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Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp

Smith, Margaret C M and Hendrix, Roger W and Dedrick, Rebekah and Mitchell, Kaitlin and Ko, Ching-Chung and Russell, Daniel and Bell, Emma and Gregory, Matthew and Bibb, Maureen J and Pethick, Florence and Jacobs-Sera, Deborah and Herron, Paul and Buttner, Mark J and Hatfull, Graham F (2013) Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. Journal of Bacteriology, 195 (21). pp. 4924-4935. ISSN 1098-5530

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Abstract

The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, 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 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.