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Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA. Int J Mol Sci 2020; 21:ijms21197389. [PMID: 33036395 PMCID: PMC7583915 DOI: 10.3390/ijms21197389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 11/17/2022] Open
Abstract
Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.
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Alekseev A, Serdakov M, Pobegalov G, Yakimov A, Bakhlanova I, Baitin D, Khodorkovskii M. Single-molecule analysis reveals two distinct states of the compressed RecA filament on single-stranded DNA. FEBS Lett 2020; 594:3464-3476. [PMID: 32880917 DOI: 10.1002/1873-3468.13922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 11/07/2022]
Abstract
The RecA protein plays a key role in bacterial homologous recombination (HR) and acts through assembly of long helical filaments around single-stranded DNA in the presence of ATP. Large-scale conformational changes induced by ATP hydrolysis result in transitions between stretched and compressed forms of the filament. Here, using a single-molecule approach, we show that compressed RecA nucleoprotein filaments can exist in two distinct interconvertible states depending on the presence of ADP in the monomer-monomer interface. Binding of ADP promotes cooperative conformational transitions and directly affects mechanical properties of the filament. Our findings reveal that RecA nucleoprotein filaments are able to continuously cycle between three mechanically distinct states that might have important implications for RecA-mediated processes of HR.
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Affiliation(s)
| | - Maksim Serdakov
- Peter the Great St Petersburg Polytechnic University, Russia
| | | | - Alexandr Yakimov
- Peter the Great St Petersburg Polytechnic University, Russia
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P. Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina, Russia
| | - Irina Bakhlanova
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P. Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina, Russia
| | - Dmitry Baitin
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute (B.P. Konstantinov of National Research Centre 'Kurchatov Institute'), Gatchina, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St Petersburg Polytechnic University, Russia
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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Boyer B, Danilowicz C, Prentiss M, Prévost C. Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res 2019; 47:7798-7808. [PMID: 31372639 PMCID: PMC6735932 DOI: 10.1093/nar/gkz667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023] Open
Abstract
Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.
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Affiliation(s)
- Benjamin Boyer
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Presently in Laboratoire Génomique Bioinformatique et Applications, EA4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
| | | | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chantal Prévost
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
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Li C, Danilowicz C, Tashjian TF, Godoy VG, Prévost C, Prentiss M. The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements. Nucleic Acids Res 2019; 47:1836-1846. [PMID: 30544167 PMCID: PMC6393298 DOI: 10.1093/nar/gky1252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 12/03/2022] Open
Abstract
Bacterial recombinational repair of double-strand breaks often begins with creation of initiating 3′ single-stranded DNA (ssDNA) tails on each side of a double-strand break (DSB). Importantly, if the RecBCD pathway is followed, RecBCD creates a gap between the sequences at 3′ ends of the initiating strands. The gap flanks the DSB and extends at least to the nearest Chi site on each strand. Once the initiating strands form ssDNA–RecA filaments, each ssDNA–RecA filament searches for homologous double-stranded DNA (dsDNA) to use as a template for the DNA synthesis needed to fill the gap created by RecBCD. Our experimental results show that the DNA synthesis requires formation of a heteroduplex dsDNA that pairs >20 contiguous bases in the initiating strand with sequence matched bases in a strand from the original dsDNA. To trigger synthesis, the heteroduplex must be near the 3′ end of the initiating strand. Those experimentally determined requirements for synthesis combined with the Chi site dependence of the function of RecBCD and the distribution of Chi sites in bacterial genomes could allow the RecBCD pathway to avoid some genomic rearrangements arising from directly induced DSBs; however, the same three factors could promote other rearrangements.
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Affiliation(s)
- Chastity Li
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | | | - Tommy F Tashjian
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Veronica G Godoy
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Chantal Prévost
- Laboratoire de BioChimie Théorique, CNRS UMR 9080, IBPC, Paris, France
| | - Mara Prentiss
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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Borgogno MV, Monti MR, Zhao W, Sung P, Argaraña CE, Pezza RJ. Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange. J Biol Chem 2015; 291:4928-38. [PMID: 26709229 DOI: 10.1074/jbc.m115.704718] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 12/30/2022] Open
Abstract
Recombination between homologous chromosomes is required for the faithful meiotic segregation of chromosomes and leads to the generation of genetic diversity. The conserved meiosis-specific Dmc1 recombinase catalyzes homologous recombination triggered by DNA double strand breaks through the exchange of parental DNA sequences. Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 must also guard against recombination between divergent sequences. How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood. We have used fluorescence resonance energy transfer to study the mechanism of Dmc1-mediated strand exchange between DNA oligonucleotides with different degrees of heterology. The efficiency of strand exchange is highly sensitive to the location, type, and distribution of mismatches. Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches near the 5' end impede strand exchange dramatically. The Hop2-Mnd1 protein complex stimulates Dmc1-catalyzed strand exchange on homologous DNA or containing a single mismatch. We observed that Dmc1 can reject divergent DNA sequences while bypassing a few mismatches in the DNA sequence. Our findings have important implications in understanding meiotic recombination. First, Dmc1 acts as an initial barrier for heterologous recombination, with the mismatch repair system providing a second level of proofreading, to ensure that ectopic sequences are not recombined. Second, Dmc1 stepping over infrequent mismatches is likely critical for allowing recombination between the polymorphic sequences of homologous chromosomes, thus contributing to gene conversion and genetic diversity.
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Affiliation(s)
- María V Borgogno
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Mariela R Monti
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Weixing Zhao
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Carlos E Argaraña
- From the Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Roberto J Pezza
- the Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, and the Department of Cell Biology, Oklahoma University Health Science Center, Oklahoma City, Oklahoma 73126
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Sansam CL, Pezza RJ. Connecting by breaking and repairing: mechanisms of DNA strand exchange in meiotic recombination. FEBS J 2015; 282:2444-57. [PMID: 25953379 PMCID: PMC4573575 DOI: 10.1111/febs.13317] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/26/2015] [Accepted: 05/06/2015] [Indexed: 01/03/2023]
Abstract
During prophase of meiosis I, homologous chromosomes interact and undergo recombination. Successful completion of these processes is required in order for the homologous chromosomes to mount the meiotic spindle as a pair. The organization of the chromosomes into pairs ensures orderly segregation to opposite poles of the dividing cell, such that each gamete receives one copy of each chromosome. Chiasmata, the cytological manifestation of crossover products of recombination, physically connect the homologs in pairs, providing a linkage that facilitates their segregation. Consequently, mutations that reduce the level of recombination are invariably associated with increased errors in meiotic chromosome segregation. In this review, we focus on recent biochemical and genetic advances in elucidating the mechanisms of meiotic DNA strand exchange catalyzed by the Dmc1 protein. We also discuss the mode by which two recombination mediators, Hop2 and Mnd1, facilitate rate-limiting steps of DNA strand exchange catalyzed by Dmc1.
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Affiliation(s)
- Christopher L Sansam
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation and the Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Roberto J Pezza
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation and the Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
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Pezza RJ, Voloshin ON, Volodin AA, Boateng KA, Bellani MA, Mazin AV, Camerini-Otero RD. The dual role of HOP2 in mammalian meiotic homologous recombination. Nucleic Acids Res 2013; 42:2346-57. [PMID: 24304900 PMCID: PMC3936763 DOI: 10.1093/nar/gkt1234] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Deletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2–MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2 alone is proficient in promoting strand invasion. We observed that a fraction of Mnd1−/− spermatocytes, which express HOP2 but apparently have inactive DMC1 and RAD51 due to lack of the HOP2–MND1 complex, exhibits a high level of chromosome synapsis and that most DSBs in these spermatocytes are repaired. This suggests that DSB repair catalyzed solely by HOP2 supports homologous chromosome pairing and synapsis. In addition, we show that in vitro HOP2 promotes the co-aggregation of ssDNA with duplex DNA, binds to ssDNA leading to unstacking of the bases, and promotes the formation of a three-strand synaptic intermediate. However, HOP2 shows distinctive mechanistic signatures as a recombinase. Namely, HOP2-mediated strand exchange does not require ATP and, in contrast to DMC1, joint molecules formed by HOP2 are more sensitive to mismatches and are efficiently dissociated by RAD54. We propose that HOP2 may act as a recombinase with specific functions in meiosis.
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Affiliation(s)
- Roberto J Pezza
- Oklahoma Medical Research Foundation, Oklahoma City, 73104 OK, USA, Department of Cell Biology, Oklahoma University Health Science Center, Oklahoma City, 73126 OK, USA, Genetics and Biochemistry Branch, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892 MD, USA, Institute of Molecular Genetics of the Russian Academy of Sciences, 123182 Moscow, Russia, Biomedical Research Center, National Institute of Aging, Baltimore, 21224 MA, USA and Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, 19102 PA, USA
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Equilibrious strand exchange promoted by DNA conformational switching. Sci Rep 2013; 3:1121. [PMID: 23350029 PMCID: PMC3553462 DOI: 10.1038/srep01121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/31/2012] [Indexed: 12/16/2022] Open
Abstract
Most of DNA strand exchange reactions in vitro are based on toehold strategy which is generally nonequilibrium, and intracellular strand exchange mediated by proteins shows little sequence specificity. Herein, a new strand exchange promoted by equilibrious DNA conformational switching is verified. Duplexes containing c-myc sequence which is potentially converted into G-quadruplex are designed in this strategy. The dynamic equilibrium between duplex and G4-DNA is response to the specific exchange of homologous single-stranded DNA (ssDNA). The SER is enzyme free and sequence specific. No ATP is needed and the displaced ssDNAs are identical to the homologous ssDNAs. The SER products and exchange kenetics are analyzed by PAGE and the RecA mediated SER is performed as the contrast. This SER is a new feature of G4-DNAs and a novel strategy to utilize the dynamic equilibrium of DNA conformations.
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Bocharova TN, Smirnova EA, Volodin AA. Linker histone H1 stimulates DNA strand exchange between short oligonucleotides retaining high sensitivity to heterology. Biopolymers 2011; 97:229-39. [PMID: 22113846 DOI: 10.1002/bip.22010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/10/2011] [Accepted: 11/15/2011] [Indexed: 12/30/2022]
Abstract
The interaction of human linker histone H1(0) with short oligonucleotides was characterized. The capability of the histone to promote DNA strand exchange in this system has been demonstrated. The reaction is reversible at saturating amounts of H1 corresponding to complete binding of the oligonucleotide substrates with the histone. In our conditions the complete saturation of DNA with the histone occurs at a ratio of one protein molecule per about 60 nucleotides irrespectively of DNA strandedness. In contrast to the DNA strand exchange promoted by RecA-like enzymes of homologous recombination the H1 promoted reaction exhibits low tolerance to interruptions of homology between oligonucleotide substrates comparable to those for the case of spontaneous strand exchange between free DNA molecules at elevated temperatures and the exchange promoted by some synthetic polycations.
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Affiliation(s)
- Tatiana N Bocharova
- Institute of Molecular Genetics of the Russian Academy of Sciences, 2 Kurchatov sq., 123182 Moscow, Russia
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Bocharova TN, Kvitko NP, Smirnova EA, Volodin AA. Bimodal character of the solubility isotherm of histone H1 complexes with short oligonucleotides. Mol Biol 2011. [DOI: 10.1134/s0026893311020026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tsai YC, Wang Y, Urena DE, Kumar S, Chen J. Heterology tolerance and recognition of mismatched base pairs by human Rad51 protein. DNA Repair (Amst) 2011; 10:363-72. [PMID: 21239234 DOI: 10.1016/j.dnarep.2010.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 12/15/2022]
Abstract
Human Rad51 (hRad51) promoted homology recognition and subsequent strand exchange are the key steps in human homologous recombination mediated repair of DNA double-strand breaks. However, it is still not clear how hRad51 deals with sequence heterology between the two homologous chromosomes in eukaryotic cells, which would lead to mismatched base pairs after strand exchange. Excessive tolerance of sequence heterology may compromise the fidelity of repair of DNA double-strand breaks. In this study, fluorescence resonance energy transfer (FRET) was used to monitor the heterology tolerance of human Rad51 mediated strand exchange reactions, in real time, by introducing either G-T or I-C mismatched base pairs between the two homologous DNA strands. The strand exchange reactions were much more sensitive to G-T than to I-C base pairs. These results imply that the recognition of homology and the tolerance of heterology by hRad51 may depend on the local structural motif adopted by the base pairs participating in strand exchange. AnhRad51 mutant protein (hRad51K133R), deficient in ATP hydrolysis, showed greater heterology tolerance to both types of mismatch base pairing, suggesting that ATPase activity may be important for maintenance of high fidelity homologous recombination DNA repair.
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Affiliation(s)
- Yu-Cheng Tsai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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RecA-Mediated Homology Search as a Nearly Optimal Signal Detection System. Mol Cell 2010; 40:388-96. [DOI: 10.1016/j.molcel.2010.10.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 02/18/2010] [Accepted: 09/08/2010] [Indexed: 11/18/2022]
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