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

Abstract

The genomes of six Listeria bacteriophages were sequenced and analyzed. Phages A006, A500, B025, P35, and P40 are members of the Siphoviridae and 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 gene tsf. 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 the tsh coding sequences is induced by overlapping proline codons and cis-acting shifty stops. Although Listeria phage 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 other Listeria phages but also to viruses infecting other members of the Firmicutes. In conclusion, our results yield insights into the composition and diversity of Listeria phages and provide new information on their function, genome adaptation, and evolution.The opportunistic pathogen Listeria monocytogenes is ubiquitous in nature and can become endemic in food processing environments, causing contamination of dairy products, meats, vegetables, and processed ready-to-eat food (14). L. monocytogenes is the causative agent of epidemic and sporadic listeriosis. The risk of infection is markedly increased among immunocompromised patients, newborns, pregnant women, and the elderly and is associated with a mortality rate of about 20 to 30% (37).Although all strains of L. monocytogenes are considered potentially pathogenic, epidemiological evidence has shown that certain serovars are more frequently associated with both sporadic cases and larger food-borne outbreaks. However, genetic variation within the virulence genes of wild-type strains appears to be limited and could not be directly linked to differences in pathogenicity (30) or environmental distribution.It is becoming increasingly clear that bacteriophages have an important role in bacterial biology, diversity, and evolution, as indicated by the advances in genome sequencing which revealed a high incidence of phage-related sequences in bacterial genomes. Many phages have been described for the genus Listeria, and lysogeny appears to be widespread (28). Availability of the genome sequences of different L. monocytogenes and L. innocua strains also revealed the...

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

“…Unlike phages of other species (Nolan et al, 2006;Dorscht et al, 2009;Sepúlveda-Robles et al, 2012), P. acnes phages show a high genetic similarity. The phages may have evolved recently under limited selection, as no clear lineages can be found among the phages studied, suggesting that these phages may be relatively new to their hosts .…”

Cryo-Electron Microscopy Structure of Lactococcal Siphophage 1358 Virion

“…Many of its genes share sequence identities with some Listeria siphophages (23), which led to the hypothesis that this uncommon lactococcal phage originated from a Listeria phage (8). Moreover, the tail of 1358 is significantly shorter than those of other lactococcal phages, and it is decorated by hairy appendages.…”

Bacteriophage P70: Unique Morphology and Unrelatedness to Other Listeria Bacteriophages

“…Nucleotide dot plot analyses against the genomes of Listeria phages 01761, A006, A118, A500, A511, B025, B053, B054, P35, and P40 (results not shown) revealed that P70 possesses a unique genome, about 50% larger than other Listeria siphoviruses and half the size of the largest known Listeria phage genomes (5,20). The genome is divided into several functional modules corresponding to lifestyle (5) but highly mosaic in nature and composed of more modules than any other known Listeria phage genomes (5,20). Major structural component-encoding genes could be identified, such as the terminase subunits, portal, major capsid protein, major tail protein, head-tail connector, and a putative tail fiber.…”

“…Although many Listeria-specific bacteriophages have been described, only a limited number have been fully sequenced (2,5,15,21,29). Most Listeria phages are temperate siphoviruses, with B054, A511, and P100 being the only described myoviruses (2,5,15). Listeria can be efficiently detected and controlled by the use of highly virulent and specific bacteriophages (2,22,23).…”