Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan.
Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, 739-8530, Japan.
Sci Rep. 2018 Mar 14;8(1):4486. doi: 10.1038/s41598-018-22239-3.
Xanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.
黄单胞菌病毒（噬菌体）XacN1 是一种新型巨型肌尾噬菌体，感染柑橘溃疡病致病菌黄单胞菌。其线性 384670bp 双链 DNA 基因组编码 592 种蛋白质，具有测序病毒基因组中最长的（66kbp）直接末端重复序列（DTR）。DTR 含有 56 个 tRNA 基因，对应所有 20 种氨基酸，是病毒基因组中报道的最多的 tRNA 基因数。密码子使用分析表明，噬菌体编码的 tRNA 倾向于靶向噬菌体高度使用但宿主较少使用的密码子。XacN1 基因组中存在这些 tRNA 基因以及另外七个与翻译相关的基因和一个 chaperonin 基因，表明噬菌体复制相对独立于宿主分子机制，这导致对该巨型噬菌体具有广泛宿主范围的预测。我们通过在感染试验中针对一系列宿主菌株证实了 XacN1 比其他柑橘溃疡病噬菌体具有更广泛的宿主范围，验证了这一预测。系统发育分析揭示了由 XacN1 和其他十个巨型噬菌体组成的噬菌体分支，表明该噬菌体群体的进化稳定的大型基因组大小。
