Complete genome of the broad-host-range Erwinia amylovora phage phiEa21-4 and its relationship to Salmonella phage felix O1

Appl Environ Microbiol. 2009 Apr;75(7):2139-47. doi: 10.1128/AEM.02352-08. Epub 2009 Jan 30.

Abstract

The first complete genome sequence for a myoviridal bacteriophage, PhiEa21-4, infecting Erwinia amylovora, Erwinia pyrifoliae, and Pantoea agglomerans strains has been determined. The unique sequence of this terminally redundant, circularly permuted genome is 84,576 bp. The PhiEa21-4 genome has a GC content of 43.8% and contains 117 putative protein-coding genes and 26 tRNA genes. PhiEa21-4 is the first phage in which a precisely conserved rho-independent terminator has been found dispersed throughout the genome, with 24 copies in all. Also notable in the PhiEa21-4 genome are the presence of tRNAs with six- and nine-base anticodon loops, the absence of a small packaging terminase subunit, and the presence of nadV, a principle component of the NAD(+) salvage pathway, which has been found in only a few phage genomes to date. PhiEa21-4 is the first reported Felix O1-like phage genome; 56% of the predicted PhiEa21-4 proteins share homology with those of the Salmonella phage. Apart from this similarity to Felix O1, the PhiEa21-4 genome appears to be substantially different, both globally and locally, from previously reported sequences. A total of 43 of the 117 genes are unique to PhiEa21-4, and 32 of the Felix O1-like genes do not appear in any phage genome sequences other than PhiEa21-4 and Felix O1. N-terminal sequencing and matrix-assisted laser desorption ionization-time of flight analysis resulted in the identification of five PhiEa21-4 genes coding for virion structural proteins, including the major capsid protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriophages / genetics*
  • Bacteriophages / isolation & purification
  • Bacteriophages / ultrastructure
  • Base Composition
  • DNA, Circular / genetics
  • DNA, Viral / genetics*
  • Erwinia amylovora / virology*
  • Genome, Viral*
  • Microscopy, Electron, Transmission
  • Molecular Sequence Data
  • Open Reading Frames
  • RNA, Transfer / genetics
  • Salmonella Phages / genetics
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid
  • Synteny
  • Viral Proteins / genetics
  • Virion / ultrastructure

Substances

  • DNA, Circular
  • DNA, Viral
  • Viral Proteins
  • RNA, Transfer

Associated data

  • GENBANK/AF320576
  • GENBANK/AJ278614
  • GENBANK/EF160123