Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: Evolution, structure, and genome organization of lactococcal bacteriophages

A complete analysis of the entire genome of the temperate lactococcal bacte riophage TP901-1 has been performed and the function of 21 of 56 TP901-1-en coded ORFs has been assigned. This knowledge has been used to propose 10 fu nctional modules each responsible for specific functions during bacteriopha ge TP901-1 proliferation. Short regions of microhomology in intergenic regi ons present in several lactococcal bacteriophages and chromosomal fragments of Lactococcus lactis are suggested to be points of exchange of genetic ma terial through homologous recombination. Our results indicate that TP901-1 may have evolved by homologous recombination between the host chromosome an d a mother phage and support the observation that phage remnants as well as prophages located in the Lactococcus chromosome contribute significantly t o bacteriophage evolution. Some proteins encoded in the early transcribed r egion of the TP901-1 genome were more homologous to proteins encoded by pha ges infecting gram-positive hosts other than L. lactis. This protein homolo gy argues for the occurrence of horizontal genetic exchange among these bac teriophages and indicates that they have access to a common gene pool. (C) 2001 Academic Press.