Recombinational repair and restart of damaged replication forks

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Abstract
Replication forks encounter problems due to causes such as chemical damage to the DNA template, from both endogenous and exogenous agents, and problems with the protein–DNA complexes that are associated with normal metabolism, such as transcribing RNA polymerases. The structure of the DNA at a damaged fork, and whether the replication proteins remain associated with the fork, might depend on whether the initial blockage affects only a single strand of the template or both strands. Replication forks might simply pause at transient protein roadblocks that are not associated with damage in the template DNA, whereas chemical damage to the template might present a far greater problem. Specialized DNA polymerases that can replicate past damaged nucleotides might bypass the lesion, but at the cost of enhanced mutation rates. However, recombination between the two newly replicated portions of the chromosome might provide an error-free way to facilitate repair or bypass of the lesion. Recombination enzymes in bacteria might facilitate the repair of damaged forks through the unwinding of the DNA at the fork to create a four-stranded Holliday junction structure. Processing of the Holliday junction, either with or without cleavage of the junction DNA, might generate a suitable DNA structure onto which replication enzymes can be reloaded. Eukaryotes might have analogous systems to deal with blocked replication forks. Potential roles in the maintenance of replication fork progression are supported by the enhanced genome instability of humans who carry mutations in those enzymes that might unwind forked DNA structures. When the original source of a replication blockage is removed or bypassed, the replication machinery must be reassembled onto the forked DNA that has been generated by recombination. In bacteria, this is achieved by a protein that recognizes specific branched-DNA structures, and recruits essential components of the replication machinery to these structures. Eukaryotes might also have the means to reassemble replication enzymes onto recombination intermediates. The complexity of replication and repair processes indicates that some coordination must occur. Specific sites of replication in the cell, and the association of recombination enzymes with these sites, supports this idea. Recent evidence pointing to the importance of recombination for successful genome duplication indicates that recombination enzymes might be viewed as accessory factors for replication. The generation of genetic diversity — the textbook view of recombination — might, therefore, be a mere side-show that arose by hijacking of replication repair enzymes during evolution.