Resolution of a hybrid cointegrate between transposons Tn501 and Tn1721 defines the recombination site

The related transposons Tn501 and Tn1721 have a 3.8 kb region in common that contains two genes (tnpA and tnpR) and a resolution site (res) required for transposition. Resolvase, the product of tnpR, catalyses site-specific recombination at res, a 186 base pair (bp) sequence located adjacent to tnpR at one end of the homology region. We describe here identification of the crossover site within res. It involved the construction of a plasmid containing copies of res (Tn501) and res (Tn1721) in direct orientation and tnpR-mediated intramolecular recombination between the two homologous (but non-identical) sites. The resulting hybrid contained Tn501 and Tn1721 fused at the crossover point. DNA sequence analysis of the recombinant indicates that recombination occurs in an 11 bp region of exact homology between Tn501 and Tn1721. The recombination site lies 161-172 bp upstream of tnpR at the transition from homology to non-homology between Tn501 and Tn1721 suggesting that site-specific recombination may have played a role in the evolution of these elements.