Contributed equally to this work.
Genome and proteome analysis of phage E3 infecting the soil-borne actinomycete Rhodococcus equi
Article first published online: 16 JAN 2013
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Environmental Microbiology Reports
Thematic Issue on Environmental Ecology of Pathogens and Resistances
Volume 5, Issue 1, pages 170–178, February 2013
How to Cite
Salifu, S. P., Valero-Rello, A., Campbell, S. A., Inglis, N. F., Scortti, M., Foley, S. and Vázquez-Boland, J. A. (2013), Genome and proteome analysis of phage E3 infecting the soil-borne actinomycete Rhodococcus equi. Environmental Microbiology Reports, 5: 170–178. doi: 10.1111/1758-2229.12028
- Issue published online: 3 FEB 2013
- Article first published online: 16 JAN 2013
- Accepted manuscript online: 20 DEC 2012 10:31AM EST
- Manuscript Accepted: 10 DEC 2012
- Manuscript Received: 7 MAR 2012
- Horserace Betting Levy Board. Grant Number: Prj-753
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.