Wilde C, Mazel D, Hochhut B, Middendorf B, Le Roux F, Carniel E, Dobrindt U, Hacker J (2008): Delineation of the recombination sites necessary for integration of pathogenicity islands II and III into the Escherichia coli 536 chromosome
Mol. Microbiol. 68 (1): 139-151. Epub 2008 Feb 26.

In uropathogenic Escherichia coli strain 536, six pathogenicity islands (PAIs) encode key virulence factors. All PAIs except PAI IV₅₃₆ are flanked by direct repeats and four of them encode integrases responsible for their chromosomal excision. To study recombination sites used for the integration by PAI II₅₃₆ and III₅₃₆ integrases, we measured site-specific recombination between the chromosomal integration site attB, and the PAI-specific attachment site attP. We show that PAI III₅₃₆ IntB, but not IntA, mediates PAI III₅₃₆ integration. Studies of integrative recombination sites of both PAIs show that, when using a large cognate attP site (839 bp for PAI II₅₃₆ and 268 bp for PAI III₅₃₆), PAI II₅₃₆ and III₅₃₆ attB sites could be reduced to 16 bp and 20 bp, respectively, without affecting recombination. Further reduction to 14 bp for PAI II₅₃₆ and 13 bp for PAI III₅₃₆ diminished recombination efficiency. Surprisingly, attP sites could also be reduced to 14 bp (PAI II₅₃₆) and 20 bp (PAI III₅₃₆). The integration host factor (IHF) and the DNA-bending HU protein do not influence PAI II₅₃₆ recombination, but IHF enhances PAI-III₅₃₆ excision and negatively affects its integration. These data suggest that PAI intasomes differ from those of lambda and P4 integrase paradigms.