Definition of the attl1 site of class 1 integrons

Integron-encoded integrases recognize two distinct types of recombination site: attl sites, found in integrons, and members of the 59-base element (59-be) family, found in the integron-associated gene cassettes. The class 1 integron integrase, Intl1, catalyses recombination between attl1 and a 59-be, two 59-be, or two attl1 sites, but events involving two attl1 sites are less efficient than the reactions in which a 59-be participates. The full attl1 site is required for high-efficiency recombination with a 59-be site. It is 65 bp in length and includes a simple site, consisting of a pair of inversely oriented Intl1-binding domains, together with two further directly oriented Intl1-binding sites designated strong and weak. However, a smaller region that contains only the simple site is sufficient to support a lower level of recombination with a complete attl1 partner and the features that determine the orientation of attl1 reside within this region. An unusual reaction between the attl1 site and a 59-be appears to be responsible for the loss of the central region of a 59-be to create a potential fusion of two adjacent gene cassettes.