Evolution of Immunity and Host Chromosome Integration Site of P2-Like Coliphages

Abstract

The amount and distribution of variation in the genomic region containing the genes in the lytic-lysogenic genetic switch and the sequence that determines the integration site into the host chromosome were analyzed for 38 P2-like phages from Escherichia coli. The genetic switch consists of two convergent mutually exclusive promoters, Pe and Pc, and two repressors, C and Cox. The immunity repressor C blocks the early Pe promoter, leading to the establishment of lysogeny. The Cox repressor blocks expression of Pc, allowing lytic growth. Phylogenetic analyses showed that the C and Cox proteins were distributed into seven distinct classes. The phylogenetic relationship differed between the two proteins, and we showed that homologous recombination plays a major role in creating alterations in the genetic switch, leading to new immunity classes. Analyses of the host integration site for these phages resulted in the discovery of a previously unknown site, and there were at least four regular integration sites. Interestingly, we found no case where phages of the same immunity class had different host attachment sites. The evolution of immunity and integration sites is complex, since it involves interactions both between the phages themselves and between phages and hosts, and often, both regulatory proteins and target DNA must change.P2-like phages are a group of related temperate phages that grow on ␥-proteobacteria and share common traits such as morphology, control of lytic versus lysogenic growth, and noninducibility by UV light (for a recent review, see reference 26). Temperate phages have the ability to reproduce by two alternative life cycles: the lytic or the lysogenic cycle. In the latter life cycle, the phage genome integrates into a specific location on the host chromosome, and most phage genes are turned off by the phage-encoded immunity repressor C. P2-like phages are prevalent in Escherichia coli strains; about 30% of the strains in the ECOR collection (28) contain P2-like prophages (27). P2-like phages that are found in other ␥-proteobacteria are more distantly related to P2 than those found in E. coli, and it seems as if the evolution of the P2-like phages tracks the evolution of their respective hosts (26; A. S. Nilsson, unpublished data). An analysis of the DNA sequence of the late structural genes of 18 P2-like isolates that grow on E. coli showed that these genes are at least 96% identical to the genes of P2 (25). Thus, these P2-like coliphages might be considered different isolates of P2, but they have been shown to have different immunities, based on their capacity to grow on bacteria lysogenized with different P2-like phages (6,9,14) and to integrate at at least two different sites in the host chromosome (22,38). Phage 186 is a more distantly related E. coli phage, and its immunity repressor, cI, differs in size and sequence from the C repressors of the P2-like coliphages in this study. In fact, both cI and Apl (the equivalent of Cox) of phage 186 are more related to the cI and Cox repressors of Ha...

Insertion Site Occupancy by stx 2 Bacteriophages Depends on the Locus Availability of the Host Strain Chromosome

“…Results showed that when the main target site was inaccessible, either due to the presence of another prophage or because of an induced mutation, prophages integrated within a secondary site located in the host chromosome. This finding is consistent with other published reports (4,16).…”

“…This can also explain the variability observed in the STEC strains. Another plausible explanation is that in double lysogens, homologous recombination between the two phages can serve as the causative agent for the selection of two different sites (16). However, since in our experiments conducted with the mutant strain there was only one phage, homologous recombination between two prophages was not possible.…”

“…That is, the second phage is integrated together with the first temperate phage or into another integration site, but not via the same attachment site (4,16). Rutkai et al (27) demonstrated the same phenomenon with their own model, in which lambdoid phages changed their insertion specificity by adapting their integrases to sequences found in secondary attachment sites.…”

“…Some studies with P2-like coliphages (16) demonstrated that conversion of a lysogen with a second P2-like phage, one that shares the same integration site as the first, results in the second phage being integrated either in tandem with the first prophage or into a secondary site. That is, the second phage is integrated together with the first temperate phage or into another integration site, but not via the same attachment site (4,16).…”

“…Several studies have attempted to characterize phage integrases (3,16,23,26,27,33). Although different families of this enzyme have been established, most of them conserve certain motifs in their protein architecture that allow attachment site recognition and phage genome-bacterial genome recombination.…”