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Characterization of the temperate phage vB_RleM_PPF1 and its site-specific integration into the Rhizobium leguminosarum F1 genome

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Abstract

Bacteriophages may play an important role in regulating population size and diversity of the root nodule symbiont Rhizobium leguminosarum, as well as participating in horizontal gene transfer. Although phages that infect this species have been isolated in the past, our knowledge of their molecular biology, and especially of genome composition, is extremely limited, and this lack of information impacts on the ability to assess phage population dynamics and limits potential agricultural applications of rhizobiophages. To help address this deficit in available sequence and biological information, the complete genome sequence of the Myoviridae temperate phage PPF1 that infects R. leguminosarum biovar viciae strain F1 was determined. The genome is 54,506 bp in length with an average G+C content of 61.9 %. The genome contains 94 putative open reading frames (ORFs) and 74.5 % of these predicted ORFs share homology at the protein level with previously reported sequences in the database. However, putative functions could only be assigned to 25.5 % (24 ORFs) of the predicted genes. PPF1 was capable of efficiently lysogenizing its rhizobial host R. leguminosarum F1. The site-specific recombination system of the phage targets an integration site that lies within a putative tRNA-Pro (CGG) gene in R. leguminosarum F1. Upon integration, the phage is capable of restoring the disrupted tRNA gene, owing to the 50 bp homologous sequence (att core region) it shares with its rhizobial host genome. Phage PPF1 is the first temperate phage infecting members of the genus Rhizobium for which a complete genome sequence, as well as other biological data such as the integration site, is available.

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Acknowledgments

This study was funded by a Saskatchewan Ministry of Agriculture, Agriculture Development Fund grant and NSERC (Natural Sciences and Engineering Research Council of Canada) Discovery Grants to MFH and CKY. APH acknowledges the support of an Alberta Ingenuity Technology Futures (AITF) graduate scholarship.

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Authors and Affiliations

  1. Department of Biological Sciences, University of Calgary, Calgary, AB, Canada

    Anupama P. Halmillawewa, Marcela Restrepo-Córdoba & Michael F. Hynes

  2. Department of Biology, University of Regina, Regina, SK, Canada

    Benjamin J. Perry & Christopher K. Yost

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  1. Anupama P. Halmillawewa
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  2. Marcela Restrepo-Córdoba
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  3. Benjamin J. Perry
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  4. Christopher K. Yost
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  5. Michael F. Hynes
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Correspondence to Michael F. Hynes.

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This study was funded by grants from the Saskatchewan Ministry of Agriculture, Agriculture Development Fund (to CKY and MFH, Grant # 20080211) and from NSERC (Natural Sciences and Engineering Research Council of Canada) (Discovery Grant # 105660 to MFH) (Discovery grant # 288281 to CKY).

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All authors declare that they have no conflict of interest with respect to this paper.

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Communicated by S. Hohmann.

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Halmillawewa, A.P., Restrepo-Córdoba, M., Perry, B.J. et al. Characterization of the temperate phage vB_RleM_PPF1 and its site-specific integration into the Rhizobium leguminosarum F1 genome. Mol Genet Genomics 291, 349–362 (2016). https://doi.org/10.1007/s00438-015-1113-8

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