Genomic and proteomic analyses of the terminally redundant genome of the Pseudomonas aeruginosa phage PaP1: establishment of genus PaP1-like phages

PLoS One. 2013 May 13;8(5):e62933. doi: 10.1371/journal.pone.0062933. Print 2013.

Abstract

We isolated and characterized a new Pseudomonas aeruginosa myovirus named PaP1. The morphology of this phage was visualized by electron microscopy and its genome sequence and ends were determined. Finally, genomic and proteomic analyses were performed. PaP1 has an icosahedral head with an apex diameter of 68-70 nm and a contractile tail with a length of 138-140 nm. The PaP1 genome is a linear dsDNA molecule containing 91,715 base pairs (bp) with a G+C content of 49.36% and 12 tRNA genes. A strategy to identify the genome ends of PaP1 was designed. The genome has a 1190 bp terminal redundancy. PaP1 has 157 open reading frames (ORFs). Of these, 143 proteins are homologs of known proteins, but only 38 could be functionally identified. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and high-performance liquid chromatography-mass spectrometry allowed identification of 12 ORFs as structural protein coding genes within the PaP1 genome. Comparative genomic analysis indicated that the Pseudomonas aeruginosa phage PaP1, JG004, PAK_P1 and vB_PaeM_C2-10_Ab1 share great similarity. Besides their similar biological characteristics, the phages contain 123 core genes and have very close phylogenetic relationships, which distinguish them from other known phage genera. We therefore propose that these four phages be classified as PaP1-like phages, a new phage genus of Myoviridae that infects Pseudomonas aeruginosa.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Composition
  • Base Sequence
  • DNA, Viral*
  • Genome, Viral*
  • Microscopy, Electron, Transmission
  • Myoviridae / classification
  • Myoviridae / genetics*
  • Myoviridae / ultrastructure
  • Open Reading Frames
  • Pancreatitis-Associated Proteins
  • Phylogeny
  • Proteomics
  • Pseudomonas Phages / classification
  • Pseudomonas Phages / genetics*
  • Pseudomonas Phages / ultrastructure
  • Pseudomonas aeruginosa / virology
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid
  • Viral Proteins / classification
  • Viral Proteins / genetics*
  • Virion / classification
  • Virion / genetics*
  • Virion / ultrastructure

Substances

  • DNA, Viral
  • Pancreatitis-Associated Proteins
  • REG3A protein, human
  • Viral Proteins

Grant support

This work was supported by grants 31070153 from the National Natural Science Foundation of China. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.