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  • Review Article
  • Published:

Recombinational repair and restart of damaged replication forks

Nature Reviews Molecular Cell Biology volume 3, pages 859–870 (2002)Cite this article

Key Points

  • 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.

Abstract

Genome duplication necessarily involves the replication of imperfect DNA templates and, if left to their own devices, replication complexes regularly run into problems. The details of how cells overcome these replicative 'hiccups' are beginning to emerge, revealing a complex interplay between DNA replication, recombination and repair that ensures faithful passage of the genetic material from one generation to the next.

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Figure 1: Potential types of replication-fork damage.
Figure 2: Restarting DNA replication by junction cleavage.
Figure 3: Restarting DNA replication without cleavage.
Figure 4: PriA-directed reloading of the replication machinery.
Figure 5: Potential mechanisms of replication restart.

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Acknowledgements

Work in the authors' laboratories is supported by the MRC (P.M. and R.G.L.) and the Wellcome Trust (R.G.L.). P.M. is a Lister Institute–Jenner Research Fellow.

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Authors and Affiliations

  1. Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK

    Peter McGlynn & Robert G. Lloyd

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  1. Peter McGlynn
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Correspondence to Peter McGlynn or Robert G. Lloyd.

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DATABASES

Entrez

DnaB

DnaC

DnaG

PriA

RecA

RecF

RecG

RecJ

RecQ

RecR

resolvase

Rqh1

Rrm3

RuvC

Sgs1

OMIM

Bloom's syndrome

Werner's syndrome

Swiss-Prot

ISWI

Mus81

Rad51

WSTF

Glossary

REPLISOME

A complex of DNA-replication enzymes that contains two DNA polymerases for leading- and lagging-strand synthesis, sliding clamps to maintain processivity, a sliding-clamp loader, a helicase to unwind the parental double-stranded DNA ahead of the advancing fork and a primase to synthesize RNA primers for discontinuous lagging-strand synthesis.

OKAZAKI FRAGMENTS

Individual lagging strand that ranges from 40–300 base pairs (bp) in eukaryotes, and 1,000–2,000 bp in bacteria.

PYRIMIDINE DIMER

Adjacent pyrimidine bases that are covalently linked in a DNA strand as a result of irradiation with UV light. Such lesions block normal replicative DNA polymerases.

RIBOSOMAL DNA CLUSTER

(rDNA). Tandem repeats of genes that encode ribosomal RNA.

TUS–TER

A complex formed by binding of the Tus protein to specific ter sequences in bacterial genomes. It blocks advancing replication forks, which allows the opposing replication fork to converge with the blocked fork to complete duplication of the circular bacterial chromosome.

REPLICATIVE HELICASE

The helicase activity required to unwind the parental double-stranded DNA ahead of the advancing replication fork, which allows the unwound strands to be used as templates for leading- and lagging-strand synthesis.

SLIDING CLAMPS

Also known as processivity factors. Protein dimers or trimers that encircle and slide along double-stranded DNA. They tether the replicative polymerase and prevent its rapid dissociation from the template DNA.

HELICASE

A protein that uses the energy of ATP hydrolysis to disrupt hydrogen bonding between two nucleic-acid strands, therefore separating the strands.

HETEROCHROMATIN

Chromatin — DNA packaged around nucleosomes — that is highly compacted as compared with most chromatin in a eukaryotic cell.

RUVABC

A Holliday-junction-specific multisubunit helicase (RuvAB) and endonuclease (RuvC) that act in concert to move and then cleave the branch point of Holliday junctions.

RECA

A recombination enzyme that catalyses strand exchange between a single strand of DNA and a homologous double-stranded DNA.

D-LOOP

A recombination intermediate that is formed by the base pairing of a single-stranded DNA with a homologous double-stranded DNA; a structure in which one strand of the dsDNA is displaced to make way for the invading strand is formed.

PRIA

Recognizes and loads the replication machinery at branched DNA structures in Escherichia coli.

CHECKPOINT

An enzyme system that ensures events, such as DNA replication, are completed before progression to the next stage of the cell cycle in eukaryotes.

RECG

A helicase that can unwind forked DNA to generate Holliday junctions, and that can also move the branch point of a Holliday junction along the DNA.

EXCISION REPAIR

The removal of damaged nucleotide residues in DNA and their replacement with the correct residue.

NEGATIVE SUPERCOILING

Almost all DNA molecules are negatively supercoiled. The DNA is twisted about itself in the direction opposite to that of the two strands of the double helix.

POSITIVE SUPERCOILING

Positively supercoiled DNA, like negatively supercoiled DNA, has a higher energy than relaxed DNA and this energy can alter local DNA structure. However, the DNA is twisted on itself in the same direction as the two strands of the double helix.

DNAB

The replicative helicase of Escherichia coli that unwinds the parental double-stranded DNA ahead of the replication fork by translocating along the lagging-strand template.

ILLEGITIMATE RECOMBINATION

Recombination between DNA sequences that share little or no homology.

TOPOISOMERASE III

An enzyme that alters the degree of supercoiling in double-stranded DNA by the transient introduction of nicks in a single strand of the DNA.

DNAG

A specialized Escherichia coli RNA polymerase, or primase, that transiently interacts with DnaB and synthesizes short stretches of RNA on the lagging-strand template. These RNAs prime lagging-strand DNA synthesis.

SOS RESPONSE

The induction of expression of a series of genes, many of which encode proteins that are involved in DNA-damage tolerance mechanisms, in response to elevated levels of DNA damage.

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McGlynn, P., Lloyd, R. Recombinational repair and restart of damaged replication forks. Nat Rev Mol Cell Biol 3, 859–870 (2002). https://doi.org/10.1038/nrm951

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