生命的基本要求是生物体DNA的复制。对大肠杆菌和枯草芽孢杆菌的研究为细菌中的DNA复制树立了范例。在大肠杆菌和枯草芽孢杆菌的复制启动过程中,复制解旋酶通过ATP酶解旋酶加载器加载到复制起点的DNA上。然而,大多数细菌不编码大肠杆菌和枯草芽孢杆菌中解旋酶加载器的同源物。最近的工作已经将DciA蛋白鉴定为预测的解旋酶操纵子,其可以执行类似于大肠杆菌和枯草芽孢杆菌中的解旋酶加载器的功能。DciA蛋白,它们由DUF721结构域(本文称为DciA结构域)的存在定义,在大多数细菌中都是保守的,但仅在分枝杆菌和变形杆菌(铜绿假单胞菌和霍乱弧菌)中进行了研究。结核分枝杆菌DciA结构域外的序列DciA是蛋白质功能所必需的,但在铜绿假单胞菌和霍乱弧菌同源物中不保守,提出了关于DciA蛋白在细菌系中的保守和进化的问题。为了全面定义DcIA蛋白家族,我们采用了计算进化的方法,并分析了整个生命树中含有DciA结构域的蛋白质的结构域结构和序列特性。这些分析确定了DciA同源物之间的谱系特异性域结构,以及广泛保守的序列结构基序。DciA蛋白的多样性代表了细菌DNA复制中解旋酶操作的演变,并强调了对该基本生物学过程进行门特异性分析的必要性。重要性尽管DNA复制对生命至关重要,在大肠杆菌和枯草芽孢杆菌以外的细菌中,这一过程仍未得到充分研究。特别是,大多数细菌不编码在大肠杆菌和枯草芽孢杆菌中DNA复制所必需的解旋酶负载蛋白。相反,大多数细菌编码DciA同源物,该同源物可能构成细菌中解旋酶操作的主要机制。然而,目前尚不清楚DciA结构和功能如何在编码DciA蛋白的不同门之间进行比较。在这项研究中,我们进行了计算进化分析,以发现DciA同源物之间的巨大多样性。这些研究为我们对细菌DNA复制机制的基本组成部分的理解提供了重大进展。
A fundamental requirement for life is the replication of an organism\'s DNA. Studies in Escherichia coli and Bacillus subtilis have set the paradigm for DNA replication in bacteria. During replication initiation in E. coli and B. subtilis, the replicative helicase is loaded onto the DNA at the origin of replication by an ATPase helicase loader. However, most bacteria do not encode homologs to the helicase loaders in E. coli and B. subtilis. Recent work has identified the
DciA protein as a predicted helicase operator that may perform a function analogous to the helicase loaders in E. coli and B. subtilis.
DciA proteins, which are defined by the presence of a DUF721 domain (termed the
DciA domain herein), are conserved in most bacteria but have only been studied in mycobacteria and gammaproteobacteria (Pseudomonas aeruginosa and Vibrio cholerae). Sequences outside the
DciA domain in Mycobacterium tuberculosis
DciA are essential for protein function but are not conserved in the P. aeruginosa and V. cholerae homologs, raising questions regarding the conservation and evolution of DciA proteins across bacterial phyla. To comprehensively define the
DciA protein family, we took a computational evolutionary approach and analyzed the domain architectures and sequence properties of DciA domain-containing proteins across the tree of life. These analyses identified lineage-specific domain architectures among DciA homologs, as well as broadly conserved sequence-structural motifs. The diversity of DciA proteins represents the evolution of helicase operation in bacterial DNA replication and highlights the need for phylum-specific analyses of this fundamental biological process. IMPORTANCE Despite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside Escherichia coli and Bacillus subtilis. In particular, most bacteria do not encode the helicase-loading proteins that are essential in E. coli and B. subtilis for DNA replication. Instead, most bacteria encode a DciA homolog that likely constitutes the predominant mechanism of helicase operation in bacteria. However, it is still unknown how DciA structure and function compare across diverse phyla that encode
DciA proteins. In this study, we performed computational evolutionary analyses to uncover tremendous diversity among DciA homologs. These studies provide a significant advance in our understanding of an essential component of the bacterial DNA replication machinery.