Site‐specific insertion of genes into integrons: role of the 59‐base element and determination of the recombination cross‐over point

From examination of published DNA sequences of genes found inserted at a specific site in integrons, all genes are shown to be associated, at their 3′ ends, with a short imperfect inverted repeat sequence, a 59‐base element or relative of this element. The similarity of the arrangement of gene inserts in the integron and in the Tn7 transposon family is described. A refined consensus for the 59‐base element is reported. Members of this family are highly diverged and the relationship of a group of longer elements to the 59‐base elements is demonstrated. The ability of 59‐base elements of different length and sequence to act as sites for recombination catalysed by the integron‐encoded DNA integrase is demonstrated, confirming that elements of this family have a common function. The ability of elements located between gene pairs to act as recombination sites has also been demonstrated. The recombination cross‐over point has been localized to the GTT triplet which is conserved in the core sites, GTTRRRY, found at the 3′ end of 59‐base elements. Recombination at the core site found in inverse orientation at the 5′ end of the 59‐base elements was not detected, and the sequences responsible for orientation of the recombination event appear to reside within the 59‐base element. A model for site‐specific insertion of genes into integrons and Tn 7‐iike transposons is proposed. Circular units consisting of a gene associated with a 59‐base element are inserted into an ancestral element which contains neither a gene nor a 59‐base element. Further genes can be inserted at one or both of the composite sites generated by the first gene‐insertion