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Review
. 2023 Jun 28;87(2):e0007822.
doi: 10.1128/mmbr.00078-22. Epub 2023 May 22.

Generation and Repair of Postreplication Gaps in Escherichia coli

Michael M Cox  1 , Myron F Goodman  2   3 , James L Keck  4 , Antoine van Oijen  5   6 , Susan T Lovett  7 , Andrew Robinson  5   6
Affiliations
Review

Generation and Repair of Postreplication Gaps in Escherichia coli

Michael M Cox et al. Microbiol Mol Biol Rev. .

Abstract

When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.

Keywords: DNA recombination; DNA repair; RecA; RecF; RecG; RecO; RecR; mutagenesis; postreplication gap; translesion DNA synthesis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
Consequences of DNA lesion repair. (A) Many DNA repair pathways, including nucleotide excision repair, base excision repair, and mismatch repair, rely on the fact that DNA is double stranded. If a lesion occurs in one strand, it can be excised from that strand to leave a DNA gap. DNA synthesis, using the undamaged complementary strand as a template, then completes the repair process in a manner that does not produce mutations. (B) The processes described above for panel A generate a transient discontinuity in one of the DNA strands. If a replication fork encounters this discontinuity before it is eliminated, a double-strand break results. The double-strand break is repaired by RecBCD and RecA in the double-strand break repair pathway.
FIG 2
FIG 2
Three possible outcomes of replisome collisions with template lesions. The outcomes are, from left to right, fork stalling and reversal, translesion DNA synthesis, and lesion skipping. Lesion skipping occurs often in bacteria and is the focus of this review.
FIG 3
FIG 3
Recombinational DNA repair of a postreplication gap mediated by the RecFOR system. The RecF protein, in a complex with RecR, targets the system to the appropriate postreplication gaps. RecO is recruited and activated, most likely via a handoff of RecR from RecF to RecO. RecOR loads a RecA filament into the gap. RecA promotes the formation of a joint molecule, which is then resolved by one of multiple pathways. Topo I, topoisomerase I.
FIG 4
FIG 4
The dnaA-dnaN-recF-gyrB operon. The recF locus is shown, along with the neighboring operon genes and putative promoters (small arrows).
FIG 5
FIG 5
DNA strand exchange reactions used to study RecA function in vitro. RecA filaments are formed on the single-stranded or gapped DNA circle. These function to pair the bound DNA with the linear duplex and promote the exchange of DNA strands, as shown.
FIG 6
FIG 6
Model for the targeting of the RecA protein specifically to lesion-containing postreplication gaps. In this scenario, the targeting of RecF to the appropriate gaps is mediated by the interaction of the RecF protein with the DnaN β-clamp. An encounter between the replisome and a lesion triggers a conformational change that disengages the replisome for lesion skipping and deposits RecF at the end of the resulting gap where the lesion was encountered. The deposited RecF forms a stabilizing complex with RecR. The RecFR complex recruits RecO, activating RecO by a handoff of RecR from RecF to RecO. RecO loads RecA into the gap to initiate repair. The gap is drawn linearly, but DNA looping could facilitate many of the described interactions. In both cases, the events shown involve sister chromosomes interacting behind the fork.
FIG 7
FIG 7
Gap-filling DNA intermediates of homologous recombination versus RecA-independent template-switching. (A) In recombination mediated by the RecFOR system and RecA, the RecA filament extracts and pairs with a strand from a duplex sister chromosome. The 3′ end of the gap can then use the sister chromosome as the template to synthesize the missing information. Pairs of branched DNA junctions are produced and can be resolved by RuvABC or RecG, restoring an intact chromosome. (B) In RecA-independent template switching, the unwinding of the nascent strands of the gapped chromosome and its replicating sister allows them to pair and promote synthesis. Branched molecules are also generated, but the factors that resolve them have not been defined. As shown in the diagram, the resulting chromosomes are noncrossovers, but an alternative resolution in both pathways can produce crossover and sister chromosome exchange.
FIG 8
FIG 8
Template switching after fork reversal. (A) A lesion on the leading strand (triangle) blocks DNA synthesis. (B) Branch migration at the fork produces a reversed fork in which both nascent strands anneal to form a nub. From this point, there are three alternative outcomes. (C) Leading nascent strand extended by DNA synthesis from the lagging-nascent-strand template. (D) Branch migration to restore the fork with lesion bypass. (C′) Alternatively, the exonucleolytic degradation of the nub by RecBCD resets the fork, backward from the original position. (D′) Because the lesion is now in dsDNA, it can be removed by excision repair. (C″) In a third scenario, the 4-strand Holliday junction (HJ) is cleaved, leaving a single-ended broken chromosome. This broken chromosome can be repaired by RecA during RecBCD-mediated double-strand break repair with the intact chromosome (not shown).
FIG 9
FIG 9
The RRS genomic element. (A) Discovery of the RRS (Replication Risk Sequence) element. Shown are genome-wide binding patterns of RecA protein to ssDNA, generated by ssGAP-Seq (444). Sharp peaks of RecA binding to ssDNA are indicated by green arrows. The RRS elements were discovered near the end of each of these regions. The RRS are positioned near the dusC and lysO genes. Both RRS are intergenic. The letters A, B, C, and D denote ter sites that are bound by the protein Tus. (B) The sequence of the RRS element. The two RRS elements in the E. coli genome differ at only 3 positions out of 222 (shown). (C) One of several predicted folding patterns that can be taken up by the RRS sequence. (D) Positioning of the RRS in the E. coli genome is shown in the center panel. RIGHT, LEFT, TER, and ORI refer to defined chromosomal macrodomains. NSL and NSR refer to left and right non-structural regions, respectively. W-strand and C-strand refers to Watson and Crick strands, respectively. Each RRS is equidistant (about 650,000 bp) from dif and symmetrically arranged around the ter macrodomain. To the right and left are shown close-ups of the RecA binding patterns in the peak adjacent to the RRS. In each case, the highest levels of RecA binding are seen near the RRS, then trailing off over a range of about 2 kbp. Enhanced RecA binding to ssDNA is seen only on the lagging strand in each case.
FIG 10
FIG 10
RRS conservation in enterobacteria. RRS elements in several other enterobacterial species are shown. They are highly conserved with respect to both sequence and positioning. Some species have more than two RRSs, but they always have one pair flanking the Ter region that encompasses the matS sites that are critical for Ter macrodomain function (450, 451).
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References

    1. De Bont R, van Larebeke N. 2004. Endogenous DNA damage in humans: a review of quantitative data. Mutagenesis 19:169–185. doi:10.1093/mutage/geh025. - DOI - PubMed
    1. Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362:709–715. doi:10.1038/362709a0. - DOI - PubMed
    1. Sancar A. 1996. DNA excision repair. Annu Rev Biochem 65:43–81. doi:10.1146/annurev.bi.65.070196.000355. - DOI - PubMed
    1. Reardon JT, Sancar A. 2005. Nucleotide excision repair. Prog Nucleic Acid Res Mol Biol 79:183–235. doi:10.1016/S0079-6603(04)79004-2. - DOI - PubMed
    1. Wozniak KJ, Simmons LA. 2022. Bacterial DNA excision repair pathways. Nat Rev Microbiol 20:465–477. doi:10.1038/s41579-022-00694-0. - DOI - PMC - PubMed

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