲基化赖氨酸的结构域展开一系列的结构和功能的研究,论文分为三部分：
第一部分为酿酒酵母SAGA复合物Sgf29亚基的结构与功能的研究。我们分别解析了Sgf29的C端tandem Tudor结构域的单体,及其与H3K4me2和H3K4me3多肽的复合物的晶体结构。Sgf29的tandem Tudor结构域的两个Tudor结构域均参与与H3K4me2/3的相互作用,两个Tudor结构域以‘'face-to-face"的方式排列,并各自含有一个带负电的结合口袋和芳香族口袋,分别与组蛋白H3A1和甲基化H3K4结合,这种新颖的结合方式使得Sgf29的tandem Tudor结构域具有更严格的底物选择性。此外,我们的体内和体外实验指出Sgf29不直接影响SAGA复合物的乙酰转移酶活性,而是通过其C端tandem Tudor(?)结构域与甲基化H3K4的相互作用调控SAGA复合物在染色质上的定位,从而影响组蛋白H3的乙酰化水平,进而调控基因的转录。
第二部分为人源异染色蛋白Cbx3(HPly)的结构和功能的研究。HP1蛋白N端Chromo结构域一直以来被人们认为可以特异性识别甲基化组蛋白H3K9,调控基因转录及DNA损伤修复等过程。我们分别解析了Cbx3Chromo结构域与组蛋白H1K26me2多肽及其与组蛋白甲基转移酶G9aK185me3多肽的复合物的晶体结构,测定了Cbx3Chromo (?)吉构域与这两种甲基化多肽的解离常数,指出Cbx3可以通过结合甲基化的组蛋白和非组蛋白蛋白发挥调控基因表达的功能。
第三部分主要是针对人源有丝分裂M期磷蛋白Mpp8的结构和功能的研究。我们分别解析了Mpp8Chromo结构域单体及其与组蛋白H3K9me3多肽的复合物的晶体结构。阐明了Mpp8Chromo结构域识别H3K9me3的分子机制,并发现Mpp8的Chromo结构域以同二聚体形式存在,在此基础上提出了同二聚体形式的Mpp8通过其Chromo结构域识别甲基化H3K9并抑制基因转录的两种模型。
Histone post-translational modifications (PTMs) is a principle component of epigenetic regulations. N-terminal tails of histones are the most accessible regions that are subjected to various PTMs such as methylation, acetylation, phosphorylation and ubiquitination and so on. PTMs are believed to function in a combinatorial pattern referred to as the "histone code". The major function of PTMs is to create sites for the recruitment of proteins with specific binding modules which subsequently stimulate downstream biological processes. In the past decades, a wealth of conserved protein domains have been identified through biochemical and biophysical assays, which specifically bind histone PTMs, including bromodomain, PHD domain, WD40repeat and domains of Royal-superfamily and so on. On account of the variety of PTMs, PTM-binding modules are involed in nearly all biological processes. Currently, numerous of PTM-binding modules have been reported to be implicated in different human disease. More complex than other PTMs, histone methylation is recognized by much more different binding modules due to the diversity of methyl lysine signals. This dissertation focuses on the members of Royal-superfamily that specifically binding methylated lysine residues.
In Chapter2, we solved the crystal structures of the tandem Tudor domain of Saccharomyces cerevisiae Sgf29and their complexes with H3K4me2and H3K4me3peptides, respectively, and show that Sgf29selectively binds H3K4me2/3marks. The tandem Tudor domains in Sgf29tightly pack against each other face-to-face. The H3A1and K4me3binding pockets created by each of the tandem Tudor domains and the fixed distance between these two pockets are the structural determinants in conferring Sgf29the ability of selectively recognizing H3K4me2/3, not other histone lysine sites. Our in vitro and in vivo functional assays show that Sgf29recognizes methylated H3K4to recruit the SAGA complex to target genes, underscoring the importance of Sgf29in gene regulation.
Chapter3presents our work on chromodomain of heterchromatin protein HP1γ (Cbx3). HP1proteins have been identified to be involved multiple biological processes including gene transcription and DNA repair. We determined the crystal structures of the human Cbx3chromodomain in complex with dimethylated histone H1K26and trimethylated G9aK185peptides, respectively. Our in vitro assay indicates Cbx3chromodomain can bind to both H1K26me2and G9aK185me3with comparable binding affinities compared to H3K9me3. The complex structures unveil that the Cbx3chromodomain specifically binds methylated histone H1K26and G9aK185through a conserved mechanism.
In Chapter4, we reported the crystal structures of human MPP8(hMPP8) chromodomain both in apo-form and in complex with the trimethylated histone H3lysine9(H3K9me3) peptide (residue1-15). Consistent with the high sequence homology of MPP8with Polycomb and HP1chromodomains, the complex structure of hMPP8-H3K9me3uncovers the detailed molecular mechanism of recruitment of MPP8chromodomain by HK9me3as well as its unexpected homodimerization. Based on the homodimerization, we build two models showing that the simultaneous binding of two histone tails to hMpp8homodimer either from the same nucleosome or from two separated nucleosomes.
第一部分为酿酒酵母SAGA复合物Sgf29亚基的结构与功能的研究。我们分别解析了Sgf29的C端tandem Tudor结构域的单体,及其与H3K4me2和H3K4me3多肽的复合物的晶体结构。Sgf29的tandem Tudor结构域的两个Tudor结构域均参与与H3K4me2/3的相互作用,两个Tudor结构域以‘'face-to-face"的方式排列,并各自含有一个带负电的结合口袋和芳香族口袋,分别与组蛋白H3A1和甲基化H3K4结合,这种新颖的结合方式使得Sgf29的tandem Tudor结构域具有更严格的底物选择性。此外,我们的体内和体外实验指出Sgf29不直接影响SAGA复合物的乙酰转移酶活性,而是通过其C端tandem Tudor(?)结构域与甲基化H3K4的相互作用调控SAGA复合物在染色质上的定位,从而影响组蛋白H3的乙酰化水平,进而调控基因的转录。
第二部分为人源异染色蛋白Cbx3(HPly)的结构和功能的研究。HP1蛋白N端Chromo结构域一直以来被人们认为可以特异性识别甲基化组蛋白H3K9,调控基因转录及DNA损伤修复等过程。我们分别解析了Cbx3Chromo结构域与组蛋白H1K26me2多肽及其与组蛋白甲基转移酶G9aK185me3多肽的复合物的晶体结构,测定了Cbx3Chromo (?)吉构域与这两种甲基化多肽的解离常数,指出Cbx3可以通过结合甲基化的组蛋白和非组蛋白蛋白发挥调控基因表达的功能。
第三部分主要是针对人源有丝分裂M期磷蛋白Mpp8的结构和功能的研究。我们分别解析了Mpp8Chromo结构域单体及其与组蛋白H3K9me3多肽的复合物的晶体结构。阐明了Mpp8Chromo结构域识别H3K9me3的分子机制,并发现Mpp8的Chromo结构域以同二聚体形式存在,在此基础上提出了同二聚体形式的Mpp8通过其Chromo结构域识别甲基化H3K9并抑制基因转录的两种模型。
Histone post-translational modifications (PTMs) is a principle component of epigenetic regulations. N-terminal tails of histones are the most accessible regions that are subjected to various PTMs such as methylation, acetylation, phosphorylation and ubiquitination and so on. PTMs are believed to function in a combinatorial pattern referred to as the "histone code". The major function of PTMs is to create sites for the recruitment of proteins with specific binding modules which subsequently stimulate downstream biological processes. In the past decades, a wealth of conserved protein domains have been identified through biochemical and biophysical assays, which specifically bind histone PTMs, including bromodomain, PHD domain, WD40repeat and domains of Royal-superfamily and so on. On account of the variety of PTMs, PTM-binding modules are involed in nearly all biological processes. Currently, numerous of PTM-binding modules have been reported to be implicated in different human disease. More complex than other PTMs, histone methylation is recognized by much more different binding modules due to the diversity of methyl lysine signals. This dissertation focuses on the members of Royal-superfamily that specifically binding methylated lysine residues.
In Chapter2, we solved the crystal structures of the tandem Tudor domain of Saccharomyces cerevisiae Sgf29and their complexes with H3K4me2and H3K4me3peptides, respectively, and show that Sgf29selectively binds H3K4me2/3marks. The tandem Tudor domains in Sgf29tightly pack against each other face-to-face. The H3A1and K4me3binding pockets created by each of the tandem Tudor domains and the fixed distance between these two pockets are the structural determinants in conferring Sgf29the ability of selectively recognizing H3K4me2/3, not other histone lysine sites. Our in vitro and in vivo functional assays show that Sgf29recognizes methylated H3K4to recruit the SAGA complex to target genes, underscoring the importance of Sgf29in gene regulation.
Chapter3presents our work on chromodomain of heterchromatin protein HP1γ (Cbx3). HP1proteins have been identified to be involved multiple biological processes including gene transcription and DNA repair. We determined the crystal structures of the human Cbx3chromodomain in complex with dimethylated histone H1K26and trimethylated G9aK185peptides, respectively. Our in vitro assay indicates Cbx3chromodomain can bind to both H1K26me2and G9aK185me3with comparable binding affinities compared to H3K9me3. The complex structures unveil that the Cbx3chromodomain specifically binds methylated histone H1K26and G9aK185through a conserved mechanism.
In Chapter4, we reported the crystal structures of human MPP8(hMPP8) chromodomain both in apo-form and in complex with the trimethylated histone H3lysine9(H3K9me3) peptide (residue1-15). Consistent with the high sequence homology of MPP8with Polycomb and HP1chromodomains, the complex structure of hMPP8-H3K9me3uncovers the detailed molecular mechanism of recruitment of MPP8chromodomain by HK9me3as well as its unexpected homodimerization. Based on the homodimerization, we build two models showing that the simultaneous binding of two histone tails to hMpp8homodimer either from the same nucleosome or from two separated nucleosomes.
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