Mechanism of repair of Mu DNA insertions

Transposable elements are ubiquitous, occupying as much as 85% of the genome of some species, and nearly 50% of the human genome, and causing DNA disruptions, mutations, and rearrangements. While transposable elements move in a variety of ways, their transposases cut and join DNA in a similar manner, all ultimately creating short flanking gaps in the target DNA. Transposition is not complete until these gaps are filled, yet this last step is still a black box. Using transposable phage Mu, we have made new discoveries that shed light on this step. We find that Mu recruits the Pol III replisome, and not gap-filling polymerases, for gap repair. Taking advantage of the high efficiency of Mu transposition and of a unique feature of its transposition intermediate, we made the surprising observation that the transpososome waits for the replisome to begin repair. When a fork runs into a gap, a double strand break (DSB) is expected: we demonstrated fork-dependent DSBs proximal to Mu. This result is consistent with genetic studies showing that recovery of Mu insertions requires the DSB repair pathway. These findings immediately suggest a model wherein the double strand break is exploited by the transpososome for coordinated repair of the two flanking gaps by the two Pol III subunits, without replicating the intervening transposon DNA. Such a maneuver constitutes a novel DNA transaction for the polymerase and for repair. These findings are of broad significance because Mu, retrotransposons and retroviruses (e.g. HIV-1) transpose by a similar mechanism.