Research Department, New England Biolabs, Ipswich, MA 01938.
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139.
Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3116-E3125. doi: 10.1073/pnas.1714812115. Epub 2018 Mar 19.
Certain viruses of bacteria (bacteriophages) enzymatically hypermodify their DNA to protect their genetic material from host restriction endonuclease-mediated cleavage. Historically, it has been known that virion DNAs from the phage ΦW-14 and the phage SP10 contain the hypermodified pyrimidines α-putrescinylthymidine and α-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 ΦW-14 and SP10, the phage M6 and the phage ViI encode kinase homologs predicted to phosphorylate 5-hmdU DNA but have uncharacterized nucleotide content [Iyer et al. (2013) 41:7635-7655]. We report here the discovery and characterization of two bases, 5-(2-aminoethoxy)methyluridine (5-emdU) and 5-(2-aminoethyl)uridine (5-edU), 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-emdU in vitro. These findings point to an unexplored diversity of DNA modifications and the underlying biochemistry of their formation.
某些细菌病毒（噬菌体）通过酶促反应对其 DNA 进行高度修饰，以保护其遗传物质免受宿主限制内切酶介导的切割。从历史上看，人们已经知道，噬菌体 ΦW-14 和噬菌体 SP10 的病毒 DNA 分别含有高度修饰的嘧啶α-腐胺基胸腺嘧啶和α-谷氨酰基胸腺嘧啶。这些碱基源自新复制的噬菌体 DNA 中 5-羟甲基-2'-脱氧尿苷（5-hmdU）通过焦磷酸化中间产物的修饰而来。与 ΦW-14 和 SP10 一样，噬菌体 M6 和噬菌体 ViI 编码激酶同源物，预测该激酶同源物可磷酸化 5-hmdU DNA，但核苷酸含量尚未确定 [Iyer 等人，（2013 年）41:7635-7655]。我们在此报告在噬菌体 ViI 和 M6 的病毒 DNA 中分别发现并鉴定了两种碱基，即 5-(2-氨乙氧基)甲基尿嘧啶（5-emdU）和 5-(2-氨基乙基)尿嘧啶（5-edU）。此外，我们还表明，噬菌体 ViI 编码的五个基因产物的重组表达足以在体外重新形成 5-emdU。这些发现表明 DNA 修饰的多样性和其形成的潜在生物化学尚未得到探索。
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