Fig. 5.

Intermolecular transposition models. a: classical replicative cointegration [108]. Modified from [98]. Donor DNA is shown in black, target DNA as a red dotted line. Replication origins on each molecule are represented by a small oval. The IS is shown as a blue box with the white arrow indicating the direction of expression of the transposase. The small directly repeated flanking sequences generated by insertion are shown as red arrows. The target sequence destined to become the new flanking repeat is indicated by white arrows. Transposition is initiated by cleavage at both terminal inverted repeats (marked 1 and 2) of the IS to generate 3’OH ends (small green circles) that attack the target site (red arrows) in what is called a strand transfer reaction. DNA replication generates a cointegrate containing two IS copies in direct repeat together with a new target site duplication (white arrows). This structure can be subsequently resolved into a plasmid identical to the original donor plasmid and a modified target plasmid carrying an IS copy flanked by target site duplications arranged as direct repeats. b: replicative cointegration by an IS6-family pseudo-transposon [8] (modified from [1]. The symbols are identical to those above. The transposon is composed of two directly repeated copies of the IS flanking a DNA segment carrying passenger gene (green) with the internal flanks represented by yellow arrows. A target plasmid is distinguished by an open oval representing the origin of replication. Transposase-mediated replicon fusion of the two molecules using one of the two flanking IS copies generates a third copy of the IS in the same orientation as the original pair. Homologous recombination, using the recA system, between any two copies can in principle occur. This will either regenerate the donor plasmid, leaving a single IS copy in the target, delete the transposon, or transfer the transposon to the target (as shown), leaving a single copy of the IS in the donor molecule