Generation and Repair of Postreplication Gaps in Escherichia coli

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. SUMMARY 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.

• Publication year

  2023

• Venue

  Microbiology and Molecular Biology Reviews

• Publication date

  2023-05-22

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1128/mmbr.00078-22PMID 37212693PMCID PMC10304936
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes

  2023cited by this paper
• RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR

  2023cited by this paper
• RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli

  2023cited by this paper
• Bacterial DNA excision repair pathways

  2022cited by this paper
• Interaction with single-stranded DNA-binding protein modulates Escherichia coli RadD DNA repair activities

  2022cited by this paper
• Single strand gap repair: The presynaptic phase plays a pivotal role in modulating lesion tolerance pathways

  2022cited by this paper
• X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain

  2022cited by this paper
• RadD is a RecA-dependent accessory protein that accelerates DNA strand exchange

  2022cited by this paper
• Host cell RecA activates a mobile element-encoded mutagenic DNA polymerase

  2022cited by this paper
• Characterization of the Escherichia coli XPD/Rad3 iron-sulfur helicase YoaA in complex with the DNA polymerase III clamp loader subunit chi (χ)

  2022cited by this paper
• How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein

  2022cited by this paper
• Elucidating Recombination Mediator Function Using Biophysical Tools

  2021cited by this paper
• Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication

  2021cited by this paper
• Alternative complexes formed by the Escherichia coli clamp loader accessory protein HolC (x) with replication protein HolD (ψ) and repair protein YoaA.

  2021cited by this paper
• Genetic Analysis of DinG Family Helicase YoaA and Its Interaction with Replication Clamp Loader Protein HolC in Escherichia coli

  2021cited by this paper
• The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ

  2021cited by this paper
• Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli.

  2021cited by this paper
• OUP accepted manuscript

  2021cited by this paper
• Genomic landscape of single-stranded DNA gapped intermediates in Escherichia coli

  2021cited by this paper
• Daughter-strand gaps in DNA replication - substrates of lesion processing and initiators of distress signalling.

  2021cited by this paper
• Redox controls RecA protein activity via reversible oxidation of its methionine residues

  2021cited by this paper
• The SOS Error-Prone DNA Polymerase V Mutasome and β-Sliding Clamp Acting in Concert on Undamaged DNA and during Translesion Synthesis

  2021cited by this paper
• Development of a single-stranded DNA-binding protein fluorescent fusion toolbox

  2020cited by this paper
• RecA‐independent recombination: Dependence on the Escherichia coli RarA protein

  2020cited by this paper
• A Comprehensive View of Translesion Synthesis in Escherichia coli

  2020cited by this paper
• Two components of DNA replication-dependent LexA cleavage

  2020cited by this paper
• Nucleotide Excision Repair

  2020cited by this paper
• Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans

  2020cited by this paper
• Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD

  2020cited by this paper
• A gatekeeping function of the replicative polymerase controls pathway choice in the resolution of lesion-stalled replisomes

  2019cited by this paper
• A Double-Strand Break Does Not Promote Neisseria gonorrhoeae Pilin Antigenic Variation

  2019cited by this paper
• Chromosome organization in bacteria: mechanistic insights into genome structure and function

  2019cited by this paper
• Replisome structure suggests mechanism for continuous fork progression and post-replication repair.

  2019cited by this paper
• DNA supercoiling and transcription in bacteria: a two-way street

  2019cited by this paper
• Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins

  2019cited by this paper
• RecFOR epistasis group: RecF and RecO have distinct localizations and functions in Escherichia coli

  2019cited by this paper
• DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair

  2019cited by this paper
• Architecture of the Escherichia coli nucleoid

  2019cited by this paper
• Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

  2019cited by this paper
• Are the intrinsically disordered linkers involved in SSB binding to accessory proteins?

  2019cited by this paper
• In vitro gap-directed translesion DNA synthesis of an abasic site involving human DNA polymerases epsilon , lambda , and beta

  2019cited by this paper
• Replisome activity slowdown after exposure to ultraviolet light in Escherichia coli

  2019cited by this paper
• Super-resolution imaging reveals changes in Escherichia coli SSB localization in response to DNA damage

  2019cited by this paper
• Near-continuously synthesized leading strands in Escherichia coli are broken by ribonucleotide excision

  2019cited by this paper
• Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

  2019cited by this paper
• Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response

  2018cited by this paper
• Chromosomal over-replication in Escherichia coli recG cells is triggered by replication fork fusion and amplified if replichore symmetry is disturbed

  2018cited by this paper
• Replication fork collapse at a protein-DNA roadblock leads to fork reversal, promoted by the RecQ helicase

  2018cited by this paper
• Replication Fork Breakage and Restart in Escherichia coli

  2018cited by this paper
• Analysis of Pilin Antigenic Variation in Neisseria meningitidis by Next-Generation Sequencing

  2018cited by this paper
• Recycling of single-stranded DNA-binding protein by the bacterial replisome

  2018cited by this paper
• DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli

  2018cited by this paper
• Movement of the RecG Motor Domain upon DNA Binding Is Required for Efficient Fork Reversal

  2018cited by this paper
• Subcellular Organization: A Critical Feature of Bacterial Cell Replication.

  2018cited by this paper
• Bacteria-to-human protein networks reveal origins of endogenous DNA damage

  2018cited by this paper
• ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair

  2018cited by this paper
• Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response

  2018cited by this paper
• Chronological Switch from Translesion Synthesis to Homology-Dependent Gap Repair In Vivo

  2018cited by this paper
• Lesion Bypass and the Reactivation of Stalled Replication Forks.

  2018cited by this paper
• Specialised DNA polymerases in Escherichia coli: roles within multiple pathways

  2018cited by this paper
• The transcription fidelity factor GreA impedes DNA break repair

  2017cited by this paper
• Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension

  2017cited by this paper
• DNA flap creation by the RarA/MgsA protein of Escherichia coli

  2017cited by this paper
• Single-molecule studies contrast ordered DNA replication with stochastic translesion synthesis

  2017cited by this paper
• PCNA ubiquitylation ensures timely completion of unperturbed DNA replication in fission yeast

  2017cited by this paper
• Template-switching during replication fork repair in bacteria.

  2017cited by this paper
• Single-molecule imaging reveals multiple pathways for the recruitment of translesion polymerases after DNA damage

  2017cited by this paper
• Staphylococcus aureus single-stranded DNA-binding protein SsbA can bind but cannot stimulate PriA helicase

  2017cited by this paper
• Mechanisms of DNA–protein crosslink repair

  2017cited by this paper
• Glutamate promotes SSB protein-protein Interactions via intrinsically disordered regions.

  2017cited by this paper
• A Magic Spot in Genome Maintenance.

  2017cited by this paper
• Building up and breaking down: mechanisms controlling recombination during replication

  2017cited by this paper
• Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme

  2017cited by this paper
• Antibiotic tolerance facilitates the evolution of resistance

  2017cited by this paper
• MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation

  2016cited by this paper
• A defect in homologous recombination leads to increased translesion synthesis in E. coli

  2016cited by this paper
• High-resolution genomic assays provide insight into the division of labor between TLS and HDR in mammalian replication of damaged DNA.

  2016cited by this paper
• DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype

  2016cited by this paper
• Figures and figure supplements Structural basis for DNA 5 ́-end resection by RecJ Kaiying

  2016cited by this paper
• Antigenic Variation in Bacterial Pathogens

  2016cited by this paper
• 25 years on and no end in sight: a perspective on the role of RecG protein

  2016cited by this paper
• Insights into the complex levels of regulation imposed on Escherichia coli DNA polymerase V.

  2016cited by this paper
• RecG Directs DNA Synthesis during Double-Strand Break Repair

  2016cited by this paper
• Structural basis for DNA 5´-end resection by RecJ

  2016cited by this paper
• Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword.

  2016cited by this paper
• Escherichia coli RadD Protein Functionally Interacts with the Single-stranded DNA-binding Protein*

  2016cited by this paper
• Tolerance of lesions in E. coli: Chronological competition between Translesion Synthesis and Damage Avoidance.

  2016cited by this paper
• Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase

  2016cited by this paper
• Recombinational branch migration by the RadA/Sms paralog of RecA in Escherichia coli

  2016cited by this paper
• A RecA Protein Surface Required for Activation of DNA Polymerase V

  2015cited by this paper
• Bacterial Proliferation: Keep Dividing and Don't Mind the Gap

  2015cited by this paper
• Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination

  2015cited by this paper
• Intrinsically disordered C-terminal tails of E. coli single-stranded DNA binding protein regulate cooperative binding to single-stranded DNA.

  2015cited by this paper
• Mycobacterium tuberculosis class II apurinic/apyrimidinic‐endonuclease/3′‐5′ exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β‐clamp

  2015cited by this paper
• Active displacement of RecA filaments by UvrD translocase activity

  2015cited by this paper
• RecF and RecR Play Critical Roles in the Homologous Recombination and Single-Strand Annealing Pathways of Mycobacteria

  2015cited by this paper
• Connecting Replication and Repair: YoaA, a Helicase-Related Protein, Promotes Azidothymidine Tolerance through Association with Chi, an Accessory Clamp Loader Protein

  2015cited by this paper
• Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function

  2015cited by this paper
• Escherichia coli radD (yejH) gene: a novel function involved in radiation resistance and double‐strand break repair

  2015cited by this paper
• Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions

  2015cited by this paper

• Escherichia coli transcription factors RapA and SspA play opposing roles in tolerance to replication/transcription conflicts after DNA damage

  2026cites this paper
• RecBCD-dependent post-UV replication restart in Escherichia coli triggers fork triplication.

  2026cites this paper
• Exploring the genetic landscape of ciprofloxacin-induced DNA supercompaction in Escherichia coli

  2025cites this paper
• Hallmarks of DNA replication stress responses in Escherichia coli and Bacillus subtilis

  2025influential citation
• Rescuing the bacterial replisome at a nick requires recombinational repair and helicase reloading

  2025cites this paper
• The Role of the RecFOR Complex in Genome Stability

  2025cites this paper
• Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli

  2024cites this paper
• BRCA2 promotes genomic integrity and therapy resistance primarily through its role in homology-directed repair.

  2024cites this paper
• The intrinsically disordered linker in the single-stranded DNA-binding protein influences DNA replication restart and recombination pathways in Escherichia coli K-12

  2024cites this paper
• RecA-dependent or independent recombination of plasmid DNA generates a conflict with the host EcoKI immunity by launching restriction alleviation

  2024cites this paper
• Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements

  2024cites this paper
• Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization

  2024cites this paper
• Dysregulated DnaB unwinding induces replisome decoupling and daughter strand gaps that are countered by RecA polymerization

  2023cites this paper
• Processing of stalled replication forks in Bacillus subtilis

  2023cites this paper
• Identification of recG genetic interactions in Escherichia coli by transposon sequencing

  2023cites this paper
• Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements

  2023cites this paper