Comparative Genome Analysis ofListeriaBacteriophages Reveals Extensive Mosaicism, Programmed Translational Frameshifting, and a Novel Prophage Insertion Site

Abstract

The genomes of sixListeriabacteriophages were sequenced and analyzed. Phages A006, A500, B025, P35, and P40 are members of theSiphoviridaeand contain double-stranded DNA genomes of between 35.6 kb and 42.7 kb. Phage B054 is a unique myovirus and features a 48.2-kb genome. Phage B025 features 3′ overlapping single-stranded genome ends, whereas the other viruses contain collections of terminally redundant, circularly permuted DNA molecules. Phages P35 and P40 have a broad host range and lack lysogeny functions, correlating with their virulent lifestyle. Phages A500, A006, and B025 integrate into bacterial tRNA genes, whereas B054 targets the 3′ end of translation elongation factor genetsf. This is the first reported case of phage integration into such an evolutionarily conserved genetic element. Peptide fingerprinting of viral proteins revealed that both A118 and A500 utilize +1 and −1 programmed translational frameshifting for generating major capsid and tail shaft proteins with C termini of different lengths. In both cases, the unusual +1 frameshift at the 3′ ends of thetshcoding sequences is induced by overlapping proline codons andcis-acting shifty stops. AlthoughListeriaphage genomes feature a conserved organization, they also show extensive mosaicism within the genome building blocks. Of particular interest is B025, which harbors a collection of modules and sequences with relatedness not only to otherListeriaphages but also to viruses infecting other members of theFirmicutes. In conclusion, our results yield insights into the composition and diversity ofListeriaphages and provide new information on their function, genome adaptation, and evolution.