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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
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.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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Del Val E, Nasser W, Abaibou H, Reverchon S. Design and comparative characterization of RecA variants. Sci Rep 2021; 11:21106. [PMID: 34702889 PMCID: PMC8548320 DOI: 10.1038/s41598-021-00589-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
RecA plays a central role in DNA repair and is a main actor involved in recombination and activation of the SOS response. It is also used in the context of biotechnological applications in recombinase polymerase isothermal amplification (RPA). In this work, we studied the biological properties of seven RecA variants, in particular their recombinogenic activity and their ability to induce the SOS response, to better understand the structure-function relationship of RecA and the effect of combined mutations. We also investigated the biochemical properties of RecA variants that may be useful for the development of biotechnological applications. We showed that Dickeya dadantii RecA (DdRecA) had an optimum strand exchange activity at 30 °C and in the presence of a dNTP mixture that inhibited Escherichia coli RecA (EcRecA). The differences between the CTD and C-tail of the EcRecA and DdRecA domains could explain the altered behaviour of DdRecA. D. radiodurans RecA (DrRecA) was unable to perform recombination and activation of the SOS response in an E. coli context, probably due to its inability to interact with E. coli recombination accessory proteins and SOS LexA repressor. DrRecA strand exchange activity was totally inhibited in the presence of chloride ions but worked well in acetate buffer. The overproduction of Pseudomonas aeruginosa RecA (PaRecA) in an E. coli context was responsible for a higher SOS response and defects in cellular growth. PaRecA was less inhibited by the dNTP mixture than EcRecA. Finally, the study of three variants, namely, EcPa, EcRecAV1 and EcRecAV2, that contained a combination of mutations that, taken independently, are described as improving recombination, led us to raise new hypotheses on the structure-function relationship and on the monomer-monomer interactions that perturb the activity of the protein as a whole.
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Affiliation(s)
- Elsa Del Val
- UMR5240, Microbiologie, Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, 11 Avenue Jean Capelle, 69621, Villeurbanne, France
- Molecular Innovation Unit, Centre Christophe Mérieux, bioMérieux, 5 Rue des Berges, 38024, Grenoble Cedex 01, France
| | - William Nasser
- UMR5240, Microbiologie, Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, 11 Avenue Jean Capelle, 69621, Villeurbanne, France
| | - Hafid Abaibou
- Molecular Innovation Unit, Centre Christophe Mérieux, bioMérieux, 5 Rue des Berges, 38024, Grenoble Cedex 01, France.
| | - Sylvie Reverchon
- UMR5240, Microbiologie, Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, 11 Avenue Jean Capelle, 69621, Villeurbanne, France.
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RecA and DNA recombination: a review of molecular mechanisms. Biochem Soc Trans 2020; 47:1511-1531. [PMID: 31654073 DOI: 10.1042/bst20190558] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 11/17/2022]
Abstract
Recombinases are responsible for homologous recombination and maintenance of genome integrity. In Escherichia coli, the recombinase RecA forms a nucleoprotein filament with the ssDNA present at a DNA break and searches for a homologous dsDNA to use as a template for break repair. During the first step of this process, the ssDNA is bound to RecA and stretched into a Watson-Crick base-paired triplet conformation. The RecA nucleoprotein filament also contains ATP and Mg2+, two cofactors required for RecA activity. Then, the complex starts a homology search by interacting with and stretching dsDNA. Thanks to supercoiling, intersegment sampling and RecA clustering, a genome-wide homology search takes place at a relevant metabolic timescale. When a region of homology 8-20 base pairs in length is found and stabilized, DNA strand exchange proceeds, forming a heteroduplex complex that is resolved through a combination of DNA synthesis, ligation and resolution. RecA activities can take place without ATP hydrolysis, but this latter activity is necessary to improve and accelerate the process. Protein flexibility and monomer-monomer interactions are fundamental for RecA activity, which functions cooperatively. A structure/function relationship analysis suggests that the recombinogenic activity can be improved and that recombinases have an inherently large recombination potential. Understanding this relationship is essential for designing RecA derivatives with enhanced activity for biotechnology applications. For example, this protein is a major actor in the recombinase polymerase isothermal amplification (RPA) used in point-of-care diagnostics.
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Lu CH, Chang TT, Cho CC, Lin HC, Li HW. Stable Nuclei of Nucleoprotein Filament and High ssDNA Binding Affinity Contribute to Enhanced RecA E38K Recombinase Activity. Sci Rep 2017; 7:14964. [PMID: 29097773 PMCID: PMC5668366 DOI: 10.1038/s41598-017-15088-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/20/2017] [Indexed: 11/10/2022] Open
Abstract
RecA plays central roles in the homologous recombination to repair double-stranded DNA break damage in E. coli. A previously identified recA strain surviving high doses of UV radiation includes a dominant RecA E38K mutation. Using single-molecule experiments, we showed that the RecA E38K variant protein assembles nucleoprotein filaments more rapidly than the wild-type RecA. We also used a single-molecule fluorescence resonance energy transfer (smFRET) experiment to compare the nucleation cluster dynamics of wild-type RecA and RecA E38K mutants on various short ssDNA substrates. At shorter ssDNA, nucleation clusters of RecA E38K form dynamically, while only few were seen in wild-type RecA. RecA E38K also forms stable nuclei by specifically lowering the dissociation rate constant, kd. These observations provide evidence that greater nuclei stability and higher ssDNA binding affinity contribute to the observed enhanced recombination activity of the RecA E38K mutant. Given that assembly of RecA nucleoprotein filaments is the first committed step in recombinational repair processes, enhancement at this step gives rise to a more efficient recombinase.
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Affiliation(s)
- Chih-Hao Lu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Ting-Tzu Chang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Chia-Chuan Cho
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hui-Cin Lin
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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Yakimov A, Pobegalov G, Bakhlanova I, Khodorkovskii M, Petukhov M, Baitin D. Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide. Nucleic Acids Res 2017; 45:9788-9796. [PMID: 28934502 PMCID: PMC5766188 DOI: 10.1093/nar/gkx687] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/24/2017] [Indexed: 01/19/2023] Open
Abstract
The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance.
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Affiliation(s)
- Alexander Yakimov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | - Georgii Pobegalov
- Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | - Irina Bakhlanova
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | | | - Michael Petukhov
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
| | - Dmitry Baitin
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P.Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina 188300, Russia.,Peter the Great St Petersburg Polytechnic University, St Petersburg 195251, Russia
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