Definition of the attI1 site of class 1 integrons

Abstract

Integron-encoded integrases recognize two distinct types of recombination site : attI 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, IntI1, catalyses recombination between attI1 and a 59-be, two 59-be, or two attI1 sites, but events involving two attI1 sites are less efficient than the reactions in which a 59-be participates. The full attI1 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 IntI1-binding domains, together with two further directly oriented IntI1-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 attI1 partner and the features that determine the orientation of attI1 reside within this region. An unusual reaction between the attI1 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.

Comparison of the structure–activity relationships of the integron-associated recombination sites attI3 and attI1 reveals common features

“…Removal of all but 15 bp of the qacE region (268 to +15 fragment) did not reduce activity, indicating that no more than 15 bp to the right of the crossover is required. Overall, these findings are similar to those obtained previously with the attI1 site (Recchia et al, 1994;Partridge et al, 2000), where progressive removal of the weak and strong binding sites reduced, then effectively abolished, site activity in reactions with a 59-be site.…”

“…Detailed studies have revealed that attI1 includes four IntI-binding sites each beginning with GTTRRRY or variations thereof ( Fig. 1a) with two in the vicinity of the recombination crossover position in inverse orientation, as expected for the simple site of a tyrosine recombinase, and two in direct orientation Gravel et al, 1998;Partridge et al, 2000). This organization is in contrast to the arrangement found in 59-be, which contain two simple sites (Stokes et al, 1997).…”

“…1a) further enhances recombination efficiency. The simple site is sufficient for recombination with a second complete attI1 site (Hansson et al, 1997;Partridge et al, 2000).…”

“…This organization is in contrast to the arrangement found in 59-be, which contain two simple sites (Stokes et al, 1997). A requirement for the two directly oriented binding sites, one of which is strong and the other weak, is only observed when the attI1 site recombines with a 59-be (Recchia et al, 1994;Partridge et al, 2000). The strong binding site (3 in Fig.…”

“…1b). Only the attI1 site from class 1 integrons has been characterized (Recchia et al, 1994;Hansson et al, 1997;Collis et al, 1998;Gravel et al, 1998;Hall et al, 1999;Partridge et al, 2000). Detailed studies have revealed that attI1 includes four IntI-binding sites each beginning with GTTRRRY or variations thereof ( Fig.…”