Bacteria have evolved diverse mechanisms to cope with the constant threat of phage predation. DndABCDE-catalysed DNA phosphorothioate modification, in which the non-bridging oxygen of the DNA sugar-phosphate backbone is replaced by sulfur, can couple with proteins encoded by the dndFGH gene cluster to provide defensive protection, albeit via an obscure mode of action. Here we present structural and biochemical insights showing that the proteins DndF, DndG and DndH form a DndFGH complex and exhibit functions that are not detected in the individual proteins, including DNA nicking and translocation activities. Interestingly, DndFGH shows preferential affinity for phosphorothioate DNA, which suppresses the DNA-stimulated ATPase activity of the complex and consequently impedes its translocation and nicking activities. This phosphorothioate binding preference is believed to account for self/non-self discrimination and enable DndFGH to specifically introduce nicking damage in invasive DNA. This study expands our knowledge of the defence mechanisms involving epigenetic markers for the protection of self-DNA.

细菌已经进化出多种机制来应对噬菌体捕食的持续威胁。DndABCDE 催化的 DNA 硫代磷酸酯修饰，其中 DNA 糖磷酸主链的非桥氧被硫取代，可以与 dndFGH 编码的蛋白质偶联基因簇提供防御性保护，尽管是通过一种模糊的作用方式。在这里，我们提出结构和生化见解，表明蛋白质 DndF、DndG 和 DndH 形成 DndFGH 复合物，并表现出在单个蛋白质中未检测到的功能，包括 DNA 切口和易位活动。有趣的是，DndFGH 显示出对硫代磷酸 DNA 的优先亲和力，这会抑制复合物的 DNA 刺激的 ATP 酶活性，从而阻碍其易位和切口活动。这种硫代磷酸酯结合偏好被认为是自我/非自我歧视的原因，并使 DndFGH 能够特异性地在侵入性 DNA 中引入切口损伤。这项研究扩展了我们对涉及用于保护自身 DNA 的表观遗传标记的防御机制的认识。