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
Fig. S1. Neighbour-joining unrooted trees of (A) DNA polymerase (E3 gp154) and (B) prohead protease (E3 gp77). Numbers in nodes are the percentage bootstrap values for 1000 replicates; values under 50% are not represented. Reference bacteriophages for accepted genera according to ICTV and NCBI taxonomy are indicated by asterisks. E3 proteins are indicated by arrows. The scale shows the number of amino acid substitutions per site. The topology of the phylogenetic trees (including the TerL tree; see Fig. 3) reproduced the branching pattern of phage phylogenies based on whole genomes (Rohwer and Edwards, 2002; Glazko et al., 2007), and most well-supported clades grouped phages classified within an established genus.
Fig. S2. Alignment of the head morphogenesis module of R. equi phage E3, enterobacteriophage HK97 and mycobacteriophages Bxz1 and Myrna. Pairwise sequence similarity between adjacent genomes is indicated by shading. HP, hypothetical protein; PAP, protease-associated protein; ThyX, FAD-dependent thymidylate synthase; HNH endo, HNH endonuclease.
Fig. S3. Neighbour-joining unrooted tree of E3 tail fibre proteins (gp86, gp88 and gp204). The numbers in nodes are the percentage bootstrap values for 1000 replicates; values under 50% are not represented. Arrows indicate E3 tail fibre proteins. The scale shows the number of amino acid substitutions per site.
Table S1. Annotation of bacteriophage E3 genome.
Table S2. E3 virion-associated proteins identified by LC-ESI-MS/MS.
Table S3. Bacterial strains used for host range analysis.
Table S4. Software used for genome annotation.
Supporting information text. E3 products for which phage homologues could not be identified or are exceptional and Supporting information references.
GenBank Accession No. HM114277.
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