Cutting out the φC31 prophage

To establish a lysogenic lifestyle, the temperate bacteriophage phi C31 integrates its genome into the chromosome of its Streptomyces host, by site-specific recombination between attP (the attachment site in the phage DNA) and attB (the chromosomal attachment site). This reaction is promoted by a phage-encoded serine recombinase Int. To return to the lytic lifestyle, the prophage excises its DNA by a similar Int-mediated reaction between the recombinant sites flanking the prophage, attL and attR. phi C31 Int has been developed into a popular experimental tool for integration of transgenic DNA into the genomes of eukaryotic organisms. However, until now it has not been possible to use Int to promote the reverse reaction, excision. In many other phages, the presence of a recombination directionality factor (RDF) protein biases the phage-encoded integrase towards prophage excision, whereas absence of the RDF favours integration; but the phi C31 RDF had proved elusive. In this issue of Molecular Microbiology, Khaleel et al. (2011) report the identification and purification of the phi C31 RDF, and show that it both promotes excision and inhibits integration by direct protein-protein interactions with Int itself.