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Lee SJ, Ahn SY, Oh HB, Kim SY, Song WS, Yoon SI. Structural and Biochemical Analysis of the Recombination Mediator Protein RecR from Campylobacter jejuni. Int J Mol Sci 2023; 24:12947. [PMID: 37629127 PMCID: PMC10454854 DOI: 10.3390/ijms241612947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The recombination mediator complex RecFOR, consisting of the RecF, RecO, and RecR proteins, is needed to initiate homologous recombination in bacteria by positioning the recombinase protein RecA on damaged DNA. Bacteria from the phylum Campylobacterota, such as the pathogen Campylobacter jejuni, lack the recF gene and trigger homologous recombination using only RecR and RecO. To elucidate the functional properties of C. jejuni RecR (cjRecR) in recombination initiation that differ from or are similar to those in RecF-expressing bacteria, we determined the crystal structure of cjRecR and performed structure-based binding analyses. cjRecR forms a rectangular ring-like tetrameric structure and coordinates a zinc ion using four cysteine residues, as observed for RecR proteins from RecF-expressing bacteria. However, the loop of RecR that has been shown to recognize RecO and RecF in RecF-expressing bacteria is substantially shorter in cjRecR as a canonical feature of Campylobacterota RecR proteins, indicating that cjRecR lost a part of the loop in evolution due to the lack of RecF and has a low RecO-binding affinity. Furthermore, cjRecR features a larger positive patch and exhibits substantially higher ssDNA-binding affinity than RecR from RecF-expressing bacteria. Our study provides a framework for a deeper understanding of the RecOR-mediated recombination pathway.
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Affiliation(s)
- Su-jin Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Si Yeon Ahn
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Han Byeol Oh
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Seung Yeon Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Wan Seok Song
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Sung-il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea
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Nirwal S, Czarnocki-Cieciura M, Chaudhary A, Zajko W, Skowronek K, Chamera S, Figiel M, Nowotny M. Mechanism of RecF-RecO-RecR cooperation in bacterial homologous recombination. Nat Struct Mol Biol 2023; 30:650-660. [PMID: 37081315 DOI: 10.1038/s41594-023-00967-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/15/2023] [Indexed: 04/22/2023]
Abstract
In bacteria, one type of homologous-recombination-based DNA-repair pathway involves RecFOR proteins that bind at the junction between single-stranded (ss) and double-stranded (ds) DNA. They facilitate the replacement of SSB protein, which initially covers ssDNA, with RecA, which mediates the search for homologous sequences. However, the molecular mechanism of RecFOR cooperation remains largely unknown. We used Thermus thermophilus proteins to study this system. Here, we present a cryo-electron microscopy structure of the RecF-dsDNA complex, and another reconstruction that shows how RecF interacts with two different regions of the tetrameric RecR ring. Lower-resolution reconstructions of the RecR-RecO subcomplex and the RecFOR-DNA assembly explain how RecO is positioned to interact with ssDNA and SSB, which is proposed to lock the complex on a ssDNA-dsDNA junction. Our results integrate the biochemical data available for the RecFOR system and provide a framework for its complete understanding.
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Affiliation(s)
- Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Anuradha Chaudhary
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Skowronek
- Biophysics and Bioanalytics Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Sebastian Chamera
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
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3
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Crystal Structure of the Recombination Mediator Protein RecO from Campylobacter jejuni and Its Interaction with DNA and a Zinc Ion. Int J Mol Sci 2022; 23:ijms23179667. [PMID: 36077065 PMCID: PMC9456098 DOI: 10.3390/ijms23179667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion. cjRecO folds into a curved rod-like structure that consists of an N-terminal domain (NTD), C-terminal domain (CTD), and Zn2+-binding domain (ZnD). The ZnD at the end of the rod-like structure coordinates three cysteine residues and one histidine residue to accommodate a Zn2+ ion. Based on an extensive comparative analysis of RecO structures and sequences, we propose that the Zn2+-binding consensus sequence of RecO is CxxC…C/HxxC/H/D. The interaction with Zn2+ is indispensable for the protein stability of cjRecO but does not seem to be required for the recombination mediator function. cjRecO also interacts with ssDNA as part of its biological function, potentially using the positively charged patch in the NTD and CTD. However, cjRecO displays a low ssDNA-binding affinity, suggesting that cjRecO requires RecR to efficiently recognize ssDNA for homologous recombination.
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ComFC mediates transport and handling of single-stranded DNA during natural transformation. Nat Commun 2022; 13:1961. [PMID: 35414142 PMCID: PMC9005727 DOI: 10.1038/s41467-022-29494-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 03/17/2022] [Indexed: 11/09/2022] Open
Abstract
The ComFC protein is essential for natural transformation, a process that plays a major role in the spread of antibiotic resistance genes and virulence factors across bacteria. However, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is involved in DNA transport through the cell membrane, and is required for the handling of the single-stranded DNA once it is delivered into the cytoplasm. The crystal structure of ComFC includes a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein's in vivo activity. Furthermore, we show that ComFC is a membrane-associated protein with affinity for single-stranded DNA. Our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.
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Shinn MK, Kozlov AG, Lohman TM. Allosteric effects of SSB C-terminal tail on assembly of E. coli RecOR proteins. Nucleic Acids Res 2021; 49:1987-2004. [PMID: 33450019 PMCID: PMC7913777 DOI: 10.1093/nar/gkaa1291] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli RecO is a recombination mediator protein that functions in the RecF pathway of homologous recombination, in concert with RecR, and interacts with E. coli single stranded (ss) DNA binding (SSB) protein via the last 9 amino acids of the C-terminal tails (SSB-Ct). Structures of the E. coli RecR and RecOR complexes are unavailable; however, crystal structures from other organisms show differences in RecR oligomeric state and RecO stoichiometry. We report analytical ultracentrifugation studies of E. coli RecR assembly and its interaction with RecO for a range of solution conditions using both sedimentation velocity and equilibrium approaches. We find that RecR exists in a pH-dependent dimer-tetramer equilibrium that explains the different assembly states reported in previous studies. RecO binds with positive cooperativity to a RecR tetramer, forming both RecR4O and RecR4O2 complexes. We find no evidence of a stable RecO complex with RecR dimers. However, binding of RecO to SSB-Ct peptides elicits an allosteric effect, eliminating the positive cooperativity and shifting the equilibrium to favor a RecR4O complex. These studies suggest a mechanism for how SSB binding to RecO influences the distribution of RecOR complexes to facilitate loading of RecA onto SSB coated ssDNA to initiate homologous recombination.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.,Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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Chaudhary SK, Elayappan M, Jeyakanthan J, Kanagaraj S. Structural and functional characterization of oligomeric states of proteins in RecFOR pathway. Int J Biol Macromol 2020; 163:943-953. [DOI: 10.1016/j.ijbiomac.2020.07.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/30/2022]
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Che S, Chen Y, Liang Y, Zhang Q, Bartlam M. Crystal structure of RecR, a member of the RecFOR DNA-repair pathway, from Pseudomonas aeruginosa PAO1. Acta Crystallogr F Struct Biol Commun 2018; 74:222-230. [PMID: 29633970 PMCID: PMC5894107 DOI: 10.1107/s2053230x18003503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/28/2018] [Indexed: 11/10/2022] Open
Abstract
DNA damage is usually lethal to all organisms. Homologous recombination plays an important role in the DNA damage-repair process in prokaryotic organisms. Two pathways are responsible for homologous recombination in Pseudomonas aeruginosa: the RecBCD pathway and the RecFOR pathway. RecR is an important regulator in the RecFOR homologous recombination pathway in P. aeruginosa. It forms complexes with RecF and RecO that can facilitate the loading of RecA onto ssDNA in the RecFOR pathway. Here, the crystal structure of RecR from P. aeruginosa PAO1 (PaRecR) is reported. PaRecR crystallizes in space group P6122, with two monomers per asymmetric unit. Analytical ultracentrifugation data show that PaRecR forms a stable dimer, but can exist as a tetramer in solution. The crystal structure shows that dimeric PaRecR forms a ring-like tetramer architecture via crystal symmetry. The presence of a ligand in the Walker B motif of one RecR subunit suggests a putative nucleotide-binding site.
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Affiliation(s)
- Shiyou Che
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Yujing Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Yakun Liang
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Qionglin Zhang
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Mark Bartlam
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 38 Tongyan Road, Tianjin 300350, People’s Republic of China
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Tang Q, Liu YP, Shan HH, Tian LF, Zhang JZ, Yan XX. ATP-dependent conformational change in ABC-ATPase RecF serves as a switch in DNA repair. Sci Rep 2018; 8:2127. [PMID: 29391496 PMCID: PMC5794780 DOI: 10.1038/s41598-018-20557-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/19/2018] [Indexed: 11/13/2022] Open
Abstract
RecF is a principal member of the RecF pathway. It interacts with RecO and RecR to initiate homologous recombination by loading RecA recombinases on single-stranded DNA and displacing single-stranded DNA-binding proteins. As an ATP-binding cassette ATPase, RecF exhibits ATP-dependent dimerization and structural homology with Rad50 and SMC proteins. However, the mechanism and action pattern of RecF ATP-dependent dimerization remains unclear. Here, We determined three crystal structures of TTERecF, TTERecF-ATP and TTERecF-ATPɤS from Thermoanaerobacter tengcongensis that reveal a novel ATP-driven RecF dimerization. RecF contains a positively charged tunnel on its dimer interface that is essential to ATP binding. Our structural and biochemical data indicate that the Walker A motif serves as a switch and plays a key role in ATP binding and RecF dimerization. Furthermore, Biolayer interferometry assay results showed that the TTERecF interacted with ATP and formed a dimer, displaying a higher affinity for DNA than that of the TTERecF monomer. Overall, our results provide a solid structural basis for understanding the process of RecF binding with ATP and the functional mechanism of ATP-dependent RecF dimerization.
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Affiliation(s)
- Qun Tang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan-Ping Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hai-Huan Shan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li-Fei Tian
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie-Zhong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Xue Yan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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Timmins J, Moe E. A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges. Comput Struct Biotechnol J 2016; 14:168-176. [PMID: 27924191 PMCID: PMC5128194 DOI: 10.1016/j.csbj.2016.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/02/2016] [Accepted: 04/07/2016] [Indexed: 10/27/2022] Open
Affiliation(s)
- Joanna Timmins
- Université Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- CEA, IBS, F-38044 Grenoble, France
| | - Elin Moe
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT the Arctic University of Norway, N-9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Av da Republica (EAN), 2780-157 Oeiras, Portugal
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Radzimanowski J, Dehez F, Round A, Bidon-Chanal A, McSweeney S, Timmins J. An 'open' structure of the RecOR complex supports ssDNA binding within the core of the complex. Nucleic Acids Res 2013; 41:7972-86. [PMID: 23814185 PMCID: PMC3763555 DOI: 10.1093/nar/gkt572] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 01/19/2023] Open
Abstract
Efficient DNA repair is critical for cell survival and the maintenance of genome integrity. The homologous recombination pathway is responsible for the repair of DNA double-strand breaks within cells. Initiation of this pathway in bacteria can be carried out by either the RecBCD or the RecFOR proteins. An important regulatory player within the RecFOR pathway is the RecOR complex that facilitates RecA loading onto DNA. Here we report new data regarding the assembly of Deinococcus radiodurans RecOR and its interaction with DNA, providing novel mechanistic insight into the mode of action of RecOR in homologous recombination. We present a higher resolution crystal structure of RecOR in an 'open' conformation in which the tetrameric RecR ring flanked by two RecO molecules is accessible for DNA binding. We show using small-angle neutron scattering and mutagenesis studies that DNA binding does indeed occur within the RecR ring. Binding of single-stranded DNA occurs without any major conformational changes of the RecOR complex while structural rearrangements are observed on double-stranded DNA binding. Finally, our molecular dynamics simulations, supported by our biochemical data, provide a detailed picture of the DNA binding motif of RecOR and reveal that single-stranded DNA is sandwiched between the two facing oligonucleotide binding domains of RecO within the RecR ring.
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Affiliation(s)
- Jens Radzimanowski
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - François Dehez
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Adam Round
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Axel Bidon-Chanal
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Sean McSweeney
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Joanna Timmins
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble cedex 9, France, Université de Lorraine, BP239, 54506 Vandoeuvre-lès-Nancy Cedex, France, CNRS, UMR N°7565, 54506 Vandoeuvre-les-Nancy, France, European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France, Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France and Institut de Biologie Structurale, CNRS/CEA/Université de Grenoble, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
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