Characterization of prophages of Lactococcus garvieae

Abstract

This report describes the morphological characterization and genome analysis of an induced prophage (PLg-TB25) from a dairy strain of Lactococcus garvieae. The phage belongs to the Siphoviridae family and its morphology is typical of other lactococcal phages. A general analysis of its genome did not reveal similarities with other lactococcal phage genomes, confirming its novelty. However, similarities were found between genes of its morphogenesis cluster and genes of Gram-positive bacteria, suggesting that this phage genome resulted from recombination events that took place in a heterogeneous microbial environment. An in silico search for other prophages in 16 L. garvieae genomes available in public databases, uncovered eight seemingly complete prophages in strains isolated from dairy and fish niches. Genome analyses of these prophages revealed three novel L. garvieae phages. The remaining prophages had homology to phages of Lactococcus lactis (P335 group) suggesting a close relationship between these lactococcal species. The similarity in GC content of L. garvieae prophages to the genomes of L. lactis phages further supports the hypothesis that these phages likely originated from the same ancestor.

Figure 1

Electron micrograph of the phage PLg-TB25 induced from strain TB25.

Figure 2

Map of the phage PLg-TB25 genome. Each arrow and number identifies an open reading frame. Black arrows identify the lysogeny module. For specific functions see Table 1.

Figure 3

Similarity matrix of 32 lactococcal phages and prophages based on the presence/absence of genes. The heatmap is generated based on the number of proteins shared by phages. Deeper shade of blue indicates a closer relationship.

Figure 4

Genomic comparison between L. garvieae phage IPLA31405b and L. lactis phage ul36.k1. Color shading was used to discriminate between ≥70% amino acid identity (dark color) and ≤69% amino acid identity (light color). The absence of shading indicates no significant similarity. The percent of amino acid identity inside the shading is representative of the aligned region only. Black arrows identify the lysogeny module.

Figure 5

Genomic comparison between L. garvieae phage IPLA31405b and L. lactis phage r1t. Color shading was used to discriminate between ≥70% amino acid identity (dark color) and ≤69% amino acid identity (light color). The absence of shading means no significant similarity. The percent of amino acid identity inside the shading is representative of the aligned region only. Black arrows identify the lysogeny module.