Abstract
BackgroundBacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank.ResultsHere, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR) and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs) that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases.ConclusionOur observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4-like phages harbour a wealth of genetic material that has not been identified previously. The mechanisms by which these genes may have arisen may differ from those previously proposed for the evolution of other bacteriophage genomes.
Highlights
Bacteriophages are an important repository of genetic diversity
The efficient and promiscuous T4-encoded recombination machinery [6] may generate a high degree of evolutionary diversity, via both homologous and non-homologous recombination between this phage genome and that of bacterial hosts or other phages
We identified a total of 750 open reading frames (ORFs) from the 5 genomes that lacked T4 orthologs
Summary
Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. The T4-like phages are a diverse group of lytic bacterial myoviruses that share genetic homologies and morphological similarities with the well-studied coliphage T4 [1,2] These phages provide an attractive model for the study of comparative genomics and phage evolution for several reasons: They possess relatively large dsDNA genomes that vary widely in size (~160–250 kb) and genetic composition. They contain host-like functions, such as nucleotide metabolism and a DNA replisome (reviewed in [3]). They experience different evolutionary constraints due to their lytic life cycle than do either their bacterial host or lysogenic bacteriophages They exist under less stringent genomic size constraints than, for example, the lambdoid phages [4]. The characteristics of the T4-like genome, its mechanism of replication, and the interactions with cellular hosts suggest that the T4-like phages constitute a natural crucible for the acquisition, evolution and dispersal of genetic information in the microbial world
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