Comparison of the Lysogeny Modules from the TemperateStreptococcus thermophilusBacteriophages TP-J34 and Sfi21: Implications for the Modular Theory of Phage Evolution

AbstractA 7.6-kb DNA segment covering the putative lysogeny module of thepac-site-containing temperateStreptococcus thermophilusbacteriophage TP-J34 was sequenced. Sequence alignment with the lysogeny module from thecos-site-containingS. thermophilusbacteriophage φSfi21 revealed areas of high sequence conservation (e.g., over theintgene), interspersed with regions of low or no sequence similarity (e.g., over thecrogene). Four of the six sharp transition zones from high to low sequence conservation were found within open reading frames coding for the CI repressor, the Anti-repressor, the Immunity protein, and a protein of unknown function. The transition points in thecIandantgenes appear to separate gene segments coding for distinct functional domains of these proteins. In addition, these two transition points were located at or near the deletion sites observed in spontaneous phage φSfi21 deletion mutants, thus suggesting these transition points as recombinational hotspots. Furthermore, the sequence at the transition point in thecIgene resembles the attachment site of the phage, suggesting the involvement of the phage integrase in at least some of the exchange reactions. Contrary to the initial formulation of the modular theory of phage evolution the unit of the evolutionary exchange in streptococcal phages is not a group of functional genes, but can be as small as a single gene. Exchange reactions can also occur within genes, possibly between gene segments encoding distinct protein domains