Mann Katherine M, Huang Deborah L, Hooppaw Anna J, Logsdon Michelle M, Richardson Kirill, Lee Hark Joon, Kimmey Jacqueline M, Aldridge Bree B, Stallings Christina L
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
PLoS Genet. 2017 Nov 27;13(11):e1007115. doi: 10.1371/journal.pgen.1007115. eCollection 2017 Nov.
DNA replication is fundamental for life, yet a detailed understanding of bacterial DNA replication is limited outside the organisms Escherichia coli and Bacillus subtilis. Many bacteria, including mycobacteria, encode no identified homologs of helicase loaders or regulators of the initiator protein DnaA, despite these factors being essential for DNA replication in E. coli and B. subtilis. In this study we discover that a previously uncharacterized protein, Rv0004, from the human pathogen Mycobacterium tuberculosis is essential for bacterial viability and that depletion of Rv0004 leads to a block in cell cycle progression. Using a combination of genetic and biochemical approaches, we found that Rv0004 has a role in DNA replication, interacts with DNA and the replicative helicase DnaB, and affects DnaB-DnaA complex formation. We also identify a conserved domain in Rv0004 that is predicted to structurally resemble the N-terminal protein-protein interaction domain of DnaA. Mutation of a single conserved tryptophan within Rv0004's DnaA N-terminal-like domain leads to phenotypes similar to those observed upon Rv0004 depletion and can affect the association of Rv0004 with DnaB. In addition, using live cell imaging during depletion of Rv0004, we have uncovered a previously unappreciated role for DNA replication in coordinating mycobacterial cell division and cell size. Together, our data support that Rv0004 encodes a homolog of the recently identified DciA family of proteins found in most bacteria that lack the DnaC-DnaI helicase loaders in E. coli and B. subtilis. Therefore, the mechanisms of Rv0004 elucidated here likely apply to other DciA homologs and reveal insight into the diversity of bacterial strategies in even the most conserved biological processes.
DNA复制是生命的基础,但除了大肠杆菌和枯草芽孢杆菌外,对细菌DNA复制的详细了解有限。许多细菌,包括分枝杆菌,都没有编码已鉴定的解旋酶装载蛋白或起始蛋白DnaA的调节因子的同源物,尽管这些因子对大肠杆菌和枯草芽孢杆菌中的DNA复制至关重要。在本研究中,我们发现人类病原体结核分枝杆菌中一种以前未被表征的蛋白质Rv0004对细菌的生存能力至关重要,并且Rv0004的缺失会导致细胞周期进程受阻。通过结合遗传和生化方法,我们发现Rv0004在DNA复制中起作用,与DNA和复制性解旋酶DnaB相互作用,并影响DnaB-DnaA复合物的形成。我们还在Rv0004中鉴定出一个保守结构域,预计其在结构上类似于DnaA的N端蛋白质-蛋白质相互作用结构域。Rv0004的DnaA N端样结构域内单个保守色氨酸的突变导致的表型与Rv0004缺失时观察到的表型相似,并可能影响Rv0004与DnaB的结合。此外,在Rv0004缺失期间使用活细胞成像,我们发现了DNA复制在协调分枝杆菌细胞分裂和细胞大小方面以前未被认识到的作用。总之,我们的数据支持Rv0004编码了最近在大多数细菌中发现的DciA家族蛋白质的同源物,这些细菌缺乏大肠杆菌和枯草芽孢杆菌中的DnaC-DnaI解旋酶装载蛋白。因此,这里阐明的Rv0004的机制可能适用于其他DciA同源物,并揭示了即使在最保守的生物学过程中细菌策略的多样性。