Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore.
School of Biological Sciences, Nanyang Technological University, Singapore.
Nucleic Acids Res. 2023 Sep 22;51(17):9214-9226. doi: 10.1093/nar/gkad657.
Bacteriophages and bacteria are engaged in a constant arms race, continually evolving new molecular tools to survive one another. To protect their genomic DNA from restriction enzymes, the most common bacterial defence systems, double-stranded DNA phages have evolved complex modifications that affect all four bases. This study focuses on modifications at position 7 of guanines. Eight derivatives of 7-deazaguanines were identified, including four previously unknown ones: 2'-deoxy-7-(methylamino)methyl-7-deazaguanine (mdPreQ1), 2'-deoxy-7-(formylamino)methyl-7-deazaguanine (fdPreQ1), 2'-deoxy-7-deazaguanine (dDG) and 2'-deoxy-7-carboxy-7-deazaguanine (dCDG). These modifications are inserted in DNA by a guanine transglycosylase named DpdA. Three subfamilies of DpdA had been previously characterized: bDpdA, DpdA1, and DpdA2. Two additional subfamilies were identified in this work: DpdA3, which allows for complete replacement of the guanines, and DpdA4, which is specific to archaeal viruses. Transglycosylases have now been identified in all phages and viruses carrying 7-deazaguanine modifications, indicating that the insertion of these modifications is a post-replication event. Three enzymes were predicted to be involved in the biosynthesis of these newly identified DNA modifications: 7-carboxy-7-deazaguanine decarboxylase (DpdL), dPreQ1 formyltransferase (DpdN) and dPreQ1 methyltransferase (DpdM), which was experimentally validated and harbors a unique fold not previously observed for nucleic acid methylases.
噬菌体和细菌之间存在着持续的军备竞赛，不断进化出新的分子工具来相互生存。为了保护其基因组 DNA 免受限制酶等最常见的细菌防御系统的侵害，双链 DNA 噬菌体进化出了复杂的修饰，影响到所有四个碱基。本研究集中于鸟嘌呤第 7 位的修饰。鉴定出了 8 种 7-脱氮鸟嘌呤的衍生物，其中包括 4 种以前未知的衍生物：2'-脱氧-7-(甲氨基)甲基-7-脱氮鸟嘌呤（mdPreQ1）、2'-脱氧-7-（甲酰氨基）甲基-7-脱氮鸟嘌呤（fdPreQ1）、2'-脱氧-7-脱氮鸟嘌呤（dDG）和 2'-脱氧-7-羧基-7-脱氮鸟嘌呤（dCDG）。这些修饰是由一种名为 DpdA 的鸟嘌呤糖基转移酶插入 DNA 中的。此前已经鉴定出三种 DpdA 亚家族：bDpdA、DpdA1 和 DpdA2。本工作还鉴定出另外两种亚家族：DpdA3 可以完全取代鸟嘌呤，而 DpdA4 则是古菌病毒所特有的。带有 7-脱氮鸟嘌呤修饰的所有噬菌体和病毒中都发现了糖基转移酶，这表明这些修饰的插入是复制后的事件。预测有三种酶参与这些新鉴定的 DNA 修饰的生物合成：7-羧基-7-脱氮鸟嘌呤脱羧酶（DpdL）、dPreQ1 甲酰基转移酶（DpdN）和 dPreQ1 甲基转移酶（DpdM），后两者经实验验证，并具有独特的折叠结构，此前在核酸甲基转移酶中未观察到。
