Termination of DNA replication drives genomic instability via multiple mechanisms.

Termination of DNA replication is a surprisingly complex process that contributes critically to genome stability and cell viability. And even though progress was made to establish the consequences that arise if termination is going awry, the precise molecular mechanisms of fork fusion events and the coordination with key factors that ensure that DNA replication is brought to a successful conclusion remain poorly understood. We therefore investigated replication termination in Escherichia coli, focusing specifically on the interplay between replication fork fusions and genomic stability, the Tus-ter replication fork trap, and key DNA-processing enzymes. By utilizing whole genome sequencing, immunoblotting, and recombination reporter assays, we demonstrate that local hyper-recombination is induced wherever forks meet and that the combined loss of factors such as RecG helicase and 3' exonucleases causes extreme over-replication in the terminus region of the chromosome. Unexpectedly, cells lacking Tus exhibit elevated R-loop levels, revealing an unanticipated connection between the fork trap and R-loop metabolism. These findings underscore the complexity of replication termination and its central role in maintaining bacterial genome stability, while providing mechanistic insights with implications for understanding replication termination in more complex organisms and developing new antimicrobial strategies.