We have studied the effect of the recA-dependent homologous recombination system of Escherichia coli on both Tn5-mediated cointegrate formation and Tn5 transposition. We demonstrate here that, whereas transposition of Tn5 is independent of the recA gene product (as has been shown by other workers), Tn5-mediated cointegrate formation is strongly dependent on recA. The structures of both the simple transpositionproducts and the cointegrates formed in a recA-background seem to be the same as those produced in a recA' background. These results provide strong evidence that Tn5 does not transpose via an obligate cointegrate intermediate and suggest that the recA effect on cointegrate formation is exerted during the process oftransposition.Transposable genetic elements are capable of insertion into many distinct nonhomologous sites in the genomes of bacteria and phage. In addition, they are known to promote the fusion of replicons (cointegrate formation) and the formation of deletions and inversions of DNA (for recent reviews see refs. 1 and 2). It has been thought that most, ifnot all, ofthe recombination events induced by transposable elements are independent of homology-requiring recombination systems, first because the recombination events are between nonhomologous sequences, and second because transposition itself and several other transposition-related processes appear to occur with equal facility in wild-type cells and cells deficient in the recA gene product (3,4). [An exception to this recA independence has recently been reported for the transposition of Tn903 from phage A to the Escherichia coli chromosome (5).]Galas and Chandler (6) have proposed that transposable elements in bacteria can be largely classified into two groups. Certain elements, including Tn3 and y8 (TnlOOO), generate 5-basepair repeats in the target DNA on insertion and appear to form unstable cointegrates as obligate intermediates in transposition. These cointegrates consist of donor and recipient replicons delimited by two directly repeated copies of the transposable element. This class of element encodes a site-specific recombination system that promotes recombination between the two directly repeated copies of the element (resolution of the cointegrate), and generates, on recombination, a copy of the donor and a copy of the recipient replicon, now also carrying the transposon (7-10).The second class ofelement, which includes Tn5, Tn9, TnlO, and Tn9O3, can be considered compound elements because they are composed of a region of DNA encoding an antibiotic resistance determinant flanked by two elements that are themselves independently transposable. Elements in this class generate 9-base-pair repeats in the target DNA on insertion. They are also. capable of fusing replicons. In contrast to cointegrate structures generated by the first class, those generated by Tn9 (11) and Tn5 -(12, 13) are quite stable. The stability of the cointegrates, together with the observation that cointegrate structures are, formed at a frequency lower ...