A virulent phage infecting Lactococcus garvieae, with homology to Lactococcus lactis phages

Abstract

A new virulent phage belonging to the Siphoviridae family and able to infect Lactococcus garvieae strains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only two L. garvieae strains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacterium Lactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness of L. garvieae phage GE1 to L. lactis phages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58 L. lactis strains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.

FIG 1

Morphology and structural proteome of phage GE1. (A) Electron micrograph of phage GE1. (B) Structural protein profiles of phages GE1 and c2. Numbers on the left indicate molecular mass of the markers (Bio-Rad) (lane M).

FIG 2

Analysis of GE1 cos region. (A) Analysis of the cos site and the flanking regions. Direct repeats (bold arrows), inverted repeats (bold, dashed arrows), A/T-rich regions, and G-rich segments are indicated. Details of the cohesive termini (rectangle) are also shown together with the site of cleavage (vertical arrows). Shading indicates nucleotides that belong to the consensus sequence found in all lactococcal phages for which the cos site has been determined. (B) Multiple alignments of λ-like R consensus sequences from Q54, GE1, and c2. Conserved nucleotides are shaded.

FIG 3

Genomic comparison of GE1, Q54, and c2 phages. ORFs from GE1 showing similarity with other phages are linked by gray shading, and the percent amino acid identity indicated is representative of the aligned region.

FIG 4

Phylogenetic tree of different lactococcal phage proteomes determined using the neighbor-joining algorithm. The bar shows the difference between the phages in amino acids.