Abstract
The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.
Highlights
Discovery of the three T-even phages (T2, T4 and T6) and their subsequent use as model systems to explore the nature of the gene and genetic mechanisms had a profound impact on the proliferation of interdisciplinary biological research
Concluding remarks Genomes of the T4-like Viruses are repositories of a diversity of genes for which no biological roles have been assigned or can be predicted on the basis of comparisons to other sequences in databases. The reference for these phages, phage T4, has been extensively studied [2,7,8] and provides a rational basis for suspecting that the diversity among its relatives is a reflection of adaptations of a core phage genome to a variety of challenges in evolution, including encounters with new host environments
Many T4 genes that are not essential for phage propagation in some bacterial hosts or genetic backgrounds are essential in others
Summary
Discovery of the three T-even phages (T2, T4 and T6) and their subsequent use as model systems to explore the nature of the gene and genetic mechanisms had a profound impact on the proliferation of interdisciplinary biological research. The Pangenome of the T4-like Viruses Collectively, the genetic backgrounds for the Core Genome of the T4 relatives examined for the current report are predicted to encode a total of ~3000 proteins that do not exhibit statistically significant sequence matches to any other proteins outside of the databases for the T4-related phages This number of ORFs is ~1.5 orders of magnitude larger than our estimate of the number of Core plus Quasicore genes in the Core Genome of these phages (Figure 1, Table 3), and might be several orders of magnitude smaller than the union of all the different ORFs that exist in T4-related phages in nature. A comprehensive listing of T4 alleles in most of the phages listed in Tables 1 and 2 can be found in Additional file 1
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