In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.

中文翻译：

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使用纳米孔测序检测噬菌体CAjan DNA中的preQ0脱氮鸟嘌呤修饰，发现在两个不同的DNA基序上存在相同的超修饰。

在与移动遗传元件（MGE）的不断进化斗争中，细菌已开发出多种防御机制，其中一些以进入的外来核酸为目标，例如限制性修饰（RM）或CRISPR-Cas系统。这些MGE中的一些，包括噬菌体，反过来又发展出不同的策略来规避这些障碍。最近显示，噬菌体CAjan和180种其他病毒在其DNA中使用7-脱氮鸟嘌呤修饰来逃避细菌RM系统。除其他外，噬菌体CAjan基因组包含编码tRNA-脱氮嘌呤修饰酶的DNA-修饰同源物的基因，以及四个7-氰基-7-脱氮鸟嘌呤合成基因。使用CRISPR-Cas9基因组编辑工具结合纳米孔测序（ONT），我们显示CAjan基因组中的7-脱氮鸟嘌呤修饰依赖于噬菌体编码的基因。修饰也是位点特异性的，主要在两个独立的DNA序列环境中发现：GA和GGC。修饰酶DpdA的同源性建模可深入了解其可能的DNA结合表面和DNA识别的一般模式。