Genome and proteome analysis of phage E3 infecting the soil-borne actinomyceteRhodococcus equi: Rhodococcusbacteriophage E3

Salifu, Samson P.; V�zquez-Boland, Jos� A.; Salifu, Samson Pandam; Valero-Rello, Ana; Campbell, Samantha A.; Inglis, Neil F.; Scortti, Mariela; Foley, Sophie; V�zquez-Boland, Jos� A

Abstract

We report on the characterization and genomic analysis of bacteriophage E3 isolated from soil and propagating in Rhodococcus equi strains. Phage E3 has a circular genome of 142 563 bp and is the first Myoviridae reported for the genus Rhodococcus and for a non-mycobacterial actinomycete. Phylogenetic analyses placed E3 in a distinct Myoviridae clade together with Mycobacterium phages Bxz1 and Myrna. The highly syntenic genomes of this myoviridal group comprise vertically evolving core phage modules flanked by hyperplastic regions specific to each phage and rich in horizontally acquired DNA. The hyperplastic regions contain numerous tRNA genes in the mycobacteriophages which are absent in E3, possibly reflecting bacterial host-specific translation-related phage fitness constraints associated with rate-limiting tRNAs. A structural proteome analysis identified 28 E3 polypeptides, including 15 not previously known to be virion-associated proteins. The E3 genome and comparative analysis provide insight into short-term genome evolution and adaptive plasticity in tailed phages from the environmental microbiome.

Citation

Salifu, S. P., Vázquez-Boland, J. A., Salifu, S. P., Valero-Rello, A., Campbell, S. A., Inglis, N. F., Scortti, M., Foley, S., & Vázquez-Boland, J. A. (2013). Genome and proteome analysis of phage E3 infecting the soil-borne actinomyceteRhodococcus equi: Rhodococcusbacteriophage E3. Environmental microbiology reports, 5(1), 170-178. https://doi.org/10.1111/1758-2229.12028

• Journal Article Type: Article
• Acceptance Date: Dec 10, 2012
• Online Publication Date: Dec 20, 2012
• Publication Date: 2013-02
• Deposit Date: Mar 20, 2014
• Publicly Available Date: Mar 20, 2014
• Journal: Environmental microbiology reports
• Print ISSN: 1758-2229
• Electronic ISSN: 1758-2229
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 5
• Issue: 1
• Pages: 170-178
• DOI: https://doi.org/10.1111/1758-2229.12028
• Keywords: bacteriophage E3; Rhodococcus equi; genome evolution; adaptive plasticity; Myoviridae
• Public URL: http://researchrepository.napier.ac.uk/id/eprint/6634
• Publisher URL: http://dx.doi.org/10.1111/1758-2229.12028
• Contract Date: Mar 20, 2014