Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions

PLoS One. 2012;7(12):e51163. doi: 10.1371/journal.pone.0051163. Epub 2012 Dec 7.

Abstract

The complete sequence of the 46,267 bp genome of the lytic bacteriophage tf specific to Pseudomonas putida PpG1 has been determined. The phage genome has two sets of convergently transcribed genes and 186 bp long direct terminal repeats. The overall genomic architecture of the tf phage is similar to that of the previously described Pseudomonas aeruginosa phages PaP3, LUZ24 and phiMR299-2, and 39 out of the 72 products of predicted tf open reading frames have orthologs in these phages. Accordingly, tf was classified as belonging to the LUZ24-like bacteriophage group. However, taking into account very low homology levels between tf DNA and that of the other phages, tf should be considered as an evolutionary divergent member of the group. Two distinguishing features not reported for other members of the group were found in the tf genome. Firstly, a unique end structure--a blunt right end and a 4-nucleotide 3'-protruding left end--was observed. Secondly, 14 single-chain interruptions (nicks) were found in the top strand of the tf DNA. All nicks were mapped within a consensus sequence 5'-TACT/RTGMC-3'. Two nicks were analyzed in detail and were shown to be present in more than 90% of the phage population. Although localized nicks were previously found only in the DNA of T5-like and phiKMV-like phages, it seems increasingly likely that this enigmatic structural feature is common to various other bacteriophages.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Breaks, Single-Stranded*
  • DNA Primers / genetics
  • Evolution, Molecular*
  • Genome Components
  • Genome, Viral / genetics*
  • Molecular Sequence Data
  • Podoviridae / genetics*
  • Pseudomonas putida / virology*
  • Sequence Analysis, DNA
  • Species Specificity

Substances

  • DNA Primers

Associated data

  • GENBANK/AM910650
  • GENBANK/AY078382
  • GENBANK/JN254801

Grants and funding

Work of LAK group was supported by the School of Biological Sciences and the QUESTOR Centre. Work in KS laboratory was supported by a Russian Academy of Science program grant in Molecular and Cellular Biology and Federal Program “Scientific and scientific-pedagogical personnel of innovative Russia 2009–2012”, state contract 02.740.11.077. NVA was partially supported by a fellowship from Charles and Johanna Busch Biomedical Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.