Chapter 4 : Bacteriophage Evolution and the Role of Phages in Host Evolution

Abstract:

Comparative analyses of phage genome sequences imply that a major component of phage evolution is large numbers of intrinsically very improbable events. In addition, there are comparable numbers of prophage sequences that are found in the genomic sequences of bacteria and, sometimes, archaea. There are stretches of sequence that match well, with abrupt transitions to regions with no detectable similarity or sometimes a different level of similarity. These transition points are considered the products of nonhomologous recombination events in the ancestry of one of the phages being compared; in this sense, they are fossils of past events in the history of the genome. It is believed that there are at least two factors that can restrict the horizontal flow of genes across the expanses of phage sequence space. Many of the beneficial genes carried by prophages appear to be morons, i.e., the genes that have entered the genome recently and are typically flanked by a transcription promoter and a terminator. The understanding of how phages evolve began in the late 1960s with the hetero duplex mapping of the chromosomes of phage lambda and some close relatives, showing that these molecules are mosaic with respect to each other. Genome sequences for such phages are just now becoming available, and the largest genome to date is 10 times as big as that of phage lambda, with a corresponding increase in gene number.