Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse ΦKZ-related phages

Abstract

The 283,757-bp double-stranded DNA genome of Pseudomonas fluorescens phage OBP shares a general genomic organization with Pseudomonas aeruginosa phage EL. Comparison of this genomic organization, assembled in syntenic genomic blocks interspersed with hyperplastic regions of the ΦKZ-related phages, supports the proposed division in the "EL-like viruses," and the "phiKZ-like viruses" within a larger subfamily. Identification of putative early transcription promoters scattered throughout the hyperplastic regions explains several features of the ΦKZ-related genome organization (existence of genomic islands) and evolution (multi-inversion in hyperplastic regions). When hidden Markov modeling was used, typical conserved core genes could be identified, including the portal protein, the injection needle, and two polypeptides with respective similarity to the 3'-5' exonuclease domain and the polymerase domain of the T4 DNA polymerase. While the N-terminal domains of the tail fiber module and peptidoglycan-degrading proteins are conserved, the observation of C-terminal catalytic domains typical for the different genera supports the further subdivision of the ΦKZ-related phages.

Fig 1

Genome sequence comparison of the ϕKZ-related phages. Genes inherited by vertical descent are shown in blue (syntenic position and orientation), red (syntenic position but inverted orientation with respect to OBP), and green (positional shift in the genome due to a multi-inversion process). Orange genes are ϕKZ-related homologs but are inconsistent with vertical descent. Genes in black have no ϕKZ-related homolog, but a homolog has been found elsewhere. Transcriptional orientation is indicated by the light blue (left to right) and pink (right to left) boxes above the OBP genome. Blocks of synteny (A, B, and C) are interspersed with hyperplastic regions.

Fig 2

Logo representation of the phage-specific promoters of phage OBP in comparison to a similar motif of phage 201ϕ2-1. When the consensus base differs, both phages often contain instances of the base characteristic of the other, indicating that these promoters may be functionally interchangeable.

Fig 3

Sequence alignment of two OBP polypeptides (Gp55 and Gp99) to the T4-like DNA polymerase (Gp43) of the enterobacterial phage RB69. RB69-Gp43 consist of an N-terminal half with an N-terminal domain (N-ter) and a 3′-5′ exonuclease domain of the DNAQ family, which is connected via a small linker (ln) to the C-terminal polymerase domain, composed of thumb, finger (Fn), and palm (PolBc) subdomains. Psi-BLAST matches are indicated in dark gray, while light gray shows similarity regions identified after alignments of the hidden Markov models of the ϕKZ relatives of both polypeptides and the HMMs of the RB69-Gp43 relatives. Asterisks indicate conserved aspartate residues.