Evolutionary patterns and processes of bacteriophages, particularly P2-like phages

Abstract: DNA sequencing of structural genes of temperate P2-like prophages from isolates of Escherichia coli bacteria showed that the difference between these genes was very small. Separate phylogenetic analyses on the genes resulted in unresolved trees, caused by a high level of homologous recombination, which implied that homologous recombination is the most important source of new genetic variation for P2-like phages infecting E. coli. The genomes of seven P2-like phages from different bacterial host families were also compared in phylogenetic analyses, that were based on the amino acid sequences of nine structural genes, the gene content of the genome, and the gene order. These analyses resulted in only one tree with high support for all branches in all analyses with one exception. It was shown that some of the genes in phage 186 had been transferred between genomes in separate branches. The results of the analyses on P2-like phages from E. coli were in sharp contrast to the results of analyses of P2-like phages from different hosts. This implies that P2-like phages from the same host belong to clonal lines that occasionally meet in the same host cell and that compete for the same resources, whereas P2-like phages from different hosts constitute discrete and separate clusters of clones that track the evolution of respective hosts. The evolutionary pattern in P2-like phages was compared to the pattern in the temperate phage P1. Phage P1 is structurally similar to P2 and use the same host, but it has genes with additional functions, similar to the genes of the host. The results from experiments of host bacteria infected with P1 with and without one of these additional genes, the ssb gene, showed that it was nonessential for the host, but a selective advantage for the phage since reproduction is guaranteed even if the host is dying. Phylogenetic analyses showed that phage P1 have had an ssb gene for a long time and that the gene has not been transferred from any known bacteria or plasmid. P2-like prophages are present in about 28% of E. coli isolates. The genetic variation among these strains seems to be low. The region corresponding to the P2 Z/fun locus was showed to contain DNA of different length at this site in many prophages. The sequences consisted of a central, highly variable AT-rich part, flanked by almost identical upstream and downstream sequences that were inverted repeats. The explanation to the diversity of genes at this site was that a site-specific recombination mechanism was acting on these sequences. The central part contained at least one open reading frame per insert, coding for proteins that in only a few cases were found in other organisms. The pattern was also found in genetically unstable regions of pathogenic bacteria. In view of all investigations, the phylogeny of P2-like phages could be described as a tree with reticulated branches. Each branch is made up by bundles of clonal lines that exchange genetic material through homologous recombination. Occasionally there is a transfer of genes between branches, but this has probably not happened many times in the last 100 million years. Each clonal line is mainly defined by the lysogenic conversion genes that it harbours, and by the ability to repress other clonal lines, but has also differentiated by selectively neutral changes in the nucleotide sequence.