Lesion Bypass and the Reactivation of Stalled Replication Forks

Abstract

Accurate transmission of the genetic information requires complete duplication of the chromosomal DNA each cell division cycle. However, the idea that replication forks would form at origins of DNA replication and proceed without impairment to copy the chromosomes has proven naive. It is now clear that replication forks stall frequently as a result of encounters between the replication machinery and template damage, slow-moving or paused transcription complexes, unrelieved positive superhelical tension, covalent protein-DNA complexes, and as a result of cellular stress responses. These stalled forks are a major source of genome instability. The cell has developed many strategies for ensuring that these obstructions to DNA replication do not result in loss of genetic information, including DNA damage tolerance mechanisms such as lesion skipping, whereby the replisome jumps the lesion and continues downstream; template switching both behind template damage and at the stalled fork; and the error-prone pathway of translesion synthesis.

Keywords: DNA lesion; lesion skipping; replication fork reversal; replication fork stalling; replication restart; template switching; translesion synthesis.

Figure 1.

Pathways of lesion bypass and replication fork reactivation. (a) a replication fork progressing from right to left that has just been stalled by a leading-strand template lesion (the black triangle). Template strands are black, nascent leading strands are green, and nascent lagging strands are red. See text for explanations of the pathways. Direct TLS by the replisome (a to c). Polymerase switching from the replicative polymerase to a specialized TLS polymerase and back to the replicative polymerase (a to d). Functional uncoupling of leading-strand DNA synthesis from template unwinding and lagging-strand synthesis (a to b). Lesion skipping (b to e). Post-replicative template switching (e to f). Replication fork reversal (b to g). Template switching in a reversed fork (g to h). Fork reset, the reversed fork is restored to the original configuration of nascent and template strands (h to i). HR-dependent replication restart for a reversed fork (h to j). Lesion removal by nucleotide excision repair at a reversed fork (g to k). Cleavage of a reversed fork by Holliday junction resolvases (k to l). HR-dependent replication restart after Holliday junction cleavage (l to m). Note that the reversed fork in (k) can also be reset directly (k to i), with the grayed out damage triangle indicating that in this pathway, the template damage would have been removed prior to fork reset. Replication at the reset fork (i) can be restarted by origin-independent replisome loading activities.