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Dumont A, Mendiboure N, Savocco J, Anani L, Moreau P, Thierry A, Modolo L, Jost D, Piazza A. Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae. Mol Cell 2024:S1097-2765(24)00657-9. [PMID: 39178861 DOI: 10.1016/j.molcel.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/26/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
Homology search is a central step of DNA double-strand break (DSB) repair by homologous recombination (HR). How it operates in cells remains elusive. We developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection drives this transition from local to genome-wide search by increasing the probability of assembling extensive NPFs. DSB end-tethering promotes coordinated search by opposite NPFs. Finally, an autonomous genetic element on chromosome III engages the NPF, which stimulates homology search in its vicinity. This work reveals the mechanism of the progressive expansion of homology search that is orchestrated by chromatin organizers, long-range resection, end-tethering, and specialized genetic elements and that exploits the stiff NPF structure conferred by Rad51 oligomerization.
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Affiliation(s)
- Agnès Dumont
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Nicolas Mendiboure
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Jérôme Savocco
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Loqmen Anani
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Pierrick Moreau
- Unité Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525, 75015 Paris, France
| | - Agnès Thierry
- Unité Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525, 75015 Paris, France
| | - Laurent Modolo
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Aurèle Piazza
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France.
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2
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Joo JH, Hong S, Higashide MT, Choi EH, Yoon S, Lee MS, Kang HA, Shinohara A, Kleckner N, Kim KP. RPA interacts with Rad52 to promote meiotic crossover and noncrossover recombination. Nucleic Acids Res 2024; 52:3794-3809. [PMID: 38340339 DOI: 10.1093/nar/gkae083] [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: 02/19/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Meiotic recombination is initiated by programmed double-strand breaks (DSBs). Studies in Saccharomyces cerevisiae have shown that, following rapid resection to generate 3' single-stranded DNA (ssDNA) tails, one DSB end engages a homolog partner chromatid and is extended by DNA synthesis, whereas the other end remains associated with its sister. Then, after regulated differentiation into crossover- and noncrossover-fated types, the second DSB end participates in the reaction by strand annealing with the extended first end, along both pathways. This second-end capture is dependent on Rad52, presumably via its known capacity to anneal two ssDNAs. Here, using physical analysis of DNA recombination, we demonstrate that this process is dependent on direct interaction of Rad52 with the ssDNA binding protein, replication protein A (RPA). Furthermore, the absence of this Rad52-RPA joint activity results in a cytologically-prominent RPA spike, which emerges from the homolog axes at sites of crossovers during the pachytene stage of the meiotic prophase. Our findings suggest that this spike represents the DSB end of a broken chromatid caused by either the displaced leading DSB end or the second DSB end, which has been unable to engage with the partner homolog-associated ssDNA. These and other results imply a close correspondence between Rad52-RPA roles in meiotic recombination and mitotic DSB repair.
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Affiliation(s)
- Jeong H Joo
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Soogil Hong
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Mika T Higashide
- Institute for Protein Research, Graduate School of Science, Osaka University, Osaka 565-0871, Japan
| | - Eui-Hwan Choi
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Deagu 41061, South Korea
| | - Seobin Yoon
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Min-Su Lee
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
| | - Akira Shinohara
- Institute for Protein Research, Graduate School of Science, Osaka University, Osaka 565-0871, Japan
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge 02138, USA
| | - Keun P Kim
- Department of Life Sciences, Chung-Ang University, Seoul 06974, South Korea
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3
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Pan Y, Zhao C, Fu W, Yang S, Lv S. Comparative analysis of structural dynamics and allosteric mechanisms of RecA/Rad51 family proteins: Integrated atomistic MD simulation and network-based analysis. Int J Biol Macromol 2024; 261:129843. [PMID: 38302027 DOI: 10.1016/j.ijbiomac.2024.129843] [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: 08/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Homologous recombination plays a key role in double-strand break repair, stalled replication fork repair, and meiosis. The RecA/Rad51 family recombinases catalyze the DNA strand invasion reaction that occurs during homologous recombination. However, the high sequence differences between homologous groups have hindered the thoroughly studies of this ancient protein family. The dynamic mechanisms of the family, particularly at the residual level, remain poorly understood. In this work, five representative RecA/Rad51 recombinase family members from all major kingdoms of living organisms: prokaryotes, eukaryotes, archaea, and viruses, were selected to explore the molecular mechanisms behind their conserved biological significance. A variety of techniques, including all-atom molecular dynamics simulation, perturbation response scanning, and protein structure network analysis, were used to examine the flexibility and correlation of protein domains, distribution of sensors and effectors and conserved hub residues. Furthermore, the potential communication routes between the ATP-binding region and the DNA-binding region of each recombinase were identified. Our results demonstrate the conserved molecular dynamics of these recombinases in the early stage of homologous recombination, including cooperative motions between regions, conserved sensing and effecting functional residue distribution, and conserved hub residues. Meanwhile, the unique ATP-DNA communication routes of each recombinase was also revealed. These results provide new insights into the mechanism of RecA/Rad51 family proteins, and provide new theoretical guidance for the development of allosteric inhibitors and the application of RecA/Rad51 family proteins.
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Affiliation(s)
- Yue Pan
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Chong Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Wenyu Fu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuo Yang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
| | - Shaowu Lv
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China; Bioarchaeology Laboratory, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
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4
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Luo SC, Yeh MC, Lien YH, Yeh HY, Siao HL, Tu IP, Chi P, Ho MC. A RAD51-ADP double filament structure unveils the mechanism of filament dynamics in homologous recombination. Nat Commun 2023; 14:4993. [PMID: 37591853 PMCID: PMC10435448 DOI: 10.1038/s41467-023-40672-5] [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: 12/28/2022] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
ATP-dependent RAD51 recombinases play an essential role in eukaryotic homologous recombination by catalyzing a four-step process: 1) formation of a RAD51 single-filament assembly on ssDNA in the presence of ATP, 2) complementary DNA strand-exchange, 3) ATP hydrolysis transforming the RAD51 filament into an ADP-bound disassembly-competent state, and 4) RAD51 disassembly to provide access for DNA repairing enzymes. Of these steps, filament dynamics between the ATP- and ADP-bound states, and the RAD51 disassembly mechanism, are poorly understood due to the lack of near-atomic-resolution information of the ADP-bound RAD51-DNA filament structure. We report the cryo-EM structure of ADP-bound RAD51-DNA filaments at 3.1 Å resolution, revealing a unique RAD51 double-filament that wraps around ssDNA. Structural analysis, supported by ATP-chase and time-resolved cryo-EM experiments, reveals a collapsing mechanism involving two four-protomer movements along ssDNA for mechanical transition between RAD51 single- and double-filament without RAD51 dissociation. This mechanism enables elastic change of RAD51 filament length during structural transitions between ATP- and ADP-states.
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Affiliation(s)
- Shih-Chi Luo
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
| | - Min-Chi Yeh
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Yu-Hsiang Lien
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Huei-Lun Siao
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, 11529, Taipei, Taiwan
| | - Peter Chi
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, 10617, Taipei, Taiwan.
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5
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Strelnikova SR, Komakhin RA. Control of meiotic crossing over in plant breeding. Vavilovskii Zhurnal Genet Selektsii 2023; 27:99-110. [PMID: 37063511 PMCID: PMC10090103 DOI: 10.18699/vjgb-23-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/11/2022] [Accepted: 09/26/2022] [Indexed: 04/18/2023] Open
Abstract
Meiotic crossing over is the main mechanism for constructing a new allelic composition of individual chromosomes and is necessary for the proper distribution of homologous chromosomes between gametes. The parameters of meiotic crossing over that have developed in the course of evolution are determined by natural selection and do not fully suit the tasks of selective breeding research. This review summarizes the results of experimental studies aimed at increasing the frequency of crossovers and redistributing their positions along chromosomes using genetic manipulations at different stages of meiotic recombination. The consequences of inactivation and/or overexpression of the SPO11 genes, the products of which generate meiotic double-strand breaks in DNA, for the redistribution of crossover positions in the genome of various organisms are discussed. The results of studies concerning the effect of inactivation or overexpression of genes encoding RecA-like recombinases on meiotic crossing over, including those in cultivated tomato (Solanum lycopersicum L.) and its interspecific hybrids, are summarized. The consequences of inactivation of key genes of the mismatch repair system are discussed. Their suppression made it possible to significantly increase the frequency of meiotic recombination between homeologues in the interspecific hybrid yeast Saccharomyces cerevisiae × S. paradoxus and between homologues in arabidopsis plants (Arabidopsis thaliana L.). Also discussed are attempts to extrapolate these results to other plant species, in which a decrease in reproductive properties and microsatellite instability in the genome have been noted. The most significant results on the meiotic recombination frequency increase upon inactivation of the FANCM, TOP3α, RECQ4, FIGL1 crossover repressor genes and upon overexpression of the HEI10 crossover enhancer gene are separately described. In some experiments, the increase of meiotic recombination frequency by almost an order of magnitude and partial redistribution of the crossover positions along chromosomes were achieved in arabidopsis while fully preserving fecundity. Similar results have been obtained for some crops.
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Affiliation(s)
- S R Strelnikova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - R A Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
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Emmenecker C, Mézard C, Kumar R. Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators. PLANT REPRODUCTION 2023; 36:17-41. [PMID: 35641832 DOI: 10.1007/s00497-022-00443-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Homologous recombination during meiosis is crucial for the DNA double-strand breaks (DSBs) repair that promotes the balanced segregation of homologous chromosomes and enhances genetic variation. In most eukaryotes, two recombinases RAD51 and DMC1 form nucleoprotein filaments on single-stranded DNA generated at DSB sites and play a central role in the meiotic DSB repair and genome stability. These nucleoprotein filaments perform homology search and DNA strand exchange to initiate repair using homologous template-directed sequences located elsewhere in the genome. Multiple factors can regulate the assembly, stability, and disassembly of RAD51 and DMC1 nucleoprotein filaments. In this review, we summarize the current understanding of the meiotic functions of RAD51 and DMC1 and the role of their positive and negative modulators. We discuss the current models and regulators of homology searches and strand exchange conserved during plant meiosis. Manipulation of these repair factors during plant meiosis also holds a great potential to accelerate plant breeding for crop improvements and productivity.
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Affiliation(s)
- Côme Emmenecker
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
- University of Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin (IJPB), CNRS, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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Ziesel A, Weng Q, Ahuja JS, Bhattacharya A, Dutta R, Cheng E, Börner GV, Lichten M, Hollingsworth NM. Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase. PLoS Genet 2022; 18:e1010407. [PMID: 36508468 PMCID: PMC9779700 DOI: 10.1371/journal.pgen.1010407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed DNA double strand breaks (DSBs). 5' end resection of the DSBs creates 3' single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and non-crossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint through the meiosis-specific effector kinase Mek1. This work shows that constitutive activation of Rad51 in Phase 1 results in a subset of DSBs being repaired by a Rad51-mediated interhomolog recombination pathway that is distinct from that of Dmc1. Strand invasion intermediates generated by Rad51 require more time to be processed into recombinants, resulting in a meiotic recombination checkpoint delay in prophase I. Without the checkpoint, Rad51-generated intermediates are more likely to involve a sister chromatid, thereby increasing Meiosis I chromosome nondisjunction. This Rad51 interhomolog recombination pathway is specifically promoted by the conserved 5'-3' helicase PIF1 and its paralog, RRM3 and requires Pif1 helicase activity and its interaction with PCNA. This work demonstrates that (1) inhibition of Rad51 during Phase 1 is important to prevent competition with Dmc1 for DSB repair, (2) Rad51-mediated meiotic recombination intermediates are initially processed differently than those made by Dmc1, and (3) the meiotic recombination checkpoint provides time during prophase 1 for processing of Rad51-generated recombination intermediates.
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Affiliation(s)
- Andrew Ziesel
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Qixuan Weng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Jasvinder S. Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Abhishek Bhattacharya
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Raunak Dutta
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Evan Cheng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - G. Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nancy M. Hollingsworth
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
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8
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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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Xu J, Zhao L, Peng S, Chu H, Liang R, Tian M, Connell PP, Li G, Chen C, Wang HW. Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination. Nucleic Acids Res 2021; 49:13135-13149. [PMID: 34871438 PMCID: PMC8682777 DOI: 10.1093/nar/gkab1141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/01/2021] [Accepted: 11/27/2021] [Indexed: 12/03/2022] Open
Abstract
Homologous recombination (HR) is a primary DNA double-strand breaks (DSBs) repair mechanism. The recombinases Rad51 and Dmc1 are highly conserved in the RecA family; Rad51 is mainly responsible for DNA repair in somatic cells during mitosis while Dmc1 only works during meiosis in germ cells. This spatiotemporal difference is probably due to their distinctive mismatch tolerance during HR: Rad51 does not permit HR in the presence of mismatches, whereas Dmc1 can tolerate certain mismatches. Here, the cryo-EM structures of Rad51-DNA and Dmc1-DNA complexes revealed that the major conformational differences between these two proteins are located in their Loop2 regions, which contain invading single-stranded DNA (ssDNA) binding residues and double-stranded DNA (dsDNA) complementary strand binding residues, stabilizing ssDNA and dsDNA in presynaptic and postsynaptic complexes, respectively. By combining molecular dynamic simulation and single-molecule FRET assays, we identified that V273 and D274 in the Loop2 region of human RAD51 (hRAD51), corresponding to P274 and G275 of human DMC1 (hDMC1), are the key residues regulating mismatch tolerance during strand exchange in HR. This HR accuracy control mechanism provides mechanistic insights into the specific roles of Rad51 and Dmc1 in DNA double-strand break repair and may shed light on the regulatory mechanism of genetic recombination in mitosis and meiosis.
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Affiliation(s)
- Jingfei Xu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Sijia Peng
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Rui Liang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Meng Tian
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Philip P Connell
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60615, USA
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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10
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Le HP, Heyer WD, Liu J. Guardians of the Genome: BRCA2 and Its Partners. Genes (Basel) 2021; 12:genes12081229. [PMID: 34440403 PMCID: PMC8394001 DOI: 10.3390/genes12081229] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/28/2022] Open
Abstract
The tumor suppressor BRCA2 functions as a central caretaker of genome stability, and individuals who carry BRCA2 mutations are predisposed to breast, ovarian, and other cancers. Recent research advanced our mechanistic understanding of BRCA2 and its various interaction partners in DNA repair, DNA replication support, and DNA double-strand break repair pathway choice. In this review, we discuss the biochemical and structural properties of BRCA2 and examine how these fundamental properties contribute to DNA repair and replication fork stabilization in living cells. We highlight selected BRCA2 binding partners and discuss their role in BRCA2-mediated homologous recombination and fork protection. Improved mechanistic understanding of how BRCA2 functions in genome stability maintenance can enable experimental evidence-based evaluation of pathogenic BRCA2 mutations and BRCA2 pseudo-revertants to support targeted therapy.
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Affiliation(s)
- Hang Phuong Le
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA; (H.P.L.); (W.-D.H.)
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA; (H.P.L.); (W.-D.H.)
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA; (H.P.L.); (W.-D.H.)
- Correspondence: ; Tel.: +1-530-752-3016
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11
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Mhaskar AN, Koornneef L, Zelensky AN, Houtsmuller AB, Baarends WM. High Resolution View on the Regulation of Recombinase Accumulation in Mammalian Meiosis. Front Cell Dev Biol 2021; 9:672191. [PMID: 34109178 PMCID: PMC8181746 DOI: 10.3389/fcell.2021.672191] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 11/19/2022] Open
Abstract
A distinguishing feature of meiotic DNA double-strand breaks (DSBs), compared to DSBs in somatic cells, is the fact that they are induced in a programmed and specifically orchestrated manner, which includes chromatin remodeling prior to DSB induction. In addition, the meiotic homologous recombination (HR) repair process that follows, is different from HR repair of accidental DSBs in somatic cells. For instance, meiotic HR involves preferred use of the homolog instead of the sister chromatid as a repair template and subsequent formation of crossovers and non-crossovers in a tightly regulated manner. An important outcome of this distinct repair pathway is the pairing of homologous chromosomes. Central to the initial steps in homology recognition during meiotic HR is the cooperation between the strand exchange proteins (recombinases) RAD51 and its meiosis-specific paralog DMC1. Despite our understanding of their enzymatic activity, details on the regulation of their assembly and subsequent molecular organization at meiotic DSBs in mammals have remained largely enigmatic. In this review, we summarize recent mouse data on recombinase regulation via meiosis-specific factors. Also, we reflect on bulk “omics” studies of initial meiotic DSB processing, compare these with studies using super-resolution microscopy in single cells, at single DSB sites, and explore the implications of these findings for our understanding of the molecular mechanisms underlying meiotic HR regulation.
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Affiliation(s)
- Aditya N Mhaskar
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
| | - Lieke Koornneef
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Erasmus MC, Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Department of Pathology, Erasmus MC, Rotterdam, Netherlands.,Department of Pathology, Erasmus MC, Rotterdam, Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, Rotterdam, Netherlands
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12
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Luo SC, Yeh HY, Lan WH, Wu YM, Yang CH, Chang HY, Su GC, Lee CY, Wu WJ, Li HW, Ho MC, Chi P, Tsai MD. Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures. Nat Commun 2021; 12:115. [PMID: 33446654 PMCID: PMC7809202 DOI: 10.1038/s41467-020-20258-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022] Open
Abstract
Both high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases. RAD51 and DMC1 recombinases catalyse high-fidelity and mismatch tolerant recombination, processes that are indispensable for the maintenance of genomic integrity. Here, the authors via cryo-EM, molecular dynamics simulation and functional analysis elucidate the structural difference between RAD51 and DMC1 with regard to mismatch tolerance.
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Affiliation(s)
- Shih-Chi Luo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wei-Hsuan Lan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yi-Min Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Guan-Chin Su
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chia-Yi Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Peter Chi
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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13
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Correll-Tash S, Lilley B, Salmons Iv H, Mlynarski E, Franconi CP, McNamara M, Woodbury C, Easley CA, Emanuel BS. Double strand breaks (DSBs) as indicators of genomic instability in PATRR-mediated translocations. Hum Mol Genet 2020; 29:3872-3881. [PMID: 33258468 DOI: 10.1093/hmg/ddaa251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/05/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Genomic instability contributes to a variety of potentially damaging conditions, including DNA-based rearrangements. Breakage in the form of double strand breaks (DSBs) increases the likelihood of DNA damage, mutations and translocations. Certain human DNA regions are known to be involved in recurrent translocations, such as the palindrome-mediated rearrangements that have been identified at the breakpoints of several recurrent constitutional translocations: t(11;22)(q23;q11), t(17;22)(q11;q11) and t(8;22) (q24;q11). These breakpoints occur at the center of palindromic AT-rich repeats (PATRRs), which suggests that the structure of the DNA may play a contributory role, potentially through the formation of secondary cruciform structures. The current study analyzed the DSB propensity of these PATRR regions in both lymphoblastoid (mitotic) and spermatogenic cells (meiotic). Initial results found an increased association of sister chromatid exchanges (SCEs) at PATRR regions in experiments that used SCEs to assay DSBs, combining SCE staining with fluorescence in situ hybridization (FISH). Additional experiments used chromatin immunoprecipitation (ChIP) with antibodies for either markers of DSBs or proteins involved in DSB repair along with quantitative polymerase chain reaction to quantify the frequency of DSBs occurring at PATRR regions. The results indicate an increased rate of DSBs at PATRR regions. Additional ChIP experiments with the cruciform binding 2D3 antibody indicate an increased rate of cruciform structures at PATRR regions in both mitotic and meiotic samples. Overall, these experiments demonstrate an elevated rate of DSBs at PATRR regions, an indication that the structure of PATRR containing DNA may lead to increased breakage in multiple cellular environments.
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Affiliation(s)
- Sarah Correll-Tash
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brenna Lilley
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Harold Salmons Iv
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elisabeth Mlynarski
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Colleen P Franconi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Meghan McNamara
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carson Woodbury
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Charles A Easley
- Department of Environmental Health Sciences, College of Public Health at the University of Georgia, Athens, GA, 30602, USA
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
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14
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Chang HY, Lee CY, Lu CH, Lee W, Yang HL, Yeh HY, Li HW, Chi P. Microcephaly family protein MCPH1 stabilizes RAD51 filaments. Nucleic Acids Res 2020; 48:9135-9146. [PMID: 32735676 PMCID: PMC7498314 DOI: 10.1093/nar/gkaa636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/30/2020] [Accepted: 07/22/2020] [Indexed: 01/19/2023] Open
Abstract
Microcephalin 1 (MCPH1) was identified from genetic mutations in patients with primary autosomal recessive microcephaly. In response to DNA double-strand breaks (DSBs), MCPH1 forms damage-induced foci and recruits BRCA2-RAD51 complex, a key component of the DSB repair machinery for homologous recombination (HR), to damage sites. Accordingly, the efficiency of HR is significantly attenuated upon depletion of MCPH1. The biochemical characteristics of MCPH1 and its functional interaction with the HR machinery had remained unclear due to lack of highly purified MCPH1 recombinant protein for functional study. Here, we established a mammalian expression system to express and purify MCPH1 protein. We show that MCPH1 is a bona fide DNA-binding protein and provide direct biochemical analysis of this MCPH family protein. Furthermore, we reveal that MCPH1 directly interacts with RAD51 at multiple contact points, providing evidence for how MCPH1 physically engages with the HR machinery. Importantly, we demonstrate that MCPH1 enhances the stability of RAD51 on single-strand DNA, a prerequisite step for RAD51-mediated recombination. Single-molecule tethered particle motion analysis showed a ∼2-fold increase in the lifetime of RAD51-ssDNA filaments in the presence of MCPH1. Thus, our study demonstrates direct crosstalk between microcephaly protein MCPH1 and the recombination component RAD51 for DSB repair.
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Affiliation(s)
- Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chia-Yi Lee
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chih-Hao Lu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Wei Lee
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Han-Lin Yang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
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15
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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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16
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Hinch AG, Becker PW, Li T, Moralli D, Zhang G, Bycroft C, Green C, Keeney S, Shi Q, Davies B, Donnelly P. The Configuration of RPA, RAD51, and DMC1 Binding in Meiosis Reveals the Nature of Critical Recombination Intermediates. Mol Cell 2020; 79:689-701.e10. [PMID: 32610038 PMCID: PMC7447979 DOI: 10.1016/j.molcel.2020.06.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/07/2020] [Accepted: 06/04/2020] [Indexed: 01/05/2023]
Abstract
Meiotic recombination proceeds via binding of RPA, RAD51, and DMC1 to single-stranded DNA (ssDNA) substrates created after formation of programmed DNA double-strand breaks. Here we report high-resolution in vivo maps of RPA and RAD51 in meiosis, mapping their binding locations and lifespans to individual homologous chromosomes using a genetically engineered hybrid mouse. Together with high-resolution microscopy and DMC1 binding maps, we show that DMC1 and RAD51 have distinct spatial localization on ssDNA: DMC1 binds near the break site, and RAD51 binds away from it. We characterize inter-homolog recombination intermediates bound by RPA in vivo, with properties expected for the critical displacement loop (D-loop) intermediates. These data support the hypothesis that DMC1, not RAD51, performs strand exchange in mammalian meiosis. RPA-bound D-loops can be resolved as crossovers or non-crossovers, but crossover-destined D-loops may have longer lifespans. D-loops resemble crossover gene conversions in size, but their extent is similar in both repair pathways.
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Affiliation(s)
| | - Philipp W Becker
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tao Li
- Howard Hughes Medical Institute, Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Hefei National Laboratory for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Clare Bycroft
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Catherine Green
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Scott Keeney
- Howard Hughes Medical Institute, Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qinghua Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK.
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17
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Rad51 facilitates filament assembly of meiosis-specific Dmc1 recombinase. Proc Natl Acad Sci U S A 2020; 117:11257-11264. [PMID: 32404423 DOI: 10.1073/pnas.1920368117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dmc1 recombinases are essential to homologous recombination in meiosis. Here, we studied the kinetics of the nucleoprotein filament assembly of Saccharomyces cerevisiae Dmc1 using single-molecule tethered particle motion experiments and in vitro biochemical assay. ScDmc1 nucleoprotein filaments are less stable than the ScRad51 ones because of the kinetically much reduced nucleation step. The lower nucleation rate of ScDmc1 results from its lower single-stranded DNA (ssDNA) affinity, compared to that of ScRad51. Surprisingly, ScDmc1 nucleates mostly on the DNA structure containing the single-stranded and duplex DNA junction with the allowed extension in the 5'-to-3' polarity, while ScRad51 nucleation depends strongly on ssDNA lengths. This nucleation preference is also conserved for mammalian RAD51 and DMC1. In addition, ScDmc1 nucleation can be stimulated by short ScRad51 patches, but not by EcRecA ones. Pull-down experiments also confirm the physical interactions of ScDmc1 with ScRad51 in solution, but not with EcRecA. Our results are consistent with a model that Dmc1 nucleation can be facilitated by a structural component (such as DNA junction and protein-protein interaction) and DNA polarity. They provide direct evidence of how Rad51 is required for meiotic recombination and highlight a regulation strategy in Dmc1 nucleoprotein filament assembly.
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18
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Zhao L, He X, Shang Y, Bao C, Peng A, Lei X, Han P, Mi D, Sun Y. Identification of potential radiation-responsive biomarkers based on human orthologous genes with possible roles in DNA repair pathways by comparison between Arabidopsis thaliana and homo sapiens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 702:135076. [PMID: 31734608 DOI: 10.1016/j.scitotenv.2019.135076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Rapid and reliable ionization radiation (IR) exposure estimation has become increasingly important in environment due to the urgent requirement of medical evaluation and treatment in the event of nuclear accident emergency. Human DNA repair genes can be identified as important candidate biomarkers to assess IR exposure, while how to find the enough sensitive and specific biomarkers in the DNA repair networks is still challenged and not fully determined. The conserved features of DNA repair pathways may facilitate interdisciplinary studies that cross the traditional boundaries between animal and plant biology, with the aim of identifying undiscovered human DNA repair genes for potential radiation-responsive biomarkers. In this work, an in silico method of homologous comparison was performed to identify the human orthologues of A. thaliana DNA repair genes, and thereby to explore the sensitive and specific human radiation-responsive genes to evaluate the IR exposure levels. The results showed that a total of 16 putative candidate genes were involved in the human DNA repair pathways of homologous recombination (HR) and non-homologous end joining (NHEJ), and most of them were confirmed by previous experiments. Additionally, we analyzed the gene expression patterns of these 16 candidate genes in several human transcript microarray datasets with different IR treatments. The results indicated that most of the gene expression levels for these candidate genes were significantly changed under different radiation treatments. Based on these results, we integrated these putative human DNA repair genes into the DNA repair pathways to propose new insights of the HR and NHEJ pathways, which can also provide the potential targets for the development of radiation biomarkers. Notably, two putative DNA repair genes, named ERCC1 and ESCO2, were identified and were considered to be the sensitive and specific biomarkers in response to γ-ray exposures.
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Affiliation(s)
- Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Xinye He
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Yuxuan Shang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Chengyu Bao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Ailin Peng
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Xiaohua Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Pei Han
- Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, China
| | - Dong Mi
- College of Science, Dalian Maritime University, Dalian, Liaoning, China.
| | - Yeqing Sun
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China.
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19
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Lu J, Wang C, Wang H, Zheng H, Bai W, Lei D, Tian Y, Xiao Y, You S, Wang Q, Yu X, Liu S, Liu X, Chen L, Jang L, Wang C, Zhao Z, Wan J. OsMFS1/ OsHOP2 Complex Participates in Rice Male and Female Development. FRONTIERS IN PLANT SCIENCE 2020; 11:518. [PMID: 32499797 PMCID: PMC7243175 DOI: 10.3389/fpls.2020.00518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/06/2020] [Indexed: 05/08/2023]
Abstract
Meiosis plays an essential role in the production of gametes and genetic diversity of posterities. The normal double-strand break (DSB) repair is vital to homologous recombination (HR) and occurrence of DNA fragment exchange, but the underlying molecular mechanism remain elusive. Here, we characterized a completely sterile Osmfs1 (male and female sterility 1) mutant which has its pollen and embryo sacs both aborted at the reproductive stage due to severe chromosome defection. Map-based cloning revealed that the OsMFS1 encodes a meiotic coiled-coil protein, and it is responsible for DSB repairing that acts as an important cofactor to stimulate the single strand invasion. Expression pattern analyses showed the OsMFS1 was preferentially expressed in meiosis stage. Subcellular localization analysis of OsMFS1 revealed its association with the nucleus exclusively. In addition, a yeast two-hybrid (Y2H) and pull-down assay showed that OsMFS1 could physically interact with OsHOP2 protein to form a stable complex to ensure faithful homologous recombination. Taken together, our results indicated that OsMFS1 is indispensable to the normal development of anther and embryo sacs in rice.
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Affiliation(s)
- Jiayu Lu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Chaolong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Haiyu Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Hai Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Wenting Bai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Dekun Lei
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Yanjia Xiao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shimin You
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Qiming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Liangming Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Ling Jang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Chunming Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhigang Zhao,
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Jianmin Wan, ;
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20
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Reitz D, Grubb J, Bishop DK. A mutant form of Dmc1 that bypasses the requirement for accessory protein Mei5-Sae3 reveals independent activities of Mei5-Sae3 and Rad51 in Dmc1 filament stability. PLoS Genet 2019; 15:e1008217. [PMID: 31790385 PMCID: PMC6907854 DOI: 10.1371/journal.pgen.1008217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 12/12/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022] Open
Abstract
During meiosis, homologous recombination repairs programmed DNA double-stranded breaks. Meiotic recombination physically links the homologous chromosomes (“homologs”), creating the tension between them that is required for their segregation. The central recombinase in this process is Dmc1. Dmc1’s activity is regulated by its accessory factors including the heterodimeric protein Mei5-Sae3 and Rad51. We use a gain-of-function dmc1 mutant, dmc1-E157D, that bypasses Mei5-Sae3 to gain insight into the role of this accessory factor and its relationship to mitotic recombinase Rad51, which also functions as a Dmc1 accessory protein during meiosis. We find that Mei5-Sae3 has a role in filament formation and stability, but not in the bias of recombination partner choice that favors homolog over sister chromatids. Analysis of meiotic recombination intermediates suggests that Mei5-Sae3 and Rad51 function independently in promoting filament stability. In spite of its ability to load onto single-stranded DNA and carry out recombination in the absence of Mei5-Sae3, recombination promoted by the Dmc1 mutant is abnormal in that it forms foci in the absence of DNA breaks, displays unusually high levels of multi-chromatid and intersister joint molecule intermediates, as well as high levels of ectopic recombination products. We use super-resolution microscopy to show that the mutant protein forms longer foci than those formed by wild-type Dmc1. Our data support a model in which longer filaments are more prone to engage in aberrant recombination events, suggesting that filament lengths are normally limited by a regulatory mechanism that functions to prevent recombination-mediated genome rearrangements. During meiosis, two rounds of division follow a single round of DNA replication to create the gametes for biparental reproduction. The first round of division requires that the homologous chromosomes become physically linked to one another to create the tension that is necessary for their segregation. This linkage is achieved through DNA recombination between the two homologous chromosomes, followed by resolution of the recombination intermediate into a crossover. Central to this process is the meiosis-specific recombinase Dmc1, and its accessory factors, which provide important regulatory functions to ensure that recombination is accurate, efficient, and occurs predominantly between homologous chromosomes, and not sister chromatids. To gain insight into the regulation of Dmc1 by its accessory factors, we mutated Dmc1 such that it was no longer dependent on its accessory factor Mei5-Sae3. Our analysis reveals that Dmc1 accessory factors Mei5-Sae3 and Rad51 have independent roles in stabilizing Dmc1 filaments. Furthermore, we find that although Rad51 is required for promoting recombination between homologous chromosomes, Mei5-Sae3 is not. Lastly, we show that our Dmc1 mutant forms abnormally long filaments, and high levels of aberrant recombination intermediates and products. These findings suggest that filaments are actively maintained at short lengths to prevent deleterious genome rearrangements.
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Affiliation(s)
- Diedre Reitz
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Jennifer Grubb
- Department of Radiation and Cellular Oncology, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Douglas K. Bishop
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Radiation and Cellular Oncology, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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21
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Ciudad T, Bellido A, Hermosa B, Andaluz E, Larriba G. DLH1, the Candida albicans homologue of the meiosis-specific DMC1, is not involved in DNA repair but catalyses spontaneous interhomologue recombination and might promote non-crossover events. Cell Microbiol 2019; 22:e13137. [PMID: 31701646 DOI: 10.1111/cmi.13137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Toni Ciudad
- Departamento de Ciencias Biomédicas, Facultad de Ciencias, Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
| | - Alberto Bellido
- Departamento de Ciencias Biomédicas, Facultad de Ciencias, Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
| | - Belén Hermosa
- Departamento de Ciencias Biomédicas, Facultad de Ciencias, Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
| | - Encarnación Andaluz
- Departamento de Ciencias Biomédicas, Facultad de Ciencias, Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
| | - Germán Larriba
- Departamento de Ciencias Biomédicas, Facultad de Ciencias, Área de Microbiología, Universidad de Extremadura, Badajoz, Spain
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22
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Steinfeld JB, Beláň O, Kwon Y, Terakawa T, Al-Zain A, Smith MJ, Crickard JB, Qi Z, Zhao W, Rothstein R, Symington LS, Sung P, Boulton SJ, Greene EC. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev 2019; 33:1191-1207. [PMID: 31371435 PMCID: PMC6719624 DOI: 10.1101/gad.328062.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
The vast majority of eukaryotes possess two DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. The evolutionary origins of this two-recombinase system remain poorly understood. Interestingly, Dmc1 can stabilize mismatch-containing base triplets, whereas Rad51 cannot. Here, we demonstrate that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family. Chimeric Rad51 mutants harboring Dmc1-specific amino acids gain the ability to stabilize heteroduplex DNA joints with mismatch-containing base triplets, whereas Dmc1 mutants with Rad51-specific amino acids lose this ability. Remarkably, RAD-51 from Caenorhabditis elegans, an organism without Dmc1, has acquired "Dmc1-like" amino acids. Chimeric C. elegans RAD-51 harboring "canonical" Rad51 amino acids gives rise to toxic recombination intermediates, which must be actively dismantled to permit normal meiotic progression. We propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.
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Affiliation(s)
- Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Ondrej Beláň
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Amr Al-Zain
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Michael J Smith
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Zhi Qi
- Center for Quantitative Biology, Peking University-Tsinghua University Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
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23
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Srs2 helicase prevents the formation of toxic DNA damage during late prophase I of yeast meiosis. Chromosoma 2019; 128:453-471. [DOI: 10.1007/s00412-019-00709-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 12/24/2022]
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24
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Stabilization of the Human DMC1 Nucleoprotein Filament. Methods Mol Biol 2019. [PMID: 31127585 DOI: 10.1007/978-1-4939-9500-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The meiosis-specific recombinase, DMC1, is important for the generation of haploids during meiosis. DMC1 forms a helical nucleoprotein filament on ssDNA overhangs located at the processed double-stranded DNA break. The DMC1 filament performs a search for homology in homologous chromosome. Once homology is located, the DMC1 filament strand invades the homologous chromosome forming a displacement loop (D-loop). These connections are needed for accurate segregation to occur later in meiosis. Because DMC1 requires numerous accessory factors and specific ionic conditions to participate in this DNA repair process, in vitro assays were developed to understand how these accessory factors influence the biochemical properties of hDMC1. This chapter describes a method that can be used to investigate the stability of the human DMC1 nucleoprotein filament under various conditions and provides insight into an important early stage in DNA double-strand break repair by homologous recombination during meiosis.
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25
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Colas I, Barakate A, Macaulay M, Schreiber M, Stephens J, Vivera S, Halpin C, Waugh R, Ramsay L. desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 in barley. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2683-2698. [PMID: 31028386 PMCID: PMC6509107 DOI: 10.1093/jxb/erz080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/28/2019] [Indexed: 05/03/2023]
Abstract
Despite conservation of the process of meiosis, recombination landscapes vary between species, with large genome grasses such as barley (Hordeum vulgare L.) exhibiting a pattern of recombination that is very heavily skewed to the ends of chromosomes. We have been using a collection of semi-sterile desynaptic meiotic mutant lines to help elucidate how recombination is controlled in barley and the role of the corresponding wild-type (WT) meiotic genes within this process. Here we applied a combination of genetic segregation analysis, cytogenetics, and immunocytology to genetically map and characterize the meiotic mutant desynaptic5 (des5). We identified an exonic insertion in the positional candidate ortholog of Disrupted Meiotic cDNA 1 (HvDMC1) on chromosome 5H of des5. des5 exhibits a severe meiotic phenotype with disturbed synapsis, reduced crossovers, and chromosome mis-segregation. The meiotic phenotype and reduced fertility of des5 is similarly observed in Hvdmc1RNAi transgenic plants and HvDMC1p:GusPlus reporter lines show DMC1 expression specifically in the developing inflorescence. The des5 mutation maintains the reading frame of the gene and exhibits semi-dominance with respect to recombination in the heterozygote indicating the value of non-knockout mutations for dissection of the control of recombination in the early stages of meiosis.
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Affiliation(s)
- Isabelle Colas
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Abdellah Barakate
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Sebastian Vivera
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Claire Halpin
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
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26
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Crickard JB, Kwon Y, Sung P, Greene EC. Dynamic interactions of the homologous pairing 2 (Hop2)-meiotic nuclear divisions 1 (Mnd1) protein complex with meiotic presynaptic filaments in budding yeast. J Biol Chem 2019; 294:490-501. [PMID: 30420424 PMCID: PMC6333877 DOI: 10.1074/jbc.ra118.006146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/02/2018] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination (HR) is a universally conserved DNA repair pathway that can result in the exchange of genetic material. In eukaryotes, HR has evolved into an essential step in meiosis. During meiosis many eukaryotes utilize a two-recombinase pathway. This system consists of Rad51 and the meiosis-specific recombinase Dmc1. Both recombinases have distinct activities during meiotic HR, despite being highly similar in sequence and having closely related biochemical activities, raising the question of how these two proteins can perform separate functions. A likely explanation for their differential regulation involves the meiosis-specific recombination proteins Hop2 and Mnd1, which are part of a highly conserved eukaryotic protein complex that participates in HR, albeit through poorly understood mechanisms. To better understand how Hop2-Mnd1 functions during HR, here we used DNA curtains in conjunction with single-molecule imaging to measure and quantify the binding of the Hop2-Mnd1 complex from Saccharomyces cerevisiae to recombination intermediates comprising Rad51- and Dmc1-ssDNA in real time. We found that yeast Hop2-Mnd1 bound rapidly to Dmc1-ssDNA filaments with high affinity and remained bound for ∼1.3 min before dissociating. We also observed that this binding interaction was highly specific for Dmc1 and found no evidence for an association of Hop2-Mnd1 with Rad51-ssDNA or RPA-ssDNA. Our findings provide new quantitative insights into the binding dynamics of Hop2-Mnd1 with the meiotic presynaptic complex. On the basis of these findings, we propose a model in which recombinase specificities for meiotic accessory proteins enhance separation of the recombinases' functions during meiotic HR.
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Affiliation(s)
- J Brooks Crickard
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Youngho Kwon
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
- the Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
- the Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229
| | - Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032,
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27
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Abstract
Meiosis is the basis for sexual reproduction and is marked by the sequential reduction of chromosome number during successive cell cycles, resulting in four haploid gametes. A central component of the meiotic program is the formation and repair of programmed double strand breaks. Recombination-driven repair of these meiotic breaks differs from recombination during mitosis in that meiotic breaks are preferentially repaired using the homologous chromosomes in a process known as homolog bias. Homolog bias allows for physical interactions between homologous chromosomes that are required for proper chromosome segregation, and the formation of crossover products ensuring genetic diversity in progeny. An important aspect of meiosis in the differential regulation of the two eukaryotic RecA homologs, Rad51 and Dmc1. In this review we will discuss the relationship between biological programs designed to regulate recombinase function.
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Affiliation(s)
- J Brooks Crickard
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
| | - Eric C Greene
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
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28
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Braslavsky I, Stavans J. Application of Algebraic Topology to Homologous Recombination of DNA. iScience 2018; 4:64-67. [PMID: 30240753 PMCID: PMC6146625 DOI: 10.1016/j.isci.2018.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/30/2018] [Accepted: 05/11/2018] [Indexed: 11/23/2022] Open
Abstract
Brouwer's fixed point theorem, a fundamental theorem in algebraic topology proved more than a hundred years ago, states that given any continuous map from a closed, simply connected set into itself, there is a point that is mapped unto itself. Here we point out the connection between a one-dimensional application of Brouwer's fixed point theorem and a mechanism proposed to explain how extension of single-stranded DNA substrates by recombinases of the RecA superfamily facilitates significantly the search for homologous sequences on long chromosomes. RecA family recombinases stretch their DNA substrates by 1.5 Stretching facilitates the search for homologous genomic targets during recombination This facilitating mechanism derives from a foundational theorem of Algebraic Topology
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Affiliation(s)
- Ido Braslavsky
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel.
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel.
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29
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Crickard JB, Kaniecki K, Kwon Y, Sung P, Lisby M, Greene EC. Regulation of Hed1 and Rad54 binding during maturation of the meiosis-specific presynaptic complex. EMBO J 2018; 37:embj.201798728. [PMID: 29444896 DOI: 10.15252/embj.201798728] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/03/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
Most eukaryotes have two Rad51/RecA family recombinases, Rad51, which promotes recombination during mitotic double-strand break (DSB) repair, and the meiosis-specific recombinase Dmc1. During meiosis, the strand exchange activity of Rad51 is downregulated through interactions with the meiosis-specific protein Hed1, which helps ensure that strand exchange is driven by Dmc1 instead of Rad51. Hed1 acts by preventing Rad51 from interacting with Rad54, a cofactor required for promoting strand exchange during homologous recombination. However, we have a poor quantitative understanding of the regulatory interplay between these proteins. Here, we use real-time single-molecule imaging to probe how the Hed1- and Rad54-mediated regulatory network contributes to the identity of mitotic and meiotic presynaptic complexes. Based on our findings, we define a model in which kinetic competition between Hed1 and Rad54 helps define the functional identity of the presynaptic complex as cells undergo the transition from mitotic to meiotic repair.
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Affiliation(s)
- J Brooks Crickard
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kyle Kaniecki
- Department of Genetics and Development, Columbia University, New York, NY, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, USA
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30
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Zhao L, Xu J, Zhao W, Sung P, Wang HW. Determining the RAD51-DNA Nucleoprotein Filament Structure and Function by Cryo-Electron Microscopy. Methods Enzymol 2018; 600:179-199. [PMID: 29458758 DOI: 10.1016/bs.mie.2017.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Homologous recombination is a universal tool for DNA double-strand break and replication fork repair, and it is catalyzed by a highly conserved family of recombinases. In eukaryotes, Rad51 is the recombinase that catalyzes the pairing of homologous DNA molecules and the exchange of strands between the paired molecules. Rad51 assembles on single-stranded DNA (ssDNA) stemming from lesion processing to form a right-handed helical polymer that engages then samples double-stranded DNA (dsDNA) for homology. Upon matching with a homologous sequence, the Rad51-bound ssDNA invades the dsDNA, leading to the formation of a DNA joint with concomitant displacement of the strand of like polarity. The Rad51-DNA filaments are amenable to structural studies using cryo-electron microscopy (cryo-EM). In particular, recent technical breakthroughs in cryo-EM have made it possible to define the structure and function of human RAD51 at near-atomic resolution. In this chapter, we describe our cryo-EM approach to capture the human RAD51 filament structures in various stages of catalysis. The approach may also be useful for related recombinases and other helical assemblies.
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Affiliation(s)
- Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jingfei Xu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | | | | | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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31
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Crickard JB, Kaniecki K, Kwon Y, Sung P, Greene EC. Spontaneous self-segregation of Rad51 and Dmc1 DNA recombinases within mixed recombinase filaments. J Biol Chem 2018; 293:4191-4200. [PMID: 29382724 DOI: 10.1074/jbc.ra117.001143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/06/2018] [Indexed: 11/06/2022] Open
Abstract
During meiosis, the two DNA recombinases Rad51 and Dmc1 form specialized presynaptic filaments that are adapted for performing recombination between homologous chromosomes. There is currently a limited understanding of how these two recombinases are organized within the meiotic presynaptic filament. Here, we used single molecule imaging to examine the properties of presynaptic complexes composed of both Rad51 and Dmc1. We demonstrate that Rad51 and Dmc1 have an intrinsic ability to self-segregate, even in the absence of any other recombination accessory proteins. Moreover, we found that the presence of Dmc1 stabilizes the adjacent Rad51 filaments, suggesting that cross-talk between these two recombinases may affect their biochemical properties. Based upon these findings, we describe a model for the organization of Rad51 and Dmc1 within the meiotic presynaptic complex, which is also consistent with in vivo observations, genetic findings, and biochemical expectations. This model argues against the existence of extensively intermixed filaments, and we propose that Rad51 and Dmc1 have intrinsic capacities to form spatially distinct filaments, suggesting that additional recombination cofactors are not required to segregate the Rad51 and Dmc1 filaments.
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Affiliation(s)
- J Brooks Crickard
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032
| | - Kyle Kaniecki
- Department of Genetics and Development, Columbia University, New York, New York, 10032, and
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, 06520
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, 06520
| | - Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032,
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32
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He WB, Tu CF, Liu Q, Meng LL, Yuan SM, Luo AX, He FS, Shen J, Li W, Du J, Zhong CG, Lu GX, Lin G, Fan LQ, Tan YQ. DMC1 mutation that causes human non-obstructive azoospermia and premature ovarian insufficiency identified by whole-exome sequencing. J Med Genet 2018; 55:198-204. [PMID: 29331980 DOI: 10.1136/jmedgenet-2017-104992] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/05/2017] [Accepted: 12/11/2017] [Indexed: 11/03/2022]
Abstract
BACKGROUND The genetic causes of the majority of male and female infertility caused by human non-obstructive azoospermia (NOA) and premature ovarian insufficiency (POI) with meiotic arrest are unknown. OBJECTIVE To identify the genetic cause of NOA and POI in two affected members from a consanguineous Chinese family. METHODS We performed whole-exome sequencing of DNA from both affected patients. The identified candidate causative gene was further verified by Sanger sequencing for pedigree analysis in this family. In silico analysis was performed to functionally characterise the mutation, and histological analysis was performed using the biopsied testicle sample from the male patient with NOA. RESULTS We identified a novel homozygous missense mutation (NM_007068.3: c.106G>A, p.Asp36Asn) in DMC1, which cosegregated with NOA and POI phenotypes in this family. The identified missense mutation resulted in the substitution of a conserved aspartic residue with asparaginate in the modified H3TH motif of DMC1. This substitution results in protein misfolding. Histological analysis demonstrated a lack of spermatozoa in the male patient's seminiferous tubules. Immunohistochemistry using a testis biopsy sample from the male patient showed that spermatogenesis was blocked at the zygotene stage during meiotic prophase I. CONCLUSIONS To the best of our knowledge, this is the first report identifying DMC1 as the causative gene for human NOA and POI. Furthermore, our pedigree analysis shows an autosomal recessive mode of inheritance for NOA and POI caused by DMC1 in this family.
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Affiliation(s)
- Wen-Bin He
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Chao-Feng Tu
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Qiang Liu
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Hunan Cancer Hospital and The Affiliated Cancer of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lan-Lan Meng
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Shi-Min Yuan
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ai-Xiang Luo
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | | | - Juan Shen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wen Li
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Chang-Gao Zhong
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Guang-Xiu Lu
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Li-Qing Fan
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.,National Engineering and Research Center of Human Stem Cell, Changsha, China
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33
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Dai J, Voloshin O, Potapova S, Camerini-Otero RD. Meiotic Knockdown and Complementation Reveals Essential Role of RAD51 in Mouse Spermatogenesis. Cell Rep 2017; 18:1383-1394. [PMID: 28178517 DOI: 10.1016/j.celrep.2017.01.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/30/2016] [Accepted: 01/11/2017] [Indexed: 12/21/2022] Open
Abstract
Meiotic homologous recombination (HR) is important for proper chromosomal segregation during gametogenesis and facilitates evolutionary adaptation via genomic reshuffling. In most eukaryotes, HR is mediated by two recombinases, the ubiquitous RAD51 and the meiosis-specific DMC1. The role of RAD51 in mammalian meiosis is unclear and study of its function is limited due to embryonic lethality of RAD51 knockouts. Here, we developed an in vivo meiotic knockdown and protein complementation system to study RAD51 during mouse spermatogenesis. We show that RAD51 is crucial during meiotic prophase and its loss leads to depletion of late prophase I spermatocytes through a p53-dependent apoptotic pathway. This phenotype is distinct from that observed in the DMC1 knockdown. Our meiotic knockdown and complementation system establishes an experimental platform for mechanistic studies of meiotic proteins with unknown functions or essential genes for which a testis-specific knockout is not possible.
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Affiliation(s)
- Jieqiong Dai
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Oleg Voloshin
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Svetlana Potapova
- Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - R Daniel Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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34
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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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35
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Lee JY, Steinfeld JB, Qi Z, Kwon Y, Sung P, Greene EC. Sequence imperfections and base triplet recognition by the Rad51/RecA family of recombinases. J Biol Chem 2017; 292:11125-11135. [PMID: 28476890 DOI: 10.1074/jbc.m117.787614] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/27/2017] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination plays key roles in double-strand break repair, rescue, and repair of stalled replication forks and meiosis. The broadly conserved Rad51/RecA family of recombinases catalyzes the DNA strand invasion reaction that takes place during homologous recombination. We have established single-stranded (ss)DNA curtain assays for measuring individual base triplet steps during the early stages of strand invasion. Here, we examined how base triplet stepping by RecA, Rad51, and Dmc1 is affected by DNA sequence imperfections, such as single and multiple mismatches, abasic sites, and single nucleotide insertions. Our work reveals features of base triplet stepping that are conserved among these three phylogenetic lineages of the Rad51/RecA family and also reveals lineage-specific behaviors reflecting properties that are unique to each recombinase. These findings suggest that Dmc1 is tolerant of single mismatches, multiple mismatches, and even abasic sites, whereas RecA and Rad51 are not. Interestingly, the presence of single nucleotide insertion abolishes recognition of an adjacent base triplet by all three recombinases. On the basis of these findings, we describe models for how sequence imperfections may affect base triplet recognition by Rad51/RecA family members, and we discuss how these models and our results may relate to the different biological roles of RecA, Rad51, and Dmc1.
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Affiliation(s)
- Ja Yil Lee
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Justin B Steinfeld
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Zhi Qi
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - YoungHo Kwon
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032 and
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36
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Zhang P, Zhang Y, Sun L, Sinumporn S, Yang Z, Sun B, Xuan D, Li Z, Yu P, Wu W, Wang K, Cao L, Cheng S. The Rice AAA-ATPase OsFIGNL1 Is Essential for Male Meiosis. FRONTIERS IN PLANT SCIENCE 2017; 8:1639. [PMID: 29021797 PMCID: PMC5624289 DOI: 10.3389/fpls.2017.01639] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/06/2017] [Indexed: 05/18/2023]
Abstract
Meiosis is crucial in reproduction of plants and ensuring genetic diversity. Although several genes involved in homologous recombination and DNA repair have been reported, their functions in rice (Oryza sativa) male meiosis remain poorly understood. Here, we isolated and characterized the rice OsFIGNL1 (OsFidgetin-like 1) gene, encoding a conserved AAA-ATPase, and explored its function and importance in male meiosis and pollen formation. The rice Osfignl1 mutant exhibited normal vegetative growth, but failed to produce seeds and displayed pollen abortion phenotype. Phenotypic comparisons between the wild-type and Osfignl1 mutant demonstrated that OsFIGNL1 is required for anther development, and that the recessive mutation of this gene causes male sterility in rice. Complementation and CRISPR/Cas9 experiments demonstrated that wild-type OsFIGNL1 is responsible for the male sterility phenotype. Subcellular localization showed that OsFIGNL1-green fluorescent protein was exclusively localized in the nucleus of rice protoplasts. Male meiosis in the Osfignl1 mutant exhibited abnormal chromosome behavior, including chromosome bridges and multivalent chromosomes at diakinesis, lagging chromosomes, and chromosome fragments during meiosis. Yeast two-hybrid assays demonstrated OsFIGNL1 could interact with RAD51A1, RAD51A2, DMC1A, DMC1B, and these physical interactions were further confirmed by BiFC assay. Taken together, our results suggest that OsFIGNL1 plays an important role in regulation of male meiosis and anther development.
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Affiliation(s)
- Peipei Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Sittipun Sinumporn
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhengfu Yang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Bin Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dandan Xuan
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zihe Li
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ping Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Weixun Wu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Kejian Wang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Liyong Cao, Shihua Cheng,
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Liyong Cao, Shihua Cheng,
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Kelso AA, Goodson SD, Chavan S, Say AF, Turchick A, Sharma D, Ledford LL, Ratterman E, Leskoske K, King AV, Attaway CC, Bandera Y, Foulger SH, Mazin AV, Temesvari LA, Sehorn MG. Characterization of the recombination activities of the Entamoeba histolytica Rad51 recombinase. Mol Biochem Parasitol 2016; 210:71-84. [PMID: 27678398 DOI: 10.1016/j.molbiopara.2016.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/10/2016] [Accepted: 09/02/2016] [Indexed: 11/29/2022]
Abstract
The protozoan parasite responsible for human amoebiasis is Entamoeba histolytica. An important facet of the life cycle of E. histolytica involves the conversion of the mature trophozoite to a cyst. This transition is thought to involve homologous recombination (HR), which is dependent upon the Rad51 recombinase. Here, a biochemical characterization of highly purified ehRad51 protein is presented. The ehRad51 protein preferentially binds ssDNA, forms a presynaptic filament and possesses ATP hydrolysis activity that is stimulated by the presence of DNA. Evidence is provided that ehRad51 catalyzes robust DNA strand exchange over at least 5.4 kilobase pairs. Although the homologous DNA pairing activity of ehRad51 is weak, it is strongly enhanced by the presence of two HR accessory cofactors, calcium and Hop2-Mnd1. The biochemical system described herein was used to demonstrate the potential for targeting ehRad51 with two small molecule inhibitors of human RAD51. We show that 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS) inhibited ehRad51 by interfering with DNA binding and attenuated encystation in Entamoeba invadens, while B02 had no effect on ehRad51 strand exchange activity. These results provide insight into the underlying mechanism of homology-directed DNA repair in E. histolytica.
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Affiliation(s)
- Andrew A Kelso
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, USA
| | - Steven D Goodson
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, USA
| | - Suchitra Chavan
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, USA; Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Amanda F Say
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Audrey Turchick
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Deepti Sharma
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - LeAnna L Ledford
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Erin Ratterman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Kristin Leskoske
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Ada V King
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | | | - Yura Bandera
- Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, SC 29634, USA; Department of Material Science and Engineering, Clemson University, Clemson, SC 29634, USA
| | - Stephen H Foulger
- Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, SC 29634, USA; Department of Material Science and Engineering, Clemson University, Clemson, SC 29634, USA
| | - Alexander V Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Lesly A Temesvari
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, USA; Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; Clemson University School of Health Research, Clemson, SC 29634, USA
| | - Michael G Sehorn
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA; Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, SC 29634, USA; Clemson University School of Health Research, Clemson, SC 29634, USA.
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38
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Lee JY, Qi Z, Greene EC. ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex. J Biol Chem 2016; 291:22218-22230. [PMID: 27587394 DOI: 10.1074/jbc.m116.740563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 01/13/2023] Open
Abstract
Homologous recombination is an important DNA repair pathway that plays key roles in maintaining genome stability. Escherichia coli RecA is an ATP-dependent DNA-binding protein that catalyzes the DNA strand exchange reactions in homologous recombination. RecA assembles into long helical filaments on single-stranded DNA, and these presynaptic complexes are responsible for locating and pairing with a homologous duplex DNA. Recent single molecule studies have provided new insights into RecA behavior, but the potential influence of ATP in the reactions remains poorly understood. Here we examine how ATP influences the ability of the RecA presynaptic complex to interact with homologous dsDNA. We demonstrate that over short time regimes, RecA presynaptic complexes sample heterologous dsDNA similarly in the presence of either ATP or ATPγS, suggesting that initial interactions do not depend on ATP hydrolysis. In addition, RecA stabilizes pairing intermediates in three-base steps, and stepping energetics is seemingly unaltered in the presence of ATP. However, the overall dissociation rate of these paired intermediates with ATP is ∼4-fold higher than with ATPγS. These experiments suggest that ATP plays an unanticipated role in promoting the turnover of captured duplex DNA intermediates as RecA attempts to align homologous sequences during the early stages of recombination.
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Affiliation(s)
- Ja Yil Lee
- From the Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032 and
| | - Zhi Qi
- the Center of Quantitative Biology & Center of Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
| | - Eric C Greene
- From the Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York 10032 and
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39
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Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8403-8412. [PMID: 27479732 DOI: 10.1021/acs.langmuir.6b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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Affiliation(s)
| | | | | | - Joshua Araya
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Erik Werner
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Ali Çakır
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , 751 24 Uppsala, Sweden
| | - Edwige B Garcin
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
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40
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Abstract
Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination.
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Affiliation(s)
- Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
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41
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Marsh ME, Scott DE, Ehebauer MT, Abell C, Blundell TL, Hyvönen M. ATP half-sites in RadA and RAD51 recombinases bind nucleotides. FEBS Open Bio 2016; 6:372-85. [PMID: 27419043 PMCID: PMC4856416 DOI: 10.1002/2211-5463.12052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination is essential for repair of DNA double-strand breaks. Central to this process is a family of recombinases, including archeal RadA and human RAD51, which form nucleoprotein filaments on damaged single-stranded DNA ends and facilitate their ATP-dependent repair. ATP binding and hydrolysis are dependent on the formation of a nucleoprotein filament comprising RadA/RAD51 and single-stranded DNA, with ATP bound between adjacent protomers. We demonstrate that truncated, monomeric Pyrococcus furiosus RadA and monomerised human RAD51 retain the ability to bind ATP and other nucleotides with high affinity. We present crystal structures of both apo and nucleotide-bound forms of monomeric RadA. These structures reveal that while phosphate groups are tightly bound, RadA presents a shallow, poorly defined binding surface for the nitrogenous bases of nucleotides. We suggest that RadA monomers would be constitutively bound to nucleotides in the cell and that the bound nucleotide might play a structural role in filament assembly.
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Affiliation(s)
- May E Marsh
- Department of Biochemistry University of Cambridge UK; Present address: Paul Scherrer Institut Villingen Switzerland
| | | | - Matthias T Ehebauer
- Department of Biochemistry University of Cambridge UK; Present address: Target Discovery Institute Nuffield Department of Medicine University of Oxford UK
| | - Chris Abell
- Department of Chemistry University of Cambridge UK
| | | | - Marko Hyvönen
- Department of Biochemistry University of Cambridge UK
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42
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BRCA2 regulates DMC1-mediated recombination through the BRC repeats. Proc Natl Acad Sci U S A 2016; 113:3515-20. [PMID: 26976601 DOI: 10.1073/pnas.1601691113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In somatic cells, BRCA2 is needed for RAD51-mediated homologous recombination. The meiosis-specific DNA strand exchange protein, DMC1, promotes the formation of DNA strand invasion products (joint molecules) between homologous molecules in a fashion similar to RAD51. BRCA2 interacts directly with both human RAD51 and DMC1; in the case of RAD51, this interaction results in stimulation of RAD51-promoted DNA strand exchange. However, for DMC1, little is known regarding the basis and functional consequences of its interaction with BRCA2. Here we report that human DMC1 interacts directly with each of the BRC repeats of BRCA2, albeit most tightly with repeats 1-3 and 6-8. However, BRC1-3 bind with higher affinity to RAD51 than to DMC1, whereas BRC6-8 bind with higher affinity to DMC1, providing potential spatial organization to nascent filament formation. With the exception of BRC4, each BRC repeat stimulates joint molecule formation by DMC1. The basis for this stimulation is an enhancement of DMC1-ssDNA complex formation by the stimulatory BRC repeats. Lastly, we demonstrate that full-length BRCA2 protein stimulates DMC1-mediated DNA strand exchange between RPA-ssDNA complexes and duplex DNA, thus identifying BRCA2 as a mediator of DMC1 recombination function. Collectively, our results suggest unique and specialized functions for the BRC motifs of BRCA2 in promoting homologous recombination in meiotic and mitotic cells.
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43
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Lee JY, Terakawa T, Qi Z, Steinfeld JB, Redding S, Kwon Y, Gaines WA, Zhao W, Sung P, Greene EC. DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases. Science 2016; 349:977-81. [PMID: 26315438 DOI: 10.1126/science.aab2666] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
DNA strand exchange plays a central role in genetic recombination across all kingdoms of life, but the physical basis for these reactions remains poorly defined. Using single-molecule imaging, we found that bacterial RecA and eukaryotic Rad51 and Dmc1 all stabilize strand exchange intermediates in precise three-nucleotide steps. Each step coincides with an energetic signature (0.3 kBT) that is conserved from bacteria to humans. Triplet recognition is strictly dependent on correct Watson-Crick pairing. Rad51, RecA, and Dmc1 can all step over mismatches, but only Dmc1 can stabilize mismatched triplets. This finding provides insight into why eukaryotes have evolved a meiosis-specific recombinase. We propose that canonical Watson-Crick base triplets serve as the fundamental unit of pairing interactions during DNA recombination.
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Affiliation(s)
- Ja Yil Lee
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Department of Biophysics, Kyoto University, Sakyo, Kyoto, Japan
| | - Zhi Qi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sy Redding
- Department of Chemistry, Columbia University, New York, NY, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - William A Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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Brown MS, Grubb J, Zhang A, Rust MJ, Bishop DK. Small Rad51 and Dmc1 Complexes Often Co-occupy Both Ends of a Meiotic DNA Double Strand Break. PLoS Genet 2015; 11:e1005653. [PMID: 26719980 PMCID: PMC4697796 DOI: 10.1371/journal.pgen.1005653] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/15/2015] [Indexed: 11/19/2022] Open
Abstract
The Eukaryotic RecA-like proteins Rad51 and Dmc1 cooperate during meiosis to promote recombination between homologous chromosomes by repairing programmed DNA double strand breaks (DSBs). Previous studies showed that Rad51 and Dmc1 form partially overlapping co-foci. Here we show these Rad51-Dmc1 co-foci are often arranged in pairs separated by distances of up to 400 nm. Paired co-foci remain prevalent when DSBs are dramatically reduced or when strand exchange or synapsis is blocked. Super-resolution dSTORM microscopy reveals that individual foci observed by conventional light microscopy are often composed of two or more substructures. The data support a model in which the two tracts of ssDNA formed by a single DSB separate from one another by distances of up to 400 nm, with both tracts often bound by one or more short (about 100 nt) Rad51 filaments and also by one or more short Dmc1 filaments.
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Affiliation(s)
- M. Scott Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Jennifer Grubb
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Annie Zhang
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Michael J. Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
| | - Douglas K. Bishop
- Department of Molecular Genetics and Cell Biology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- Department of Radiation and Cellular Oncology, University of Chicago, Cummings Life Science Center, Chicago, Illinois, United States of America
- * E-mail:
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Abstract
The genome of spinach single chromosome complement is about 1000 Mbp, which is the model material to study the molecular mechanisms of plant sex differentiation. The cytological study showed that the biggest spinach chromosome (chromosome 1) was taken as spinach sex chromosome. It had three alleles of sex-related X,X(m) and Y. Many researchers have been trying to clone the sex-determining genes and investigated the molecular mechanism of spinach sex differentiation. However,there are no successful cloned reports about these genes. A new technology combining chromosome microdissection with hybridization-specific amplification (HSA) was adopted. The spinach Y chromosome degenerate oligonucleotide primed-PCR (DOP-PCR) products were hybridized with cDNA of the male spinach flowers in florescence. The female spinach genome was taken as blocker and cDNA library specifically expressed in Y chromosome was constructed. Moreover, expressed sequence tag (EST) sequences in cDNA library were cloned, sequenced and bioinformatics was analysed. There were 63 valid EST sequences obtained in this study. The fragment size was between 53 and 486 bp. BLASTn homologous alignment indicated that 12 EST sequences had homologous sequences of nucleic acids, the rest were new sequences. BLASTx homologous alignment indicated that 16 EST sequences had homologous protein-encoding nucleic acid sequence. The spinach Y chromosome-specific EST sequences laid the foundation for cloning the functional genes, specifically expressed in spinach Y chromosome. Meanwhile, the establishment of the technology system in the research provided a reference for rapid cloning of other biological sex chromosome-specific EST sequences.
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Kelso AA, Say AF, Sharma D, Ledford LL, Turchick A, Saski CA, King AV, Attaway CC, Temesvari LA, Sehorn MG. Entamoeba histolytica Dmc1 Catalyzes Homologous DNA Pairing and Strand Exchange That Is Stimulated by Calcium and Hop2-Mnd1. PLoS One 2015; 10:e0139399. [PMID: 26422142 PMCID: PMC4589404 DOI: 10.1371/journal.pone.0139399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/12/2015] [Indexed: 01/03/2023] Open
Abstract
Meiosis depends on homologous recombination (HR) in most sexually reproducing organisms. Efficient meiotic HR requires the activity of the meiosis-specific recombinase, Dmc1. Previous work shows Dmc1 is expressed in Entamoeba histolytica, a eukaryotic parasite responsible for amoebiasis throughout the world, suggesting this organism undergoes meiosis. Here, we demonstrate Dmc1 protein is expressed in E. histolytica. We show that purified ehDmc1 forms presynaptic filaments and catalyzes ATP-dependent homologous DNA pairing and DNA strand exchange over at least several thousand base pairs. The DNA pairing and strand exchange activities are enhanced by the presence of calcium and the meiosis-specific recombination accessory factor, Hop2-Mnd1. In combination, calcium and Hop2-Mnd1 dramatically increase the rate of DNA strand exchange activity of ehDmc1. The biochemical system described herein provides a basis on which to better understand the role of ehDmc1 and other HR proteins in E. histolytica.
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Affiliation(s)
- Andrew A. Kelso
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Amanda F. Say
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Deepti Sharma
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - LeAnna L. Ledford
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Audrey Turchick
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher A. Saski
- Clemson University Genomics and Computational Biology Laboratory, Institute for Translational Genomics, Clemson, South Carolina, United States of America
| | - Ada V. King
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher C. Attaway
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
- Clemson University School of Health Research, Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Michael G. Sehorn
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Clemson University School of Health Research, Clemson, South Carolina, United States of America
- Center for Optical Materials Science and Engineering Technologies, Clemson University, Clemson, South Carolina, United States of America
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Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
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48
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Chang HY, Liao CY, Su GC, Lin SW, Wang HW, Chi P. Functional Relationship of ATP Hydrolysis, Presynaptic Filament Stability, and Homologous DNA Pairing Activity of the Human Meiotic Recombinase DMC1. J Biol Chem 2015; 290:19863-73. [PMID: 26088134 DOI: 10.1074/jbc.m115.666289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 11/06/2022] Open
Abstract
DMC1 and RAD51 are conserved recombinases that catalyze homologous recombination. DMC1 and RAD51 share similar properties in DNA binding, DNA-stimulated ATP hydrolysis, and catalysis of homologous DNA strand exchange. A large body of evidence indicates that attenuation of ATP hydrolysis leads to stabilization of the RAD51-ssDNA presynaptic filament and enhancement of DNA strand exchange. However, the functional relationship of ATPase activity, presynaptic filament stability, and DMC1-mediated homologous DNA strand exchange has remained largely unexplored. To address this important question, we have constructed several mutant variants of human DMC1 and characterized them biochemically to gain mechanistic insights. Two mutations, K132R and D223N, that change key residues in the Walker A and B nucleotide-binding motifs ablate ATP binding and render DMC1 inactive. On the other hand, the nucleotide-binding cap D317K mutant binds ATP normally but shows significantly attenuated ATPase activity and, accordingly, forms a highly stable presynaptic filament. Surprisingly, unlike RAD51, presynaptic filament stabilization achieved via ATP hydrolysis attenuation does not lead to any enhancement of DMC1-catalyzed homologous DNA pairing and strand exchange. This conclusion is further supported by examining wild-type DMC1 with non-hydrolyzable ATP analogues. Thus, our results reveal an important mechanistic difference between RAD51 and DMC1.
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Affiliation(s)
- Hao-Yen Chang
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Chia-Yu Liao
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Guan-Chin Su
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Sheng-Wei Lin
- the Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan, and
| | - Hong-Wei Wang
- the Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peter Chi
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan, the Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan, and
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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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Kang HA, Shin HC, Kalantzi AS, Toseland CP, Kim HM, Gruber S, Peraro MD, Oh BH. Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination. Nucleic Acids Res 2015; 43:3841-56. [PMID: 25740648 PMCID: PMC4402518 DOI: 10.1093/nar/gkv172] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/20/2015] [Indexed: 11/14/2022] Open
Abstract
In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2-Mnd1 reveals that it forms a curved rod-like structure consisting of three leucine zippers and two kinked junctions. One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra α-helices to form a helical bundle-like structure. Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament. Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations. These findings allow us to propose a model explaining how Hop2-Mnd1 juxtaposes Dmc1-bound ssDNA with distorted recipient double-stranded DNA and thus facilitates strand invasion.
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Affiliation(s)
- Hyun-Ah Kang
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Ho-Chul Shin
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea Functional Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Alexandra-Styliani Kalantzi
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Christopher P Toseland
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am, Klopferspitz 18, 82152 Martinsried, Germany
| | - Hyun-Min Kim
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Stephan Gruber
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am, Klopferspitz 18, 82152 Martinsried, Germany
| | - Matteo Dal Peraro
- Laboratory for Biomolecular Modeling, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), and Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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