Amare Benhur, Mo Anthea, Khan Noorisah, Sowa Dana J, Warner Monica M, Tetenych Andriana, Andres Sara N
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
Front Mol Biosci. 2021 Nov 25;8:787709. doi: 10.3389/fmolb.2021.787709. eCollection 2021.
DNA double-strand breaks are the most lethal form of damage for living organisms. The non-homologous end joining (NHEJ) pathway can repair these breaks without the use of a DNA template, making it a critical repair mechanism when DNA is not replicating, but also a threat to genome integrity. NHEJ requires proteins to anchor the DNA double-strand break, recruit additional repair proteins, and then depending on the damage at the DNA ends, fill in nucleotide gaps or add or remove phosphate groups before final ligation. In eukaryotes, NHEJ uses a multitude of proteins to carry out processing and ligation of the DNA double-strand break. Bacterial NHEJ, though, accomplishes repair primarily with only two proteins-Ku and LigD. While Ku binds the initial break and recruits LigD, it is LigD that is the primary DNA end processing machinery. Up to three enzymatic domains reside within LigD, dependent on the bacterial species. These domains are a polymerase domain, to fill in nucleotide gaps with a preference for ribonucleotide addition; a phosphoesterase domain, to generate a 3'-hydroxyl DNA end; and the ligase domain, to seal the phosphodiester backbone. To date, there are no experimental structures of wild-type LigD, but there are x-ray and nuclear magnetic resonance structures of the individual enzymatic domains from different bacteria and archaea, along with structural predictions of wild-type LigD via AlphaFold. In this review, we will examine the structures of the independent domains of LigD from different bacterial species and the contributions these structures have made to understanding the NHEJ repair mechanism. We will then examine how the experimental structures of the individual LigD enzymatic domains combine with structural predictions of LigD from different bacterial species and postulate how LigD coordinates multiple enzymatic activities to carry out DNA double-strand break repair in bacteria.
DNA双链断裂是生物体最致命的损伤形式。非同源末端连接（NHEJ）途径可以在不使用DNA模板的情况下修复这些断裂，这使其成为DNA不复制时的关键修复机制，但同时也对基因组完整性构成威胁。NHEJ需要蛋白质来锚定DNA双链断裂，招募其他修复蛋白，然后根据DNA末端的损伤情况，填补核苷酸缺口或在最终连接之前添加或去除磷酸基团。在真核生物中，NHEJ使用多种蛋白质来进行DNA双链断裂的加工和连接。然而，细菌的NHEJ主要仅通过两种蛋白质——Ku和LigD来完成修复。虽然Ku结合初始断裂并招募LigD，但LigD才是主要的DNA末端加工机制。根据细菌种类的不同，LigD中最多存在三个酶结构域。这些结构域分别是：一个聚合酶结构域，用于填补核苷酸缺口，优先添加核糖核苷酸；一个磷酸二酯酶结构域，用于产生3'-羟基DNA末端；以及连接酶结构域，用于封闭磷酸二酯主链。迄今为止，尚无野生型LigD的实验结构，但有来自不同细菌和古细菌的单个酶结构域的X射线和核磁共振结构，以及通过AlphaFold对野生型LigD的结构预测。在本综述中，我们将研究来自不同细菌物种的LigD独立结构域的结构，以及这些结构对理解NHEJ修复机制所做的贡献。然后，我们将研究单个LigD酶结构域的实验结构如何与来自不同细菌物种的LigD结构预测相结合，并推测LigD如何协调多种酶活性以在细菌中进行DNA双链断裂修复。
