人源NSD家族蛋白质的PHD5-C5HCH模块的结构与功能研究
摘要
NSD家族蛋白质的三个成员,NSD1, NSD2(WHSC1, MMSET)和NSD3(WHSC1L1),在生物体的发育过程中起重要的作用,并与多种人类遗传疾病和癌症相关。但是目前依旧缺乏这些蛋白质在生物体发育过程中起的作用和致病机理的研究。
NSD家族三个成员的结构域排布与同源性相似,其典型特征是在蛋白质C末端包含了一段大概有700个氨基酸残基的高度相似的区域。该区域包含了一个SET酶活结构域,一个PWWP结构域,五个PHD锌指,和一个NSD家族特有的富含半胱氨酸和组氨酸的结构域(C5HCH结构域)。这个区域里面,SET酶活结构域是目前探索得较多的一个结构域,其酶活性质是H3K36特异性单甲基和二甲基转移酶。H3K36甲基化在各种生物过程中起着重要的作用,所产生效应的关键因素在于其在基因上的定位。鉴于这三个蛋白质的功能并不冗余,而且具体原因未明,探索NSD家族这些H3K36甲基转移酶的潜在结合组蛋白的结构域的功能是很重要的。这有助于了解NSD家族蛋白质如何被募集到基因组的指定位置,从而发挥功能,进而阐明NSD家族蛋白质突变的致病机理。
我们利用多种体外相互作用实验方法阐明了NSD3C末端的PHD5-C5HCH模块特异识别包含着非修饰H3K4和三甲基H3K9的组蛋白H3N端小肽的机制。解析了PHD5-C5HCHNSD3的单体结构,及其和H31-7, H31-15,H31-15K9me3小肽的复合物结构。这些结构显示PHD5-C5HCH模块是一个串联的PHD-PHD-like模块,但是仅有PHD5识别组蛋白H3小肽。高分辨率的结构使得我们能够清楚的解析PHD5NSD3识别H3N端小肽的分子机制。序列比对显示,螯合二价锌离子和PHD5-C5HCH模块疏水核心的氨基酸在NSD家族蛋白质的三个成员里面都是十分保守的,这暗示NSD家族三个成员的PHD5-C5HCH模块在三级结构上是保守的。进一步的结构分析和突变实验显示,虽然这三个PHD5-C5HCH可能具有保守的三级结构,但是在组蛋白H3尾巴识别机制上却是有明显的差异。PHD-C5HCHNSD2识别非修饰H3K4,但是在H3K9的识别上倾向于非修饰K9状态,而NSD3则偏爱H3K9me3。PHD-C5HCHNSDI与组蛋白没有直接的相互作用。这些差异是由PHD5的组蛋白结合面上的少量氨基酸差异引起的。我们的结果揭示H3K36的甲基化可能与H3K4和H3K9的识别有所联系。同时,NSD家族的PHD5-C5HCH模块识别组蛋白H3能力的不同,可能会募集NSD家族蛋白质到基因组不同的位置,从而导致了NSD家族三个蛋白质功能上的多样性。
The NSD family of SET domain-containing histone methyl-transferases includes NSD1, NSD2(also known as WHSC1, Wolf-Hirschhorn syndrome candidate1or MMSET, multiple myeloma SET), and NSD3(also known as WHSC1L1, WHSC1like1). All three NSD proteins have been directly linked to multiple human diseases. Although highly relevant to human health and diseases, only a few details have been published regarding the mechanism of NSD family action.
A striking feature of the three NSD proteins is that they are highly similar within the block of about700amino acids, which contains a catalytic SET domain with its pre-and post-domains, a PWWP domain, five PHD fingers, and an NSD-specific Cys-His rich domain (C5HCH). However, the similar domain architecture of the three NSD family members does not indicate a functional redundancy. The SET domains of the three NSD proteins have been confirmed to have highly specific H3K36mono-or dimethylase activities. H3K36methylation has been implicated in multiple biological processes, and the biological consequences of such modification are largely determined by the location of the gene where the methylated H3K36mark is placed. Because the NSD proteins also contain several histone Readers, one attractive possibility is that these Readers recruit the NSD H3K36methyltransferases to their specific gene sites, thus lead to distinct biological outcomes. Therefore, the molecular mechanishm of the Reader domains to recognize the chromatin is critical to undertand their biological impact and the rationale of functional redundancy of NSD proteins.
Herein, we used several in vitro binding assays to identify the histone binding ability of the C-terminal PHD5-C5HCH module of NSD3. We demonstrate that the PHD5-C5HCH module of NSD3prefers to bind H3N-termianl peptide containing unmodified H3K4and trimethylated H3K9. We solved the high resolution crystal structures of PHD5-C5HCHNSD3in its apo and holo states with unmodified H3residues1-7(H31-7),1-15(H31-15), and1-15with lysine9trimethylated (H31-15K9me3), respectively. These structures reveal an integrated tandem PHD-PHD-like fold with H3peptide bound only on the surface of PHD5and provide the structural basis for the peptide recognition by PHD5of NSD3. Further mutagenesis and peptide binding assays show that PHD5-C5HCHNSD1does not bind to H3, and the PHD5-C5HCH module of NSD2(PHD5-C5HCHNSD2) prefers to bind to unmodified H3K4and H3K9. This is likely due to a minor sequence change at the H3binding surface. Our findings suggest that PHD5-C5HCHs of the NSD family are conserved in the overall structure but vary in H3recognition. These variable recognitions may play a role in the localization of these H3K36methyltransferases to different genome sites and are consistent with the distinct and non-redundant functions of NSD proteins. Our results also imply a link between the deposition of H3K36methylation and the recognition of H3K4and H3K9.
NSD家族三个成员的结构域排布与同源性相似,其典型特征是在蛋白质C末端包含了一段大概有700个氨基酸残基的高度相似的区域。该区域包含了一个SET酶活结构域,一个PWWP结构域,五个PHD锌指,和一个NSD家族特有的富含半胱氨酸和组氨酸的结构域(C5HCH结构域)。这个区域里面,SET酶活结构域是目前探索得较多的一个结构域,其酶活性质是H3K36特异性单甲基和二甲基转移酶。H3K36甲基化在各种生物过程中起着重要的作用,所产生效应的关键因素在于其在基因上的定位。鉴于这三个蛋白质的功能并不冗余,而且具体原因未明,探索NSD家族这些H3K36甲基转移酶的潜在结合组蛋白的结构域的功能是很重要的。这有助于了解NSD家族蛋白质如何被募集到基因组的指定位置,从而发挥功能,进而阐明NSD家族蛋白质突变的致病机理。
我们利用多种体外相互作用实验方法阐明了NSD3C末端的PHD5-C5HCH模块特异识别包含着非修饰H3K4和三甲基H3K9的组蛋白H3N端小肽的机制。解析了PHD5-C5HCHNSD3的单体结构,及其和H31-7, H31-15,H31-15K9me3小肽的复合物结构。这些结构显示PHD5-C5HCH模块是一个串联的PHD-PHD-like模块,但是仅有PHD5识别组蛋白H3小肽。高分辨率的结构使得我们能够清楚的解析PHD5NSD3识别H3N端小肽的分子机制。序列比对显示,螯合二价锌离子和PHD5-C5HCH模块疏水核心的氨基酸在NSD家族蛋白质的三个成员里面都是十分保守的,这暗示NSD家族三个成员的PHD5-C5HCH模块在三级结构上是保守的。进一步的结构分析和突变实验显示,虽然这三个PHD5-C5HCH可能具有保守的三级结构,但是在组蛋白H3尾巴识别机制上却是有明显的差异。PHD-C5HCHNSD2识别非修饰H3K4,但是在H3K9的识别上倾向于非修饰K9状态,而NSD3则偏爱H3K9me3。PHD-C5HCHNSDI与组蛋白没有直接的相互作用。这些差异是由PHD5的组蛋白结合面上的少量氨基酸差异引起的。我们的结果揭示H3K36的甲基化可能与H3K4和H3K9的识别有所联系。同时,NSD家族的PHD5-C5HCH模块识别组蛋白H3能力的不同,可能会募集NSD家族蛋白质到基因组不同的位置,从而导致了NSD家族三个蛋白质功能上的多样性。
The NSD family of SET domain-containing histone methyl-transferases includes NSD1, NSD2(also known as WHSC1, Wolf-Hirschhorn syndrome candidate1or MMSET, multiple myeloma SET), and NSD3(also known as WHSC1L1, WHSC1like1). All three NSD proteins have been directly linked to multiple human diseases. Although highly relevant to human health and diseases, only a few details have been published regarding the mechanism of NSD family action.
A striking feature of the three NSD proteins is that they are highly similar within the block of about700amino acids, which contains a catalytic SET domain with its pre-and post-domains, a PWWP domain, five PHD fingers, and an NSD-specific Cys-His rich domain (C5HCH). However, the similar domain architecture of the three NSD family members does not indicate a functional redundancy. The SET domains of the three NSD proteins have been confirmed to have highly specific H3K36mono-or dimethylase activities. H3K36methylation has been implicated in multiple biological processes, and the biological consequences of such modification are largely determined by the location of the gene where the methylated H3K36mark is placed. Because the NSD proteins also contain several histone Readers, one attractive possibility is that these Readers recruit the NSD H3K36methyltransferases to their specific gene sites, thus lead to distinct biological outcomes. Therefore, the molecular mechanishm of the Reader domains to recognize the chromatin is critical to undertand their biological impact and the rationale of functional redundancy of NSD proteins.
Herein, we used several in vitro binding assays to identify the histone binding ability of the C-terminal PHD5-C5HCH module of NSD3. We demonstrate that the PHD5-C5HCH module of NSD3prefers to bind H3N-termianl peptide containing unmodified H3K4and trimethylated H3K9. We solved the high resolution crystal structures of PHD5-C5HCHNSD3in its apo and holo states with unmodified H3residues1-7(H31-7),1-15(H31-15), and1-15with lysine9trimethylated (H31-15K9me3), respectively. These structures reveal an integrated tandem PHD-PHD-like fold with H3peptide bound only on the surface of PHD5and provide the structural basis for the peptide recognition by PHD5of NSD3. Further mutagenesis and peptide binding assays show that PHD5-C5HCHNSD1does not bind to H3, and the PHD5-C5HCH module of NSD2(PHD5-C5HCHNSD2) prefers to bind to unmodified H3K4and H3K9. This is likely due to a minor sequence change at the H3binding surface. Our findings suggest that PHD5-C5HCHs of the NSD family are conserved in the overall structure but vary in H3recognition. These variable recognitions may play a role in the localization of these H3K36methyltransferases to different genome sites and are consistent with the distinct and non-redundant functions of NSD proteins. Our results also imply a link between the deposition of H3K36methylation and the recognition of H3K4and H3K9.
引文
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