Chromosome duplication initiates via the assembly of replication fork complexes at defined
origins, from where they proceed in opposite directions until they fuse with a converging fork.
Recent work highlights that the completion of DNA replication is highly complex in both pro- and
eukaryotic cells. In this study we have investigated how 3’ and 5’ exonucleases contribute towards
the successful termination of chromosome duplication in Escherichia coli. We show that the
absence of 3’ exonucleases can trigger levels of over-replication in the termination area robust enough to allow successful chromosome duplication in the absence of oriC firing. Over-replication
is completely abolished if replication fork complexes are prevented from fusing by chromosome
linearization. Our data strongly support the idea that 3’ flaps are generated as replication fork
complexes fuse. In the absence of 3’ exonucleases, such as ExoI, these 3’ flaps can be converted
into 5’ flaps, which are degraded by 5’ exonucleases, such as ExoVII and RecJ. Our data support
the idea that multiple protein activities are required to process fork fusion intermediates. They
highlight the complexity of fork fusions and further support the idea that the termination area
evolved to contain fork fusion-mediated pathologies