Evolutionary Relationships among Actinophages and a Putative Adaptation for Growth in Streptomyces spp.
Evolutionary Relationships among Actinophages and a Putative Adaptation for Growth in Streptomyces spp.
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DOI：
10.1128/jb.00618-13
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发表时间：
2013-11-01
影响因子：
3.2
通讯作者：
Hatfull, Graham F.
中科院分区：
文献类型：
--
作者：
Smith, Margaret C. M.;Hendrix, Roger W.;Hatfull, Graham F.
八个链霉菌的基因组序列，其中四个是分离的这项研究。噬菌体R4、TG 1、phi Hau 3和SV 1先前已被分离，并已被用作理解和遗传操纵链霉菌属的工具。我们还提取了五个明显完整的原噬菌体从最近的链霉菌。基因组计划，并在数据库中的六个噬菌体基因组，我们分析了所有19个链霉菌噬菌体基因组，以了解它们之间的关系，以及其他放线菌噬菌体，特别是分枝杆菌噬菌体。其中15个链霉菌属的基因组被分成4个相关的基因组簇。虽然R4样噬菌体与其他噬菌体不具有核苷酸序列相似性，但它们显然与A簇分枝杆菌噬菌体具有共同的祖先，共享许多蛋白质同源物，共同的基因同线性和相似的阻遏物-stoperator调控系统。R4样噬菌体phi Hau 3和前噬菌体StrepC.1（来自链霉菌属菌株C）似乎劫持了链霉菌的独特适应，即，使用罕见的UUA密码子，以控制必需的噬菌体蛋白，即末端酶的翻译。委内瑞拉链霉菌广义转导噬菌体SV 1被用来预测不同链霉菌属的其他广义转导噬菌体的存在。
The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, phi Hau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating Streptomyces spp. We also extracted five apparently intact prophages from recent Streptomyces spp. genome projects and, together with six phage genomes in the database, we analyzed all 19 Streptomyces phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the Streptomyces phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage phi Hau3 and the prophage StrepC.1 (from Streptomyces sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The Streptomyces venezuelae generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different Streptomyces species.