Multiple pathways process stalled replication forks

Abstract

Impairment of replication fork progression is a serious threat to living organisms and a potential source of genome instability. Studies in prokaryotes have provided evidence that inactivated replication forks can restart by the reassembly of the replication machinery. Several strategies for the processing of inactivated replication forks before replisome reassembly have been described. Most of these require the action of recombination proteins, with different proteins being implicated, depending on the cause of fork arrest. The action of recombination proteins at blocked forks is not necessarily accompanied by a strand-exchange reaction and may prevent rather than repair fork breakage. These various restart pathways may reflect different structures at stalled forks. We review here the different strategies of fork processing elicited by different kinds of replication impairments in prokaryotes and the variety of roles played by recombination proteins in these processes.W ork from several laboratories has established that in bacteria, a recombination event can lead to the establishment of a unidirectional replication fork (reviewed in refs. 1-3). These observations extend the concept of a direct recombination-replication connection, originally proposed Ϸ30 years ago from studies of bacteriophage T4 and replication. Furthermore, the existence of recombination-dependent replication in yeast suggests that this connection may be a widely distributed phenomenon (4, 5).Considering the tight control of replication initiation at chromosomal origins, the assembly of a complete replisome at recombination intermediates, independently of time and place, is paradoxical. One of the raisons d'être of this potentially dangerous process was revealed by the finding that recombination intermediates form at inactivated replication forks and are used for replication restart. However, studies of the replicationrecombination connection in Escherichia coli have indicated that recombination proteins do not necessarily catalyze strand exchange at blocked forks and rather act in a variety of reactions that depend on the origin of the arrest. We review here the diversity of fates of inactivated replication forks in bacteria, as well as our present knowledge of the roles played by recombination proteins during replication restart. DNA Double-Strand End Repair in BacteriaAlmost 30 years ago, Higgins et al. (6) proposed that blocked replication forks could be isomerized into a four-way Holliday junction (HJ) with a DNA double-strand end, which could permit DNA repair and then continuation of replication (Fig. 1, step A). The test of the model, performed by treatment of mammalian cells with a DNA-damaging agent, was inconclusive (7). However, more recent studies in E. coli suggest that such replication fork reversal plays a crucial role in replication restart in bacteria (8,9).A key aspect of the replication fork reversal model is that it generates a DNA double-strand end at blocked forks without chromosome breakage. In E. coli, the enzyme th...

Resolving Holliday Junctions with Escherichia coli UvrD Helicase

“…This is consistent with in vitro experiments that have shown UvrD to be capable of removing RecA molecules from DNA thereby disrupting a recombination event (9,18,18,19). It has also been suggested that UvrD could act to resolve the intermediate formed by replication fork regression so that the lesion may be repaired or bypassed immediately (16,20).…”

Minding the gap: The underground functions of BRCA1 and BRCA2 at stalled replication forks

“…A key intermediate in this type of genomic instability is thought to be the double strand break (DSB), and a large body of evidence now implicates DSB repair defects in cancer susceptibility. In the absence of extrinsic DNA damage, most chromosomal DSBs in cycling cells, and the associated chromosomal rearrangements, are thought to arise during the S phase of the cell cycle as a result of replication across a damaged DNA template [3][4][5][6].…”

“…The DSG has received less attention than its illustrious cousin, the DSB, but recent work in model organisms has reawakened interest in the DSG as a potential intermediate in genomic instability and cancer [7]. DSBs and DSGs can be repaired in an error-free manner by sister chromatid recombination (SCR), a mechanism whereby the damaged chromatid uses the intact sister as a template for repair by homologous recombination (HR) [5,8,9]. SCR competes with alternative error-prone pathways for repair of DSBs and DSGs and is therefore an important bulwark against the threats of genomic instability and cancer.…”

Topological locking restrains replication fork reversal

“…Despite the solid genetic evidence supporting this model, the molecular characterization of HLJs formed in vivo and an estimation of the extent of fork regression are still scarce (11-13). Moreover, replication restart after fork stalling was also suggested to occur by means of mechanisms that do not necessarily need fork reversal (FR) (8,14).…”