Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp

Abstract

The horizontal transfer of genes by mobile genetic elements such as plasmids and phages can accelerate genome diversification of Vibrio spp., affecting their physiology, pathogenicity, and ecological character. In this study, sequence analysis of three plasmids from Vibrio spp. previously isolated from salt marsh sediment revealed the remarkable diversity of these elements. Plasmids p0908 (81.4 kb), p23023 (52.5 kb), and p09022 (31.0 kb) had a predicted 99, 64, and 32 protein-coding sequences and G+C contents of 49.2%, 44.7%, and 42.4%, respectively. A phylogenetic tree based on concatenation of the host 16S rRNA and rpoA nucleotide sequences indicated p23023 and p09022 were isolated from strains most closely related to V. mediterranei and V. campbellii, respectively, while the host of p0908 forms a clade with V. fluvialis and V. furnissii. Many predicted proteins had amino acid identities to proteins of previously characterized phages and plasmids (24 to 94%). Predicted proteins with similarity to chromosomally encoded proteins included RecA, a nucleoid-associated protein (NdpA), a type IV helicase (UvrD), and multiple hypothetical proteins. Plasmid p0908 had striking similarity to enterobacteria phage P1, sharing genetic organization and amino acid identity for 23 predicted proteins. This study provides evidence of genetic exchange between Vibrio plasmids, phages, and chromosomes among diverse Vibrio spp.

FIG. 1.

A concatenation of 16S rRNA and rpoA nucleotide sequences of the plasmid hosts, Vibrio sp. strains 0908, 23023, and 09022, was used to determine relatedness of the hosts to other Vibrio spp. as examined in a previous study (60). The neighbor-joining method with the Jukes-Cantor model of distance estimation (30) was used to generate the tree with a concatenation of 16S rRNA (1,452 nucleotides) and rpoA (772 nucleotides) sequences. Bootstrap values represent 1,000 replications, and only those with values of ≥50 are shown.

FIG. 2.

Genetic organization and amino acid conservation of predicted CDSs of p0908 compared to CDSs of enterobacteria phage P1. Shading indicates regions with amino acid similarity, while the protein lengths (number of amino acids) are designated under each arrow and approximated by the arrow size. The orientation of each arrow indicates the direction of transcription. Vertical lines indicate the presence of additional genes that are not shown.

FIG. 3.

Phylogenetic comparison of the predicted amino acid sequence encoded by CDS24 of p23023 with RecA amino acid sequences representing most Vibrio spp. and additional members of the Vibrionaceae available in GenBank as of March 2007. Distantly related proteobacteria were included as outgroups. A neighbor-joining tree was constructed in MEGA (33) using the Poisson correction (42). Bootstrap values were generated over 1,000 replications and are indicated where the value was ≥50.

FIG. 4.

Sequence alignment of RecA amino acid sequences of CDS24 from p23023 with those sequences encoded on the genomes of V. splendidus, V. parahaemolyticus, and E. coli. The V. mediterranei RecA sequence was a partial sequence obtained from a multilocus sequence analysis of Vibrio spp. (60). The RecA signature motif (4), P-loop motif (Walker A motif) involved in ATP binding (6), loop L1 motif involved in binding of double-stranded DNA (24, 54), and the loop L2 motif for binding single-stranded DNA (24, 54) are all indicated.