Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA.
Center for Women's Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri, USA.
J Bacteriol. 2022 Aug 16;204(8):e0016322. doi: 10.1128/jb.00163-22. Epub 2022 Jul 26.
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. 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.
生命的一个基本要求是复制生物体的 DNA。在大肠杆菌和枯草芽孢杆菌中的研究为细菌中的 DNA 复制设定了范例。在大肠杆菌和枯草芽孢杆菌的复制起始过程中，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，大多数细菌不编码与大肠杆菌和枯草芽孢杆菌中的解旋酶加载器同源的基因。最近的工作已经确定 DciA 蛋白是一种预测的解旋酶操纵子，它可能具有与大肠杆菌和枯草芽孢杆菌中的解旋酶加载器类似的功能。DciA 蛋白由 DUF721 结构域（本文中称为 DciA 结构域）定义，在大多数细菌中保守，但仅在分枝杆菌和γ变形菌（铜绿假单胞菌和霍乱弧菌）中研究过。结核分枝杆菌 DciA 蛋白中 DciA 结构域外的序列对于蛋白质功能至关重要，但在铜绿假单胞菌和霍乱弧菌的同源物中不保守，这引发了关于 DciA 蛋白在细菌门之间的保守性和进化的问题。为了全面定义 DciA 蛋白家族，我们采用了计算进化方法，分析了生命之树中包含 DciA 结构域的蛋白质的结构域架构和序列特性。这些分析确定了 DciA 同源物中的谱系特异性结构域架构，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进化，并强调了对这个基本生物学过程进行特定于门的分析的必要性。尽管 DNA 复制对生命至关重要，但在大肠杆菌和枯草芽孢杆菌之外的细菌中，这一过程的研究仍不够充分。特别是，大多数细菌不编码在大肠杆菌和枯草芽孢杆菌中对 DNA 复制至关重要的解旋酶加载蛋白。相反，大多数细菌编码 DciA 同源物，它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 的结构和功能如何在编码 DciA 蛋白的不同门之间比较。在这项研究中，我们进行了计算进化分析，以揭示 DciA 同源物之间的巨大多样性。这些研究为我们理解细菌 DNA 复制机制的一个重要组成部分提供了重要进展。
