Molecular consequences of deletion formation mediated by the transposon TN9

Abstract

Insertion elements and transposons stimulate deletion formation, mediating the elimination of neighbouring host sequences at a high rate compared to the background of deletions occurring in their absence. The (non-lethal) deletions generated by a variety of transposable elements end at or near the terminus of the element¹ (for reviews see refs 2–4). The finding that transposable elements generate the repetition of a short segment of host DNA on either side of the integrated element^5,6 raises new questions about deletion formation at the sequence level. Do the deletions terminate at the precise endpoint of the element and remove the repeated sequence, or do they end within it or leave it intact? Is deletion formation linked to the transposition process? To study the above questions we have used the transposon Tn9, which carries the genetic determinants for chloramphenicol resistance flanked on either side by the insertion sequence IS1^7,8 (in the same orientation), and which like IS1 generates a nine base pair repeat upon integration^5,6,9. Starting with a Tn9 integrated into the lacI gene of Escherichia coli, we examined deletions extending into the neighbouring lacZ and lacY genes. Sequence analysis, reported below, shows that after deletion formation the ends of the transposon remain intact, although one copy of the repeated 9 base pairs is removed by the deletion, fusing the end of Tn9 to host sequences several thousand base pairs away (in these cases). (Studies with Tn3¹⁰, IS1¹¹ and IS2¹² are consistent with these results.) We also find that the Tn9-distal end of the deletions terminate preferentially within the same region of DNA in which Tn9 insertion points cluster, suggesting that the processes of deletion formation and transposition share a common pathway.