Characterization of the genome of the dairy Lactobacillus helveticus bacteriophage {Phi}AQ113

Abstract

The complete genomic sequence of the dairy Lactobacillus helveticus bacteriophage ΦAQ113 was determined. Phage ΦAQ113 is a Myoviridae bacteriophage with an isometric capsid and a contractile tail. The final assembled consensus sequence revealed a linear, circularly permuted, double-stranded DNA genome with a size of 36,566 bp and a G+C content of 37%. Fifty-six open reading frames (ORFs) were predicted, and a putative function was assigned to approximately 90% of them. The ΦAQ113 genome shows functionally related genes clustered together in a genome structure composed of modules for DNA replication/regulation, DNA packaging, head and tail morphogenesis, cell lysis, and lysogeny. The identification of genes involved in the establishment of lysogeny indicates that it may have originated as a temperate phage, even if it was isolated from natural cheese whey starters as a virulent phage, because it is able to propagate in a sensitive host strain. Additionally, we discovered that the ΦAQ113 phage genome is closely related to Lactobacillus gasseri phage KC5a and Lactobacillus johnsonii phage Lj771 genomes. The phylogenetic similarities between L. helveticus phage ΦAQ113 and two phages that belong to gut species confirm a possible common ancestral origin and support the increasing consideration of L. helveticus as a health-promoting organism.

Fig 1

Transmission electron micrograph of phage ΦAQ113.

Fig 2

Restriction analysis of ΦAQ113 DNA. The phage DNA was digested with BglII, HhaI, PstI, HaeIII, MspI, EcoRI, and EcoRV. Lanes M1 and M2, 1-kb Plus and λ-HindIII DNA ladders; A and B indicate that the digests were unheated and heated prior to electrophoresis, respectively.

Fig 3

Analysis of the phage ΦAQ113 structural proteins. After purifications of ΦAQ113 by PEG precipitation, the purified phage proteins were separated by SDS-PAGE. The structural proteins from the main bands were identified by MS and MS/MS (see the text for details). Band 1, sheath tail protein; band 2, major head protein; band 3, sheath tail protein.

Fig 4

Comparison of the gene order and orientation of the genomes of L. helveticus ΦAQ113, L. gasseri ΦKC5a, and L. johnsonii ΦLj771 using Mauve genome alignment software. The figure was generated by the Mauve rearrangement viewer. Each of the three genomes is displayed horizontally with homologous locally colinear blocks outlined and connected with lines. The height of the similarity profile inside each block corresponds to the average level of conservation in that region of the genome sequence.