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(NAS Colloquium) Links Between Recombination and Replication: Vital Roles of Recombination (2002)
Proceedings of the National Academy of Sciences (PNAS)

Page
63
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Colloquium on Links Between Recombination and Replication: Vital Roles of Recombination

might completely block the leading strand polymerase, but allow lagging strand synthesis to continue some way beyond the block (15, 17). Thus, a block on the leading strand template may be one type of event that leads to a stalled replication fork having a local structure similar to the fork used in Fig. 3A, lanes 5–8. It may be no coincidence that this fork is bound preferentially by RecG. Recent studies suggest that stalled replication forks can be processed by formation of a Holliday junction to create a substrate that can be branch migrated and cleaved by the RuvABC complex (5). The free DNA end generated by this cleavage [Fig. 1A (i)] can then be acted on by RecBCD and RecA to generate a D-loop. This D-loop can then act as a target for PriA-mediated assembly of a new replication fork at the D-loop (1). Alternatively, the free DNA end spooled out by regression of a stalled fork may be acted on by RecBCD directly to allow RecA-catalyzed D-loop formation, followed by subsequent cleavage of the Holliday junction by RuvABC (5, 13). However, replication can also be reestablished in a manner that requires not only PriA but also RecG, and that can proceed without the need for RuvABC-directed cleavage of the regressed fork (8). How can replication be restarted from a stalled fork without formation of a D-loop? PriA preferentially binds to forks with the 3′ end of a leading strand present at the branch point (32). PriA can also assemble a competent replication complex that can utilize this 3′ end for priming of replication (11). However, in the absence of the 3′-OH group of a leading strand at a stalled fork there would be no means to prime leading strand synthesis. The conclusion that RecG preferentially binds forks that possess a lagging strand, whereas PriA has a higher affinity for forks with a leading strand, suggests that RecG may facilitate PriA-dependent replisome reloading when the stalled fork does not initially possess a 3′-OH group at the junction point to prime leading strand synthesis. How this might be achieved is not known. However, it has been suggested that RecG may promote a template switching reaction in which formation of a Holliday junction by RecG allows extension of the stalled leading strand by using the nascent lagging strand as a template (ref. 8; Fig. 1). The ability of RecG to unwind the leading and lagging strands at fork structures, together with the high initial binding affinity of RecG for forks possessing a lagging strand, support this model. Branch migration of the Holliday junction in the reverse direction would regenerate a fork that now had a leading strand 3’OH for binding by PriA and subsequent priming of leading strand synthesis by DNA polymerase III. Thus, the opposing binding affinities of RecG and PriA at fork structures might reflect the ability of RecG to bind and unwind stalled forks that cannot be directly targeted by PriA to reload an active replisome. We are currently investigating whether such a mechanism underlies the observed genetic interaction between RecG and PriA (33).

We thank Lynda Harris for outstanding technical support and Gary Sharples for critical reading of the manuscript. This work was supported by a program grant from the Medical Research Council to R.G.L. and Gary Sharples. P.M. is a Lister Institute-Jenner Research Fellow.

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Front Matter (R1-R3)
Links between recombination and replication: Vital roles of recombination (8172-8172)
Historical overview: Searching for replication help in all of the rec places (8173-8180)
Rescue of arrested replication forks by homologous recombination (8181-8188)
Circles: The replication-recombination-chromosome segregation connection (8189-8195)
Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination (8196-8202)
Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant (8203-8210)
RecA protein promotes the regression of stalled replication forks in vitro (8211-8218)
Topological challenges to DNA replication: Conformations at the fork (8219-8226)
Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation (8227-8234)
Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled (8235-8240)
Single-strand interruptions in replicating chromosomes cause double-strand breaks (8241-8246)
Handoff from recombinase to replisome: Insights from transportation (8247-8254)
Break-induced replication: A review and an example in budding yeast (8255-8262)
Links between replication and recombination in Saccharomyces cerevisiae: A hypersensitive requirement for homologous recombination in the absence of Rad27 activity (8263-8269)
Evidence that replication fork components catalyze establishment of cohesion between sister chromatids (8270-8275)
Rad52 forms DNA repair and recombination centers during S phase (8276-8282)
A yeast gene, MGS1, encoding a DNA-dependent AAA+ ATPase is required to maintain genome stability (8283-8289)
The tight linkage between DNA replication and double-strand break repair in bacteriophage T4 (8290-8297)
Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNA replication and repair (8298-8305)
Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer (8306-8311)
Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: A versatile couple with roles in replication and recombination (8312-8318)
Instability of repetitive DNA sequences: The role of replication in multiple mechanisms (8319-8325)
Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences (8326-8333)
Stationary-phase mutation in the bacterial chromosome: Recombination protein and DNA polymerase IV dependence (8334-8341)
Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination (8342-8349)
Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli (8350-8354)
Accuracy of lesion bypass by yeast and human DNA polymerase n (8355-8360)
ATP bound to the orgin recognition complex is important for preRC formation (8361-8367)
Creating a dynamic picture of the sliding clamp during T4 DNA polymerases holoenzyme assembly by using fluorescence resonance energy transfer (8368-8375)
Interaction of the ß sliding clamp with MutS, ligase, and DNA polymerase I (8376-8380)
Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase (8381-8387)
Homologous DNA recombination in vertebrate cells (8388-8394)
Meiotic recombination and chromosome segregation in Schizosaccharomyces pombe (8395-8402)
Manipulating the mammalian genome by homologous recombination (8403-8410)
Assembly of RecA-like recombinases: Distinct roles for mediator proteins in mitosis and meiosis (8411-8418)
Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA (8419-8424)
Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material (8425-8432)
The synaptic activity of HsDmc1, a human reccombination protein specific to meiosis (8433-8439)
Complex formation by the human RAD51C and XRCC3 recombination repair proteins (8440-8446)
Rad54 protein stimulates the postsynaptic phase of Rad51 protein-mediated DNA strand exchange (8447-8453)
The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA (8454-8460)
DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination (8461-8468)
Colloquium Program (8469-8471)