Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses
Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses
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DOI：
10.1073/pnas.1714812115
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发表时间：
2018-04-03
影响因子：
11.1
通讯作者：
Weigele, Peter R.
中科院分区：
文献类型：
--
作者：
Lee, Yan-Jiun;Dai, Nan;Weigele, Peter R.
细菌的某些病毒（噬菌体）酶促超修饰其DNA以保护其遗传物质免受宿主限制性内切核酸酶介导的切割。历史上，已知来自Delftia噬菌体FW-14和芽孢杆菌属噬菌体SP10的病毒体DNA分别含有高度修饰的嘧啶α-腐胺基胸苷和α-谷氨酰胸苷。这些碱基来源于新复制的噬菌体DNA中5-羟甲基-2 '-脱氧尿苷（5-hmdU）通过焦磷酸化中间体的修饰。与FW-14和SP10一样，假单胞菌噬菌体M6和沙门氏菌噬菌体ViI编码预测磷酸化5-hmdU DNA但具有未表征的核苷酸含量的激酶同系物[Iyer等人（2013）Nucleic Acids Res 41：7635-7655]。我们在这里报告的两个碱基，5-（2-氨基乙氧基）甲基尿苷（5-NeOmdU）和5-（2-氨基乙基）尿苷（5-NedU）的发现和表征，在病毒体DNA的ViI和M6的，分别。此外，我们表明，重组表达的5个基因产物编码的噬菌体VII是足以重建5-NeOmdU在体外形成。这些发现指出了DNA修饰的未探索的多样性及其形成的潜在生物化学。
Certain viruses of bacteria (bacteriophages) enzymatically hyper-modify their DNA to protect their genetic material from host restriction endonuclease-mediated cleavage. Historically, it has been known that virion DNAs from the Delftia phage FW-14 and the Bacillus phage SP10 contain the hypermodified pyrimidines alpha-putrescinylthymidine and alpha-glutamylthymidine, respectively. These bases derive from the modification of 5-hydroxymethyl-2'-deoxyuridine (5-hmdU) in newly replicated phage DNA via a pyrophosphorylated intermediate. Like FW-14 and SP10, the Pseudomonas phage M6 and the Salmonella phage ViI encode kinase homologs predicted to phosphorylate 5-hmdU DNA but have uncharacterized nucleotide content [Iyer et al. (2013) Nucleic Acids Res 41:7635-7655]. We report here the discovery and characterization of two bases, 5-(2-aminoethoxy) methyluridine (5-NeOmdU) and 5-(2-aminoethyl) uridine (5-NedU), in the virion DNA of ViI and M6 phages, respectively. Furthermore, we show that recombinant expression of five gene products encoded by phage ViI is sufficient to reconstitute the formation of 5-NeOmdU in vitro. These findings point to an unexplored diversity of DNA modifications and the underlying biochemistry of their formation.