Characterisation of specific and secondary recombination sites recognised by the integron DNA integrase

Integrons determine a site-specific recombination system which is responsible for the acquisition of genes, particularly antibiotic resistance genes. The integrase encoded by integrons recognises two distinct classes of recombination sites. The first is the family of imperfect inverted repeats, known as 59-base elements, which are associated with the mobile gene cassettes. The second consists of a single site into which the cassettes are inserted. This site, here designated attl, is located adjacent to the int gene in the recipient integron structure. The attl site has none of the recognisable features of members of the 59-base element family except for a seven-base core site, GTTRRRY, at the recombination crossover point. Using a conduction assay to quantitate site activity, the sequence required for maximal attl site activity was confined to a region of >39 and ≤70 bases. Both integrative and excisive site-specific recombination events involving attl and a 59-base element site were demonstrated, but no evidence for events involving two attl sites was obtained. Integrase-mediated recombination between a 59-base element and several secondary sites in pACYC184 with the consensus GNT occurred at low frequency, and such events could potentially lead to insertion of gene cassettes at many non-specific sites.