Physical properties of phage 299

Evolution of immunity and host chromosome integration site of P2-like coliphages

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.

Detection of homologous recombination among bacteriophage P2 relatives

Sequencing of five late genes from 18 isolates of P2-like bacteriophages showed that these are at least 96% identical to the genes of phage P2. A maximum-parsimony phylogenetic analysis of these genes showed excess homoplasy of a magnitude three to six times higher than that expected. Examination of the distribution of the number of homoplasies at parsimoniously informative sites and incompatibility matrices of such sites revealed a pattern typical for extensive recombination. It has been shown that phage P2 probably incorporated some functionally complete genes or gene modules by recombination with other phages or with different hosts, but homologous recombination within genes has previously not been shown. In this paper we demonstrate that homologous recombination between P2-like bacteriophages occurs randomly at multiple breakpoints in five late genes. The rate of recombination is high but, since some phages were sampled decades apart and in different parts of the world, this has to be viewed on an evolutionary time scale. The applicability of different methods used for detection of recombination breakpoints and estimation of rates of recombination in bacteriophages is discussed.

Characterization of phage 18, an unstable coliphage

Phage 18, a noninducible coliphage, is quite unstable and therefore difficult to study. Newly developed very gentle lysis and mounting techniques yielded isolated virions for examination by electron microscopy. The phage has a contractile tail with a length of 130 nm and an isometric head with a capsid diameter of 50 nm. Phage 18 is similar in morphology to phage P2 but is heteroimmune to it. DNA extracted from a clear-plaque mutant of phage 18 was subjected to BamHI restriction endonuclease digestion and was found to be easily distinguishable from the published restriction patterns for P2, phage 299, or phage 186 DNA. The genome size was calculated to be 33.5 kb. Using the DNA melting point, phage 18 DNA (G+C) content was determined to be 55.0% and its buoyant density was determined to be 1.715.

Comparisons of the distribution of nucleotides and common sequences in deoxyribonucleic acid from selected bacteriophages

Results from comparisons of deoxyribonucleic acid (DNA) from several classes of bacteriophages suggest that most phage chromosomes contain either a homogeneous distribution of nucleotides or are made up of a few, rather large segments of different quanine plus cytosine (G + C) contents which are internally homogeneous. Among those temperate phages tested, most contained segmented DNA. Comparisons of sequence similarities among segments from lambdoid phage DNA species revealed the following order in relatedness to lambda: 82 (and 434) > 21 > 424 > phi80. Most common sequences are found in the highest G + C segments, which in lambda contain head and tail genes. Hybridization tests with lambda and 186 or P2 DNA species verified that the lambdoids and 186 and P2 belong to two distinct groups. There are fewer homologous sequences between the DNA species of coliphages lambda and P2 or 186 than there are between the DNA species of coliphage lambda and salmonella phage P22.