The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80

Virol J. 2013 Oct 18:10:308. doi: 10.1186/1743-422X-10-308.

Abstract

Background: Bacteriophage EC1-UPM is an N4-like bacteriophage which specifically infects Escherichia coli O78:K80, an avian pathogenic strain that causes colibacillosis in poultry. The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic similarities and differences.

Results: Bacteriophage EC1-UPM displays a very similar codon usage profile with its host and does not contain any tRNA gene. Comparative genomics analysis reveals close resemblance of bacteriophage EC1-UPM to three N4-like bacteriophages namely vB_EcoP_G7C, IME11 and KBNP21 with a total of 44 protein coding genes shared at 70% identity threshold. The genomic region coding for the tail fiber protein was found to be unique in bacteriophage EC1-UPM. Further annotation of the tail fiber protein using HHpred, a highly sensitive homology detection tool, reveals the presence of protein structure homologous to various polysaccharide processing proteins in its C-terminus. Leveraging on the availability of multiple N4-like bacteriophage genome sequences, the core genes of N4-like bacteriophages were identified and used to perform a multilocus phylogenetic analysis which enabled the construction of a phylogenetic tree with higher confidence than phylogenetic trees based on single genes.

Conclusion: We report for the first time the complete genome sequence of a N4-like bacteriophage which is lytic against avian pathogenic Escherichia coli O78:K80. A novel 928 amino acid residues tail fiber protein was identified in EC1-UPM which may be useful to further the understanding of phage-host specificity. Multilocus phylogenetic analysis using core genes of sequenced N4-like phages showed that the evolutionary relationship correlated well with the pattern of host specificity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Birds
  • Cluster Analysis
  • Coliphages / genetics*
  • Coliphages / isolation & purification*
  • DNA, Viral / chemistry*
  • DNA, Viral / genetics*
  • Escherichia coli / isolation & purification
  • Escherichia coli / virology*
  • Genome, Viral*
  • Molecular Sequence Data
  • Phylogeny
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid
  • Viral Proteins / genetics

Substances

  • DNA, Viral
  • Viral Proteins

Associated data

  • GENBANK/KC206276