Repair of transposable phage Mu DNA insertions begins only when the E. coli replisome collides with the transpososome

Summary We report a new cellular interaction between the infecting transposable phage Mu and the host Escherichia coli replication machinery during repair of Mu insertions, which involves filling‐in of short target gaps on either side of the insertion, concomitant with degradation of extraneous long flanking DNA (FD) linked to Mu. Using the FD as a marker to follow repair, we find that after transposition into the chromosome, the unrepaired Mu is indefinitely stable until the replication fork arrives at the insertion site, whereupon the FD is rapidly degraded. When the fork runs into a Mu target gap, a double strand end (DSE) will result; we demonstrate fork‐dependent DSEs proximal to Mu. These findings suggest that Pol III stalled at the transpososome is exploited for co‐ordinated repair of both target gaps flanking Mu without replicating the intervening 37 kb of Mu, disassembling the stable transpososome in the process. This work is relevant to all transposable elements, including retroviral elements like HIV‐1, which share with Mu the common problem of repair of their flanking target gaps. When transposable phage Mu infects E. coli, its linear genome (black), attached to extraneous flanking DNA (red) is protected by phage N protein until Mu transposes into the chromosome. Only when the Pol III replisome runs into the Mu transpososome does this DNA become susceptible to degradation. Pol III fills the target DNA gaps generated during transposition to repair the insertion and complete the transposition event.