1
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Petiot V, White CI, Da Ines O. DNA-binding site II is required for RAD51 recombinogenic activity in Arabidopsis thaliana. Life Sci Alliance 2024; 7:e202402701. [PMID: 38803223 PMCID: PMC11106524 DOI: 10.26508/lsa.202402701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Homologous recombination is a major pathway for the repair of DNA double strand breaks, essential both to maintain genomic integrity and to generate genetic diversity. Mechanistically, homologous recombination involves the use of a homologous DNA molecule as a template to repair the break. In eukaryotes, the search for and invasion of the homologous DNA molecule is carried out by two recombinases, RAD51 in somatic cells and RAD51 and DMC1 in meiotic cells. During recombination, the recombinases bind overhanging single-stranded DNA ends to form a nucleoprotein filament, which is the active species in promoting DNA invasion and strand exchange. RAD51 and DMC1 carry two major DNA-binding sites-essential for nucleofilament formation and DNA strand exchange, respectively. Here, we show that the function of RAD51 DNA-binding site II is conserved in the plant, Arabidopsis. Mutation of three key amino acids in site II does not affect RAD51 nucleofilament formation but inhibits its recombinogenic activity, analogous to results from studies of the yeast and human proteins. We further confirm that recombinogenic function of RAD51 DNA-binding site II is not required for meiotic double-strand break repair when DMC1 is present. The Arabidopsis AtRAD51-II3A separation of function mutant shows a dominant negative phenotype, pointing to distinct biochemical properties of eukaryotic RAD51 proteins.
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Affiliation(s)
- Valentine Petiot
- https://ror.org/052d1cv78 Institut Génétique, Reproduction et Développement (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles I White
- https://ror.org/052d1cv78 Institut Génétique, Reproduction et Développement (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Olivier Da Ines
- https://ror.org/052d1cv78 Institut Génétique, Reproduction et Développement (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
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2
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Liu S, Shinohara A, Furukohri A. Fanconi anemia-associated mutation in RAD51 compromises the coordinated action of DNA-binding and ATPase activities. J Biol Chem 2023; 299:105424. [PMID: 37924868 PMCID: PMC10716581 DOI: 10.1016/j.jbc.2023.105424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease caused by a defect in DNA repair pathway for DNA interstrand crosslinks. These crosslinks can potentially impede the progression of the DNA replication fork, consequently leading to DNA double-strand breaks. Heterozygous RAD51-Q242R mutation has been reported to cause FA-like symptoms. However, the molecular defect of RAD51 underlying the disease is largely unknown. In this study, we conducted a biochemical analysis of RAD51-Q242R protein, revealing notable deficiencies in its DNA-dependent ATPase activity and its ATP-dependent regulation of DNA-binding activity. Interestingly, although RAD51-Q242R exhibited the filament instability and lacked the ability to form displacement loop, it efficiently stimulated the formation of displacement loops mediated by wild-type RAD51. These findings facilitate understanding of the biochemical properties of the mutant protein and how RAD51 works in the FA patient cells.
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Affiliation(s)
- Sijia Liu
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Asako Furukohri
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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3
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Heemskerk T, van de Kamp G, Essers J, Kanaar R, Paul MW. Multi-scale cellular imaging of DNA double strand break repair. DNA Repair (Amst) 2023; 131:103570. [PMID: 37734176 DOI: 10.1016/j.dnarep.2023.103570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Live-cell and high-resolution fluorescence microscopy are powerful tools to study the organization and dynamics of DNA double-strand break repair foci and specific repair proteins in single cells. This requires specific induction of DNA double-strand breaks and fluorescent markers to follow the DNA lesions in living cells. In this review, where we focused on mammalian cell studies, we discuss different methods to induce DNA double-strand breaks, how to visualize and quantify repair foci in living cells., We describe different (live-cell) imaging modalities that can reveal details of the DNA double-strand break repair process across multiple time and spatial scales. In addition, recent developments are discussed in super-resolution imaging and single-molecule tracking, and how these technologies can be applied to elucidate details on structural compositions or dynamics of DNA double-strand break repair.
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Affiliation(s)
- Tim Heemskerk
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gerarda van de Kamp
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Maarten W Paul
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
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4
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Meng J, Qiu Y, Zhang Y, Zhao H, Shi S. CMI: CRISPR/Cas9 Based Efficient Multiplexed Integration in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1408-1414. [PMID: 36853024 DOI: 10.1021/acssynbio.2c00591] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Genomic integration is the preferred method for gene expression in microbial industrial production. However, traditional homologous recombination based multiplexed integration methods often suffer from low integration efficiency and complex experimental procedures. Here, we report a CRISPR/Cas9 based multiplexed integration (CMI) system in Saccharomyces cerevisiae, which can achieve quadruple integration at an individual locus without pre-engineering the host. A fused protein, Cas9-Brex27, was used as a bait to attract Rad51 recombinase to the proximity of the double-strand breaks introduced by the CRISPR/Cas9 system. The efficiency of quadruple integration was increased to 53.9% with 40 bp homology arms (HAs) and 78% with 100 bp HAs. CMI was applied to integrate a heterologous mogrol biosynthetic pathway consisting of four genes in a one-step transformation and offered an efficient solution for multiplexed integration. This method expands the synthetic biology toolbox of S. cerevisiae.
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Affiliation(s)
- Jie Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Qiu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yueping Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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5
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Meschichi A, Zhao L, Reeck S, White C, Da Ines O, Sicard A, Pontvianne F, Rosa S. The plant-specific DDR factor SOG1 increases chromatin mobility in response to DNA damage. EMBO Rep 2022; 23:e54736. [PMID: 36278395 PMCID: PMC9724665 DOI: 10.15252/embr.202254736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Homologous recombination (HR) is a conservative DNA repair pathway in which intact homologous sequences are used as a template for repair. How the homology search happens in the crowded space of the cell nucleus is, however, still poorly understood. Here, we measure chromosome and double-strand break (DSB) site mobility in Arabidopsis thaliana, using lacO/LacI lines and two GFP-tagged HR reporters. We observe an increase in chromatin mobility upon the induction of DNA damage, specifically at the S/G2 phases of the cell cycle. This increase in mobility is lost in the sog1-1 mutant, a central transcription factor of the DNA damage response in plants. Also, DSB sites show particularly high mobility levels and their enhanced mobility requires the HR factor RAD54. Our data suggest that repair mechanisms promote chromatin mobility upon DNA damage, implying a role of this process in the early steps of the DNA damage response.
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Affiliation(s)
- Anis Meschichi
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Lihua Zhao
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Svenja Reeck
- John Innes Centre, Norwich Research ParkNorwichUK
| | - Charles White
- Institut Génétique Reproduction et Développement (iGReD)Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERMClermont‐FerrandFrance
| | - Olivier Da Ines
- Institut Génétique Reproduction et Développement (iGReD)Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERMClermont‐FerrandFrance
| | - Adrien Sicard
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP)Université de Perpignan Via DomitiaPerpignanFrance
| | - Stefanie Rosa
- Plant Biology DepartmentSwedish University of Agricultural SciencesUppsalaSweden
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6
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DMC1 attenuates RAD51-mediated recombination in Arabidopsis. PLoS Genet 2022; 18:e1010322. [PMID: 36007010 PMCID: PMC9451096 DOI: 10.1371/journal.pgen.1010322] [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: 07/05/2022] [Revised: 09/07/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Ensuring balanced distribution of chromosomes in gametes, meiotic recombination is essential for fertility in most sexually reproducing organisms. The repair of the programmed DNA double strand breaks that initiate meiotic recombination requires two DNA strand-exchange proteins, RAD51 and DMC1, to search for and invade an intact DNA molecule on the homologous chromosome. DMC1 is meiosis-specific, while RAD51 is essential for both mitotic and meiotic homologous recombination. DMC1 is the main catalytically active strand-exchange protein during meiosis, while this activity of RAD51 is downregulated. RAD51 is however an essential cofactor in meiosis, supporting the function of DMC1. This work presents a study of the mechanism(s) involved in this and our results point to DMC1 being, at least, a major actor in the meiotic suppression of the RAD51 strand-exchange activity in plants. Ectopic expression of DMC1 in somatic cells renders plants hypersensitive to DNA damage and specifically impairs RAD51-dependent homologous recombination. DNA damage-induced RAD51 focus formation in somatic cells is not however suppressed by ectopic expression of DMC1. Interestingly, DMC1 also forms damage-induced foci in these cells and we further show that the ability of DMC1 to prevent RAD51-mediated recombination is associated with local assembly of DMC1 at DNA breaks. In support of our hypothesis, expression of a dominant negative DMC1 protein in meiosis impairs RAD51-mediated DSB repair. We propose that DMC1 acts to prevent RAD51-mediated recombination in Arabidopsis and that this down-regulation requires local assembly of DMC1 nucleofilaments. Essential for fertility and responsible for a major part of genetic variation in sexually reproducing species, meiotic recombination establishes the physical linkages between homologous chromosomes which ensure their balanced segregation in the production of gametes. These linkages, or chiasmata, result from DNA strand exchange catalyzed by the RAD51 and DMC1 recombinases and their numbers and distribution are tightly regulated. Essential for maintaining chromosomal integrity in mitotic cells, the strand-exchange activity of RAD51 is downregulated in meiosis, where it plays a supporting role to the activity of DMC1. Notwithstanding considerable attention from the genetics community, precisely why this is done and the mechanisms involved are far from being fully understood. We show here in the plant Arabidopsis that DMC1 can downregulate RAD51 strand-exchange activity and propose that this may be a general mechanism for suppression of RAD51-mediated recombination in meiosis.
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7
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Hu C, Wallace N. Beta HPV Deregulates Double-Strand Break Repair. Viruses 2022; 14:v14050948. [PMID: 35632690 PMCID: PMC9146468 DOI: 10.3390/v14050948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Beta human papillomavirus (beta HPV) infections are common in adults. Certain types of beta HPVs are associated with nonmelanoma skin cancer (NMSC) in immunocompromised individuals. However, whether beta HPV infections promote NMSC in the immunocompetent population is unclear. They have been hypothesized to increase genomic instability stemming from ultraviolet light exposure by disrupting DNA damage responses. Implicit in this hypothesis is that the virus encodes one or more proteins that impair DNA repair signaling. Fluorescence-based reporters, next-generation sequencing, and animal models have been used to test this primarily in cells expressing beta HPV E6/E7. Of the two, beta HPV E6 appears to have the greatest ability to increase UV mutagenesis, by attenuating two major double-strand break (DSB) repair pathways, homologous recombination, and non-homologous end-joining. Here, we review this dysregulation of DSB repair and emerging approaches that can be used to further these efforts.
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8
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Olivier M, Charbonnel C, Amiard S, White CI, Gallego ME. RAD51 and RTEL1 compensate telomere loss in the absence of telomerase. Nucleic Acids Res 2019; 46:2432-2445. [PMID: 29346668 PMCID: PMC5861403 DOI: 10.1093/nar/gkx1322] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/09/2018] [Indexed: 11/23/2022] Open
Abstract
Replicative erosion of telomeres is naturally compensated by telomerase and studies in yeast and vertebrates show that homologous recombination can compensate for the absence of telomerase. We show that RAD51 protein, which catalyzes the key strand-invasion step of homologous recombination, is localized at Arabidopsis telomeres in absence of telomerase. Blocking the strand-transfer activity of the RAD51 in telomerase mutant plants results in a strikingly earlier onset of developmental defects, accompanied by increased numbers of end-to-end chromosome fusions. Imposing replication stress through knockout of RNaseH2 increases numbers of chromosome fusions and reduces the survival of these plants deficient for telomerase and homologous recombination. This finding suggests that RAD51-dependent homologous recombination acts as an essential backup to the telomerase for compensation of replicative telomere loss to ensure genome stability. Furthermore, we show that this positive role of RAD51 in telomere stability is dependent on the RTEL1 helicase. We propose that a RAD51 dependent break-induced replication process is activated in cells lacking telomerase activity, with RTEL1 responsible for D-loop dissolution after telomere replication.
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Affiliation(s)
- Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Cyril Charbonnel
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
| | - Maria E Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293 - INSERM U1103 - Université Clermont Auvergne, Faculté de Médecine. 28, place Henri Dunant - BP38 63001 Clermont-Ferrand Cedex 1, France
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9
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Kobayashi W, Liu E, Ishii H, Matsunaga S, Schlögelhofer P, Kurumizaka H. Homologous pairing activities of Arabidopsis thaliana RAD51 and DMC1. J Biochem 2019; 165:289-295. [PMID: 30517709 DOI: 10.1093/jb/mvy105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/03/2018] [Indexed: 01/17/2023] Open
Abstract
In eukaryotes, homologous recombination plays a pivotal role in both genome maintenance and generation of genetic diversity. Eukaryotic RecA homologues, RAD51 and DMC1, are key proteins in homologous recombination that promote pairing between homologous DNA sequences. Arabidopsis thaliana is a prominent model plant for studying eukaryotic homologous recombination. However, A. thaliana RAD51 and DMC1 have not been biochemically characterized. In the present study, we purified A. thaliana RAD51 (AtRAD51) and DMC1 (AtDMC1). Biochemical analyses revealed that both AtRAD51 and AtDMC1 possess ATP hydrolyzing activity, filament formation activity and homologous pairing activity in vitro. We then compared the homologous pairing activities of AtRAD51 and AtDMC1 with those of the Oryza sativa and Homo sapiens RAD51 and DMC1 proteins.
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Affiliation(s)
- Wataru Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Enwei Liu
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Hajime Ishii
- Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, Japan
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, A-1030 Vienna, Austria
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
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10
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Waterman DP, Zhou F, Li K, Lee CS, Tsabar M, Eapen VV, Mazzella A, Haber JE. Live cell monitoring of double strand breaks in S. cerevisiae. PLoS Genet 2019; 15:e1008001. [PMID: 30822309 PMCID: PMC6415866 DOI: 10.1371/journal.pgen.1008001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/13/2019] [Accepted: 02/01/2019] [Indexed: 11/19/2022] Open
Abstract
We have used two different live-cell fluorescent protein markers to monitor the formation and localization of double-strand breaks (DSBs) in budding yeast. Using GFP derivatives of the Rad51 recombination protein or the Ddc2 checkpoint protein, we find that cells with three site-specific DSBs, on different chromosomes, usually display 2 or 3 foci that may coalesce and dissociate. This motion is independent of Rad52 and microtubules. Rad51-GFP, by itself, is unable to repair DSBs by homologous recombination in mitotic cells, but is able to form foci and allow repair when heterozygous with a wild type Rad51 protein. The kinetics of formation and disappearance of a Rad51-GFP focus parallels the completion of site-specific DSB repair. However, Rad51-GFP is proficient during meiosis when homozygous, similar to rad51 “site II” mutants that can bind single-stranded DNA but not complete strand exchange. Rad52-RFP and Rad51-GFP co-localize to the same DSB, but a significant minority of foci have Rad51-GFP without visible Rad52-RFP. We conclude that co-localization of foci in cells with 3 DSBs does not represent formation of a homologous recombination “repair center,” as the same distribution of Ddc2-GFP foci was found in the absence of the Rad52 protein. Double strand breaks (DSBs) pose the greatest threat to the fidelity of an organism’s genome. While much work has been done on the mechanisms of DSB repair, the arrangement and interaction of multiple DSBs within a single cell remain unclear. Using two live-cell fluorescent DSB markers, we show that cells with 3 site-specific DSBs usually form 2 or 3 foci that can may coalesce into fewer foci but also dissociate. The aggregation and mobility of DSBs into a single focus does not depend on the Rad52 recombination protein that is required for various mechanisms of homologous recombination, suggesting that merging of DSBs does not reflect formation of a homologous recombination repair center.
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Affiliation(s)
- David P. Waterman
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Felix Zhou
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Kevin Li
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Cheng-Sheng Lee
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael Tsabar
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Vinay V. Eapen
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Allison Mazzella
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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11
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Singh G, Da Ines O, Gallego ME, White CI. Analysis of the impact of the absence of RAD51 strand exchange activity in Arabidopsis meiosis. PLoS One 2017; 12:e0183006. [PMID: 28797117 PMCID: PMC5552350 DOI: 10.1371/journal.pone.0183006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/27/2017] [Indexed: 11/21/2022] Open
Abstract
The ploidy of eukaryote gametes must be halved to avoid doubling of numbers of chromosomes with each generation and this is carried out by meiosis, a specialized cell division in which a single chromosomal replication phase is followed by two successive nuclear divisions. With some exceptions, programmed recombination ensures the proper pairing and distribution of homologous pairs of chromosomes in meiosis and recombination defects thus lead to sterility. Two highly related recombinases are required to catalyse the key strand-invasion step of meiotic recombination and it is the meiosis-specific DMC1 which is generally believed to catalyse the essential non-sister chromatid crossing-over, with RAD51 catalysing sister-chromatid and non-cross-over events. Recent work in yeast and plants has however shown that in the absence of RAD51 strand-exchange activity, DMC1 is able to repair all meiotic DNA breaks and surprisingly, that this does not appear to affect numbers of meiotic cross-overs. In this work we confirm and extend this conclusion. Given that more than 95% of meiotic homologous recombination in Arabidopsis does not result in inter-homologue crossovers, Arabidopsis is a particularly sensitive model for testing the relative importance of the two proteins-even minor effects on the non-crossover event population should produce detectable effects on crossing-over. Although the presence of RAD51 protein provides essential support for the action of DMC1, our results show no significant effect of the absence of RAD51 strand-exchange activity on meiotic crossing-over rates or patterns in different chromosomal regions or across the whole genome of Arabidopsis, strongly supporting the argument that DMC1 catalyses repair of all meiotic DNA breaks, not only non-sister cross-overs.
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Affiliation(s)
- Gunjita Singh
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Olivier Da Ines
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
| | - Charles I. White
- Génétique, Reproduction et Dévelopement, UMR CNRS 6293 - INSERM U1103 - Université Cleront Auvergne Campus Universitaire des Cézeaux, Aubiere, France
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12
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Kobayashi W, Hosoya N, Machida S, Miyagawa K, Kurumizaka H. SYCP3 regulates strand invasion activities of RAD51 and DMC1. Genes Cells 2017; 22:799-809. [DOI: 10.1111/gtc.12513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/14/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Wataru Kobayashi
- Laboratory of Structural Biology; Graduate School of Advanced Science and Engineering, Waseda University; 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo 162-8480 Japan
| | - Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine; Graduate School of Medicine, The University of Tokyo; Tokyo 113-8655 Japan
| | - Shinichi Machida
- Laboratory of Structural Biology; Graduate School of Advanced Science and Engineering, Waseda University; 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo 162-8480 Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine; Graduate School of Medicine, The University of Tokyo; Tokyo 113-8655 Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology; Graduate School of Advanced Science and Engineering, Waseda University; 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo 162-8480 Japan
- Institute for Medical-oriented Structural Biology; Waseda University; 2-2 Wakamatsu-cho, Shinjuku-ku Tokyo 162-8480 Japan
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Kobayashi W, Takaku M, Machida S, Tachiwana H, Maehara K, Ohkawa Y, Kurumizaka H. Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing. Sci Rep 2016; 6:24228. [PMID: 27052786 PMCID: PMC4823753 DOI: 10.1038/srep24228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/22/2016] [Indexed: 01/17/2023] Open
Abstract
In eukaryotes, genomic DNA is compacted as chromatin, in which histones and DNA form the nucleosome as the basic unit. DMC1 and RAD51 are essential eukaryotic recombinases that mediate homologous chromosome pairing during homologous recombination. However, the means by which these two recombinases distinctly function in chromatin have remained elusive. Here we found that, in chromatin, the human DMC1-single-stranded DNA complex bypasses binding to the nucleosome, and preferentially promotes homologous pairing at the nucleosome-depleted regions. Consistently, DMC1 forms ternary complex recombination intermediates with the nucleosome-free DNA or the nucleosome-depleted DNA region. Surprisingly, removal of the histone tails improperly enhances the nucleosome binding by DMC1. In contrast, RAD51 does not specifically target the nucleosome-depleted region in chromatin. These are the first demonstrations that the chromatin architecture specifies the sites to promote the homologous recombination reaction by DMC1, but not by RAD51.
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Affiliation(s)
- Wataru Kobayashi
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Motoki Takaku
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science &Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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