Courcelle's group used two-dimensional gel electrophoresis to examine the shapes of a replicating bacterial plasmid. Advancing replication forks yielded the expected Y-shaped structure. But UV-induced lesions stalled the replication fork and produced X-shaped structures. These structures represent the nascent DNA backing up from the apex of a Y-shaped fork. The stalled structures were processed by RecQ and RecJ and maintained by RecA and RecF, which are the same proteins that promote homologous DNA pairing during recombinational processes.
A mid-replication stall is “like catching a cell with its pants down,” according to Courcelle. “It can't live as one and a half cells for eternity,” he says. Unchecked free DNA ends are recombinogenic. Fork stabilization by these Rec proteins may be essential for preventing unwanted mitotic recombination and its potentially cancerous consequences. In addition, fork regression and Rec binding probably delays replication long enough for repair enzymes or SOS polymerases either to repair the lesion or to replicate past it. Whether RecA and RecF recruit repair enzymes or simply maintain an open fork remains to be determined. ▪