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RecQ解旋酶分子特性的研究
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摘要
Waston和Crick提出DNA双螺旋结构后,不仅引导人们发现了DNA聚合酶,它作用于DNA以一条链为模板聚合形成一条新的DNA链;而且也让科学家们寻找到一种酶能够在DNA复制时破坏互补碱基对的氢键结构而打开DNA双螺旋结构。随后,相似功能的酶在RNA复制中也被发现。这类酶被科学家称为解旋酶。解旋酶是一类能解开核苷酸双链的酶,它广泛存在于从病毒到人类等多种生物体中。自1976年人类在大肠杆菌(Esherichia Coli E.coli)中发现了第一个解旋酶,至今已有上百种解旋酶被发现,而且这一酶家族成员还在不断扩大。
     解旋酶广泛存在于多种生物体中,有些生物还同时具有多种不同类型的解旋酶。尽管解旋酶种类繁多,人们在研究过程中发现,这类蛋白酶在其氨基酸序列上有一定的同源性和相似性。分析表明,这些同源序列在进化过程中构成了几个高度保守的区域,这些区域执行不同的酶功能。人们根据酶的二维结构和一级序列,把解旋酶分为几大家族来分类研究。经过多年的研究,人们发现解旋酶具有多种功能,在细胞内它们参与DNA复制、修复、转录重组以及RNA接拼、核糖体组装、蛋白质翻译,端粒稳定。最近,还发现个别解旋酶甚至参与机体天然免疫反应机制。解旋酶已不仅仅只是分开核酸双链结构的一类酶,它的生物功能远不止此。
     解旋酶第二大家族中的RecQ解旋酶亚家族在核酸代谢过程中起了关键的作用,这一家族参与DNA复制、DNA修复、重组、转录甚至端粒稳定机制。人们发现在人体中存在RECQ1、BLM、WRN、RECQ4和RECQ5这五种RecQ解旋酶家族成员。其中,BLM、WRN、RECQ4编码基因缺陷会导致人类相应的疾病发生,它们分别为Bloom综合症(BS)、Werner综合症(WS)、Rothmund-Thomson综合症(RTS)、RAPADILINO综合症和Baller-Gerold综合症。这些疾病虽然在人类中都是极其罕见的隐形遗传疾病,但是在分子水平都表现为基因组高度不稳定性、染色体异常(染色体断裂、缺失、重排、姐妹染色体交换等)和对DNA损伤因子敏感性增加。在临床上表现为过早衰老、Ⅱ型糖尿病、骨质疏松、动脉硬化和极度容易发生癌症。大部分病人都是最终发生不同癌症而死亡。这一临床共同现象引起了人们的关注和研究热潮。对解旋酶的结构功能、作用机制的研究不仅可以认清核酸代谢过程,还能帮助我们揭示癌症发病的某些相关机理。同时了解病毒解旋酶的结构与功能,为抗病毒药物的研制提供了新的靶点和思路。
     解旋酶具有四大基本生物化学活性:NTP水解活性、DNA或RNA结合活性、核酸链解链活性和核酸链退火配对活性。在二价金属离子(比如Mg~(2+))和NTP的存在下,解旋酶便表现出水解NTP的性质,大部分酶水解ATP和dATP,一些酶则能水解其他的核苷酸,比如TIP和GTP。当解旋酶与DNA或RNA结合后,利用水解核苷酸产生的能量,推动酶在核酸链上的移动,从而解开互补的两条核酸链。随着研究的深入,人们发现有些解旋酶在核酸修复过程中能促使核酸链配对重组。这使得我们意识到解旋酶在基因稳定过程中的作用越来越重要。但是并不是所有的解旋酶成员都表现出这四种基本生化功能,这与酶自身的结构有密切的关系,酶的结构决定了它所能表现的作用机制和生化活性。长期以来,科学家们一直研究探索解旋酶的结构与其功能间的相互关系,力求发现解旋酶本质的运作机制。
     RecQ解旋酶家族尽管蛋白种类繁多,在氨基酸序列上同源性不高,但有限的同源序列构成了数个典型的功能区域:从N端向C端方向,分别为位于氨基酸序列中间段的解旋酶核心区域,RecQ C端区域(RecQ-Ct)和解旋酶RNase D保守区域(HRDC),这些区域具有不同的功能,并相互协调共同执行解旋酶的运作机制。解旋酶核心区域是解旋酶标志性结构,它由一段高度保守的氨基酸序列组成,含有7个保守区域,负责结合NTP、NTP水解和DNA结合。RecQ-Ct区域是RecQ解旋酶家族唯一含有的结构特征,但不是所有RecQ成员都含有这一结构域。RecQ-Ct区域包含两个重要的亚结构域:由四个α螺旋和四个保守的半胱氨酸残基组成的结构平台,因能特异结合锌离子而被命名为锌结合区域或锌指结构(zinc-binding motif,zincfinger,ZBM);序列上不太保守的翼型螺旋亚结构域(winged-helix,WH)。目前发现RecQ-Ct结构域主要负责酶与核酸的结合、酶自身的折叠作用。HRDC区域位于解旋酶氨基酸序列的C端,在部分RecQ成员中缺失,对这一结构域的认识甚浅,一些研究表明HRDC区域能够增强解旋酶对NTP水解和解链活性。虽然解旋酶不同的结构域负责不同的酶功能,但解旋酶核心区域、RecQ-Ct和HRDC区域并不是各自独立的,它们互相之间相互作用相互协调,共同完成酶的生理作用机制。
     本文就以RecQ解旋酶家族中BLM、RECQ5和枯草杆菌RecQ(Bacillus subtilisRecQ)为实验对象,来研究解旋酶不同结构域之间是如何相互影响、相互牵制。从而了解解旋酶结构与其功能相互间的关系,揭示解旋酶的作用机制。
     首先我们把焦点放在RecQ解旋酶的RecQ-Ct区域,想了解这一区域是如何与解旋酶核心区域相互作用,相互之间存在何种联系,来共同维持解旋酶整体的酶活性平衡。我们以RECQ5为研究模型,RECQ5是人体5种解旋酶之一,虽然至今未发现它与任何人类疾病有关,但是有实验证明RECQ5与BLM蛋白密切相关,能协助BLM蛋白维持染色体的平衡。而且RECQ5解旋酶天然存在三种异构体:RECQ5α、REQ5β和RECQ5γ。其中REQ5β最大,含有解旋酶核心区域和RecQ-Ct区域,相对的RECQ5α最小,只含有解旋酶核心区域结构。这两种异构体成为研究RecQ-Ct结构域功能,和解旋酶核心结构域相互关系最理想的天然模型。实验结果揭示,RECQ5α既没有ATP水解能力,也不表现解链活性,却展示出对互补核酸链的退火配对作用。REQ5β则表现出较弱的退火配对能力和较强的解链活性。一系列实验证明,其中RecQ-Ct区域的保守结构—锌结合区域起到了重要作用,不仅增加酶对DNA的结合能力,而且起到了分子开关的作用,能够通过对DNA结合的增强来抑制解旋酶核心区域的退火配对活性,同时改变蛋白构型启动解链过程。我们率先提出RecQ-Ct区域锌指结构与解旋酶核心区域相互作用的机制模型,初步揭示两者之间的相互联系,了解RecQ解旋酶结构与结构之间,结构与功能间的相互关系。
     在对RecQ解旋酶核心区域与RecQ-Ct区域认识的基础上,进一步研究位于氨基酸序列最C端的HRDC区域的功能,探究HRDC与解旋酶核心区域、RecQ-Ct区域的相互关系。本文利用RecQ解旋酶家族中枯草杆菌RecQ(Bacillus subtilis RecQ,SubRecQ)亚家族为研究模型,它由两个成员组成。这两种RecQ解旋酶的典型结构差异在于一个含有HRDC区域,而另一个则HRDC区域缺失。为研究提供了理想的天然结构模型。结果表明,具有HRDC区域的SubRecQ酶,表现出解旋酶基本的生化活性,并能有效地解开一些DNA复制与修复中DNA错误结构甚至是Holliday结构。相对地,SubRecQ如果缺失HRDC区域,虽能具有较弱ATP水解活性,解链活性,但无法解开某些复杂的DNA复制与修复中间体结构,同时也不具有解开Holliday结构的能力。两种解旋酶的DNA结合活性与DNA退火配对活性无明显差异。分析认为,HRDC结构能辅助增强解旋酶的ATP水解活性与解链活性,在解开复杂的DNA结构过程中起到了关键的作用。
     RecQ解旋酶家族中的BLM蛋白是迄今在人体中发现的5种解旋酶之一,BLM编码基因的缺陷会导致疾病Bloom综合症的发生。而且BLM蛋白具有RecQ解旋酶家族典型的结构特征,因此它成为理想的研究模型。本实验室致力于BLM蛋白生化活性的研究已有多年,发现完整的BLM蛋白能表现出解旋酶全部的基本生物功能,也了解了其各个结构区域负责哪些酶功能。在研究其结构与功能的相互关系的过程中我们发现,BLM蛋白的解旋酶核心区域含有高度保守的精氨酸残基靠近于与其结合的ATPγ磷酸位置,称为精氨酸指结构。我们推测这一结构负责ATP的结合与水解活性。蛋白结构分析表明,BLM蛋白解旋酶核心区域还有两个保守的精氨酸残基—R979与R982。突变这两个残基位点后,发现BLM对ATP的水解能力明显下降,同时丧失解链能力,但对ATP结合与DNA结合能力并无影响。R982突变体的ATP水解和解链活性减弱幅度比R979突变体更为明显。运用目前公认的精氨酸指检测试剂—原钒酸盐(Vi)探测BLM蛋白的精氨酸指结构,Vi能与镁离子、ADP和酶形成复合物,从而抑制酶对核苷酸5'端三磷酸催化活性,试验结果表明Vi能非竞争性抑制R982精氨酸残基对ATP的水解作用,对R979精氨酸无抑制作用,从而确定BLM蛋白R982氨基酸残基形成了精氨酸指结构。我们还发现R982精氨酸指能与其周围其他一些解旋酶核心区域的重要残基相互作用,促进对ATP的招募和水解。在此我们也从一个新的角度揭示解旋酶是如何与ATP和核酸结合启动ATP的水解,随后引起蛋白构型变化并将水解产生的化学能源用于解链过程的作用机制。
     解旋酶的结构是其生化活性的前提,不同保守功能区域分别具有不同的功能,彼此之间相互作用,互相协调,来完成酶的整个运作机制。除了解旋酶核心区域外,RecQ-Ct与HRDC区域也是解旋酶重要的结构,结构的缺失与突变会不同程度影响酶的功能,增加或者减弱某些酶活性。解旋酶结构特征的完整保证了其在细胞中维持核酸代谢稳定的重要地位。
In the cells, the unwinding of double-stranded polynucleotides is catalyzed by helicases that exist in all kingdoms of life from virus to human. RecQ family helicases play essential roles in nucleic acid metabolism by facilitating cellular processes including genome replication, DNA repair, recombination, transcription and telomere maintenance. In human, five RecQ family members named RECQ1, BLM, WRN, RECQ4 and RECQ5, have been identified. Defects in BLM, WRN and RECQ4 will give rise to autosomal recessive disorders and predisposition to cancer. In addition to the highly conserved helicase core domain containing seven helicase motifs, most RecQ family helicases have a unique RecQ C-terminal domain (RecQ-Ct) and the Helicase RNase D conserved domain (HRDC). In the present studies, we focus on the intra-functional mechanisms of some important members of RecQ family helicases.
     Firstly, we have chosen two natural isoforms of human RECQ5 helicase as models to study the functional modulation of the helicase core domain by the zinc-binding domain. Here we show that a truncated variant of the human RECQ5βhelicase comprised of the conserved helicase domain only, a splice variant named RECQ5α, possesses neither ATPase nor DNA unwinding activities, but surprisingly displays a strong strand annealing activity. Quantitative measurements indicate that the regulatory role of the zinc-binding motif of RECQ5βis achieved by enhancing the DNA binding affinity of the helicase. More important, the zinc-binding motif of RECQ5βis found to act as a molecular switch that suppresses the strand-annealing activity of the helicase domain and triggers DNA-unwinding activity of the enzyme through enhancing DNA binding.
     Subsequently, we analyzed the biochemical properties of two isoforms of Bacillus subtilis RecQ helicases: SubL and SubS. Between them, SubS naturally lacks the HRDC domain. Our studies demonstrate that the HRDC domain is crucial in Bacillus subtilis RecQ helicases in unwinding of DNA replication/repair intermediates such as Holliday junction and kappa junction. The enzyme with HRDC domain shows stronger ATPase activity and DNA unwinding and annealing activities than the other one. These results allow us to speculate on the importance of HRDC domain in the basic activities of RecQ family helicases.
     In the last part, we investigated the existence and role of the arginine finger in the Bloom syndrome protein (BLM) in ATP hydrolysis and energy coupling. Our studies demonstrate that R982 is the residue located near theγ-phosphate of ATP which functions as a BLM arginine finger. Our finding further indicates that the arginine finger interacts with other conserved motifs aroundγ-phosphate of the nucleotide to carry out the functions as a complex network.
引文
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