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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

Authors

Samson P. Salifu

Jos� A. V�zquez-Boland

Samson Pandam Salifu

Ana Valero-Rello

Neil F. Inglis

Mariela Scortti

Jos� A V�zquez-Boland



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.

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

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Publisher Licence URL
http://creativecommons.org/licenses/by-nc-nd/4.0/

Copyright Statement
This is the peer reviewed version of the following article: Samson P. Salifu, Ana Valero-Rello, Samantha A. Campbell, Neil F. Inglis, Mariela Scortti, Sophie Foley, and José A. Vazquez-Boland (2013) - Genomic and proteomic analysis of phage E3 infecting the
soil-borne actinomycete Rhodococcus equi, Environmental Microbiology Reports, 5 (1), 170-178, which has been published in final form at http://dx.doi.org/10.1111/1758-2229.12028. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.




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