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Zou M, Shabala S, Zhao C, Zhou M. Molecular mechanisms and regulation of recombination frequency and distribution in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:86. [PMID: 38512498 PMCID: PMC10957645 DOI: 10.1007/s00122-024-04590-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
KEY MESSAGE Recent developments in understanding the distribution and distinctive features of recombination hotspots are reviewed and approaches are proposed to increase recombination frequency in coldspot regions. Recombination events during meiosis provide the foundation and premise for creating new varieties of crops. The frequency of recombination in different genomic regions differs across eukaryote species, with recombination generally occurring more frequently at the ends of chromosomes. In most crop species, recombination is rare in centromeric regions. If a desired gene variant is linked in repulsion with an undesired variant of a second gene in a region with a low recombination rate, obtaining a recombinant plant combining two favorable alleles will be challenging. Traditional crop breeding involves combining desirable genes from parental plants into offspring. Therefore, understanding the mechanisms of recombination and factors affecting the occurrence of meiotic recombination is important for crop breeding. Here, we review chromosome recombination types, recombination mechanisms, genes and proteins involved in the meiotic recombination process, recombination hotspots and their regulation systems and discuss how to increase recombination frequency in recombination coldspot regions.
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Affiliation(s)
- Meilin Zou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, 6009, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia.
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2
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Tsubouchi H. The Hop2-Mnd1 Complex and Its Regulation of Homologous Recombination. Biomolecules 2023; 13:biom13040662. [PMID: 37189409 DOI: 10.3390/biom13040662] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Homologous recombination (HR) is essential for meiosis in most sexually reproducing organisms, where it is induced upon entry into meiotic prophase. Meiotic HR is conducted by the collaborative effort of proteins responsible for DNA double-strand break repair and those produced specifically during meiosis. The Hop2-Mnd1 complex was originally identified as a meiosis-specific factor that is indispensable for successful meiosis in budding yeast. Later, it was found that Hop2-Mnd1 is conserved from yeasts to humans, playing essential roles in meiosis. Accumulating evidence suggests that Hop2-Mnd1 promotes RecA-like recombinases towards homology search/strand exchange. This review summarizes studies on the mechanism of the Hop2-Mnd1 complex in promoting HR and beyond.
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Affiliation(s)
- Hideo Tsubouchi
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Kanagawa, Japan
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3
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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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4
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Bomblies K. Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis. PLANT REPRODUCTION 2023; 36:107-124. [PMID: 36149479 PMCID: PMC9957869 DOI: 10.1007/s00497-022-00448-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/10/2022] [Indexed: 05/29/2023]
Abstract
Polyploidy, which arises from genome duplication, has occurred throughout the history of eukaryotes, though it is especially common in plants. The resulting increased size, heterozygosity, and complexity of the genome can be an evolutionary opportunity, facilitating diversification, adaptation and the evolution of functional novelty. On the other hand, when they first arise, polyploids face a number of challenges, one of the biggest being the meiotic pairing, recombination and segregation of the suddenly more than two copies of each chromosome, which can limit their fertility. Both for developing polyploidy as a crop improvement tool (which holds great promise due to the high and lasting multi-stress resilience of polyploids), as well as for our basic understanding of meiosis and plant evolution, we need to know both the specific nature of the challenges polyploids face, as well as how they can be overcome in evolution. In recent years there has been a dramatic uptick in our understanding of the molecular basis of polyploid adaptations to meiotic challenges, and that is the focus of this review.
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Affiliation(s)
- Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Plant Molecular Biology, Department of Biology, ETH Zürich, Zurich, Switzerland.
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5
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Thangavel G, Hofstatter PG, Mercier R, Marques A. Tracing the evolution of the plant meiotic molecular machinery. PLANT REPRODUCTION 2023; 36:73-95. [PMID: 36646915 PMCID: PMC9957857 DOI: 10.1007/s00497-022-00456-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Meiosis is a highly conserved specialised cell division in sexual life cycles of eukaryotes, forming the base of gene reshuffling, biological diversity and evolution. Understanding meiotic machinery across different plant lineages is inevitable to understand the lineage-specific evolution of meiosis. Functional and cytogenetic studies of meiotic proteins from all plant lineage representatives are nearly impossible. So, we took advantage of the genomics revolution to search for core meiotic proteins in accumulating plant genomes by the highly sensitive homology search approaches, PSI-BLAST, HMMER and CLANS. We could find that most of the meiotic proteins are conserved in most of the lineages. Exceptionally, Arabidopsis thaliana ASY4, PHS1, PRD2, PRD3 orthologs were mostly not detected in some distant algal lineages suggesting their minimal conservation. Remarkably, an ancestral duplication of SPO11 to all eukaryotes could be confirmed. Loss of SPO11-1 in Chlorophyta and Charophyta is likely to have occurred, suggesting that SPO11-1 and SPO11-2 heterodimerisation may be a unique feature in land plants of Viridiplantae. The possible origin of the meiotic proteins described only in plants till now, DFO and HEIP1, could be traced and seems to occur in the ancestor of vascular plants and Streptophyta, respectively. Our comprehensive approach is an attempt to provide insights about meiotic core proteins and thus the conservation of meiotic pathways across plant kingdom. We hope that this will serve the meiotic community a basis for further characterisation of interesting candidates in future.
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Affiliation(s)
- Gokilavani Thangavel
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | | | - Raphaël Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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6
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Daradur J, Kesserwan M, Freese NH, Loraine AE, Riggs CD. Genomic targets of HOP2 are enriched for features found at recombination hotspots. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525520. [PMID: 36747711 PMCID: PMC9900786 DOI: 10.1101/2023.01.25.525520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
HOP2 is a conserved protein that plays a positive role in homologous chromosome pairing and a separable role in preventing illegitimate connections between nonhomologous chromosome regions during meiosis. We employed ChIP-seq to discover that Arabidopsis HOP2 binds along the length of all chromosomes, except for centromeric and nucleolar organizer regions, and no binding sites were detected in the organelle genomes. A large number of reads were assigned to the HOP2 locus itself, yet TAIL-PCR and SNP analysis of the aligned sequences indicate that many of these reads originate from the transforming T-DNA, supporting the role of HOP2 in preventing nonhomologous exchanges. The 292 ChIP-seq peaks are largely found in promoter regions and downstream from genes, paralleling the distribution of recombination hotspots, and motif analysis revealed that there are several conserved sequences that are also enriched at crossover sites. We conducted coimmunoprecipitation of HOP2 followed by LC-MS/MS and found enrichment for several proteins, including some histone variants and modifications that are also known to be associated with recombination hotspots. We propose that HOP2 may be directed to chromatin motifs near double strand breaks, where homology checks are proposed to occur.
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Affiliation(s)
- Jenya Daradur
- Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C1A4, Canada
| | - Mohamad Kesserwan
- Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C1A4, Canada
| | - Nowlan H. Freese
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, N.C. USA
| | - Ann E. Loraine
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, N.C. USA
| | - C. Daniel Riggs
- Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C1A4, Canada
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7
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Sankaranarayanan S, Jamshed M, Delmas F, Yeung EC, Samuel MA. Identification and characterization of a female gametophyte defect in sdk1-7 +/- abi3-6 +/- heterozygotes of Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2020; 15:1780038. [PMID: 32657242 PMCID: PMC8570737 DOI: 10.1080/15592324.2020.1780038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Successful reproduction in angiosperms is dependent on the highly synchronous development of their male and female gametophytes and the ensuing fusion of the gametes from these reproductive tissue types. When crossing a T-DNA insertion line sdk1-7-/-(Salk_024564), one of the S-domain receptor kinases involved in ABA responses with a fast neutron deletion line abi3-6-/-, the F1 heterozygotes (sdk1-7+/-abi3-6 +/-) displayed 50% ovule abortion suggesting a likely gametophytic defects. We identified and characterized an early stage female gametophyte developmental defect in the heterozygous mutant ovules. Recombination frequency analysis of the F2 progenies from selfed heterozygotes revealed a possible pseudo-linkage of sdk1-7 and abi3-6 suggesting a reciprocal translocation event in the heterozygote. Our study emphasizes the importance of robust analysis to distinguish gametophytic defect phenotypes caused by genetic interactions and that resulting from possible chromosomal translocation events.
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Affiliation(s)
- Subramanian Sankaranarayanan
- Department of Biological Sciences, BI 392, University of Calgary, Calgary, Alberta, Canada
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Muhammad Jamshed
- Department of Biological Sciences, BI 392, University of Calgary, Calgary, Alberta, Canada
- Frontier Agri-Science, Port Hope, Ontario, Canada
| | - Frédéric Delmas
- UMR1332 BFP, INRAE, Université De Bordeaux, Villenave d’Ornon, France
| | - Edward C. Yeung
- Department of Biological Sciences, BI 392, University of Calgary, Calgary, Alberta, Canada
| | - Marcus A. Samuel
- Department of Biological Sciences, BI 392, University of Calgary, Calgary, Alberta, Canada
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8
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Liu H, Cao A, Yang L, Wang J. Rice Female Meiosis: Genome-Wide mRNA, Small RNA, and DNA Methylation Analysis During Ovule Development. Methods Mol Biol 2020; 2061:267-280. [PMID: 31583666 DOI: 10.1007/978-1-4939-9818-0_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Meiosis is an essential process in sexual life cycle, not only for the genomic stability maintenance but also for the genetic diversity creation through recombination. In rice ovule, megaspore mother cells undergo meiosis to form megaspores; then the functional megaspore performs three rounds of mitoses to form female gametophyte. However, the mechanism of gene expression and regulation in female meiosis process is still poorly understood. As important gene regulatory factors, miRNAs and DNA methylation are widely involved in plant meiosis and ovule development. In order to systematically study the potential mechanism of gene expression and regulation in female meiosis, ovules at megaspore mother cell meiosis stage, functional megaspore mitosis stage, and mature female gametophytes are collected to perform genome-wide RNA sequencing, small RNA sequencing, and bisulfite sequencing. Through bioinformatics analysis, we obtained many differentially expressed genes, miRNAs, and differentially methylated genes related to female meiosis. These data may provide important clues for further revealing the mechanism of female meiosis in rice.
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Affiliation(s)
- Helian Liu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Aqin Cao
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Liyu Yang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Jianbo Wang
- College of Life Sciences, Wuhan University, Wuhan, China.
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9
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Xue M, Wang J, Jiang L, Wang M, Wolfe S, Pawlowski WP, Wang Y, He Y. The Number of Meiotic Double-Strand Breaks Influences Crossover Distribution in Arabidopsis. THE PLANT CELL 2018; 30:2628-2638. [PMID: 30282794 PMCID: PMC6241269 DOI: 10.1105/tpc.18.00531] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/17/2018] [Accepted: 09/30/2018] [Indexed: 05/06/2023]
Abstract
Meiotic recombination generates genetic diversity and ensures proper chromosome segregation. Recombination is initiated by the programmed formation of double-strand breaks (DSBs) in chromosomal DNA by DNA Topoisomerase VI-A Subunit (SPO11), a topoisomerase-like enzyme. Repair of some DSBs leads to the formation of crossovers (COs). In most organisms, including plants, the number of DSBs greatly exceeds the number of COs and which DSBs become CO sites is tightly controlled. The CO landscape is affected by DNA sequence and epigenome features of chromosomes as well as by global mechanisms controlling recombination dynamics. The latter are poorly understood and their effects on CO distribution are not well elucidated. To study how recombination dynamics affects CO distribution, we engineered Arabidopsis thaliana plants to carry hypomorphic alleles of SPO11-1 Two independent transgenic lines showed ∼30% and 40% reductions in DSB numbers, which were commensurate with the dosage of the SPO11-1 transcript. The reduction in DSB number resulted in proportional, although smaller, reductions of the number of COs. Most interestingly, CO distribution along the chromosomes was dramatically altered, with substantially fewer COs forming in pericentromeric chromosome regions. These results indicate that SPO11 activity, and the resulting DSB numbers are major factors shaping the CO landscape.
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Affiliation(s)
- Ming Xue
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Jun Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Luguang Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Minghui Wang
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
- Bioinformatics Facility, Cornell University, Ithaca, New York 14853
| | - Sarah Wolfe
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
| | | | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
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10
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Sarma S, Pandey AK, Sharma K, Ravi M, Sreelakshmi Y, Sharma R. MutS-Homolog2 silencing generates tetraploid meiocytes in tomato ( Solanum lycopersicum). PLANT DIRECT 2018; 2:e00017. [PMID: 31245679 PMCID: PMC6508528 DOI: 10.1002/pld3.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 09/07/2017] [Accepted: 09/12/2017] [Indexed: 05/16/2023]
Abstract
MSH2 is the core protein of MutS-homolog family involved in recognition and repair of the errors in the DNA. While other members of MutS-homolog family reportedly regulate mitochondrial stability, meiosis, and fertility, MSH2 is believed to participate mainly in mismatch repair. The search for polymorphism in MSH2 sequence in tomato accessions revealed both synonymous and nonsynonymous SNPs; however, SIFT algorithm predicted that none of the SNPs influenced MSH2 protein function. The silencing of MSH2 gene expression by RNAi led to phenotypic abnormalities in highly silenced lines, particularly in the stamens with highly reduced pollen formation. MSH2 silencing exacerbated formation of UV-B-induced thymine dimers and blocked light-induced repair of the dimers. The MSH2 silencing also affected the progression of male meiosis to a varying degree with either halt of meiosis at zygotene stage or formation of diploid tetrads. The immunostaining of male meiocytes with centromere localized CENPC (centromere protein C) antibody showed the presence of 48 univalent along with 24 bivalent chromosomes suggesting abnormal tetraploid meiosis. The mitotic cells of root tips of silenced lines showed diploid nuclei but lacked intervening cell plates leading to cells with syncytial nuclei. Thus, we speculate that tetraploid pollen mother cells may have arisen due to the fusion of syncytial nuclei before the onset of meiosis. It is likely that in addition to mismatch repair (MMR), MSH2 may have an additional role in regulating ploidy stability.
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Affiliation(s)
- Supriya Sarma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
- Present address:
Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Arun Kumar Pandey
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
- Present address:
International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kapil Sharma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
| | - Maruthachalam Ravi
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramKeralaIndia
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
| | - Rameshwar Sharma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesSchool of Life SciencesUniversity of HyderabadHyderabadIndia
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11
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Fitzgerald TL, Powell JJ, Stiller J, Weese TL, Abe T, Zhao G, Jia J, McIntyre CL, Li Z, Manners JM, Kazan K. An assessment of heavy ion irradiation mutagenesis for reverse genetics in wheat (Triticum aestivum L.). PLoS One 2015; 10:e0117369. [PMID: 25719507 PMCID: PMC4342231 DOI: 10.1371/journal.pone.0117369] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 12/22/2014] [Indexed: 11/19/2022] Open
Abstract
Reverse genetic techniques harnessing mutational approaches are powerful tools that can provide substantial insight into gene function in plants. However, as compared to diploid species, reverse genetic analyses in polyploid plants such as bread wheat can present substantial challenges associated with high levels of sequence and functional similarity amongst homoeologous loci. We previously developed a high-throughput method to identify deletions of genes within a physically mutagenized wheat population. Here we describe our efforts to combine multiple homoeologous deletions of three candidate disease susceptibility genes (TaWRKY11, TaPFT1 and TaPLDß1). We were able to produce lines featuring homozygous deletions at two of the three homoeoloci for all genes, but this was dependent on the individual mutants used in crossing. Intriguingly, despite extensive efforts, viable lines possessing homozygous deletions at all three homoeoloci could not be produced for any of the candidate genes. To investigate deletion size as a possible reason for this phenomenon, we developed an amplicon sequencing approach based on synteny to Brachypodium distachyon to assess the size of the deletions removing one candidate gene (TaPFT1) in our mutants. These analyses revealed that genomic deletions removing the locus are relatively large, resulting in the loss of multiple additional genes. The implications of this work for the use of heavy ion mutagenesis for reverse genetic analyses in wheat are discussed.
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Affiliation(s)
- Timothy L. Fitzgerald
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- * E-mail: (TLF); (KK)
| | - Jonathan J. Powell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Terri L. Weese
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama, 351–0198, Japan
| | - Guangyao Zhao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - C. Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
| | - Zhongyi Li
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Black Mountain Laboratories, Clunies Ross St, Acton, ACT, 2601, Australia
| | - John M. Manners
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Black Mountain Laboratories, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture Flagship, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Brisbane, QLD, 4067, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, 4072, Australia
- * E-mail: (TLF); (KK)
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12
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Abstract
Homology search and DNA strand-exchange reactions are central to homologous recombination in meiosis. During meiosis, these processes are regulated such that the probability of choosing a homolog chromatid as recombination partner is enhanced relative to that of choosing a sister chromatid. This regulatory process occurs as homologous chromosomes pair in preparation for assembly of the synaptonemal complex. Two strand-exchange proteins, Rad51 and Dmc1, cooperate in regulated homology search and strand exchange in most organisms. Here, we summarize studies on the properties of these two proteins and their accessory factors. In addition, we review current models for the assembly of meiotic strand-exchange complexes and the possible mechanisms through which the interhomolog bias of recombination partner choice is achieved.
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Affiliation(s)
- M Scott Brown
- Department of Radiation and Cellular Oncology, and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637
| | - Douglas K Bishop
- Department of Radiation and Cellular Oncology, and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637
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13
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Qin Y, Zhao L, Skaggs MI, Andreuzza S, Tsukamoto T, Panoli A, Wallace KN, Smith S, Siddiqi I, Yang Z, Yadegari R, Palanivelu R. ACTIN-RELATED PROTEIN6 Regulates Female Meiosis by Modulating Meiotic Gene Expression in Arabidopsis. THE PLANT CELL 2014; 26:1612-1628. [PMID: 24737671 PMCID: PMC4036575 DOI: 10.1105/tpc.113.120576] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 03/14/2014] [Accepted: 03/23/2014] [Indexed: 05/02/2023]
Abstract
In flowering plants, meiocytes develop from subepidermal cells in anthers and ovules. The mechanisms that integrate gene-regulatory processes with meiotic programs during reproductive development remain poorly characterized. Here, we show that Arabidopsis thaliana plants deficient in ACTIN-RELATED PROTEIN6 (ARP6), a subunit of the SWR1 ATP-dependent chromatin-remodeling complex, exhibit defects in prophase I of female meiosis. We found that this meiotic defect is likely due to dysregulated expression of meiotic genes, particularly those involved in meiotic recombination, including DMC1 (DISRUPTED MEIOTIC cDNA1). Analysis of DMC1 expression in arp6 mutant plants indicated that ARP6 inhibits expression of DMC1 in the megasporocyte and surrounding nonsporogeneous ovule cells before meiosis. After cells enter meiosis, however, ARP6 activates DMC1 expression specifically in the megasporocyte even as it continues to inhibit DMC1 expression in the nonsporogenous ovule cells. We further show that deposition of the histone variant H2A.Z, mediated by the SWR1 chromatin-remodeling complex at the DMC1 gene body, requires ARP6. Therefore, ARP6 regulates female meiosis by determining the spatial and temporal patterns of gene expression required for proper meiosis during ovule development.
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Affiliation(s)
- Yuan Qin
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Lihua Zhao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Megan I Skaggs
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | | | - Tatsuya Tsukamoto
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Aneesh Panoli
- Center for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Kirsten N Wallace
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Steven Smith
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona 85721
| | - Imran Siddiqi
- Center for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Zhenbiao Yang
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Ramin Yadegari
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
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14
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Pezza RJ, Voloshin ON, Volodin AA, Boateng KA, Bellani MA, Mazin AV, Camerini-Otero RD. The dual role of HOP2 in mammalian meiotic homologous recombination. Nucleic Acids Res 2013; 42:2346-57. [PMID: 24304900 PMCID: PMC3936763 DOI: 10.1093/nar/gkt1234] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Deletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2–MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2 alone is proficient in promoting strand invasion. We observed that a fraction of Mnd1−/− spermatocytes, which express HOP2 but apparently have inactive DMC1 and RAD51 due to lack of the HOP2–MND1 complex, exhibits a high level of chromosome synapsis and that most DSBs in these spermatocytes are repaired. This suggests that DSB repair catalyzed solely by HOP2 supports homologous chromosome pairing and synapsis. In addition, we show that in vitro HOP2 promotes the co-aggregation of ssDNA with duplex DNA, binds to ssDNA leading to unstacking of the bases, and promotes the formation of a three-strand synaptic intermediate. However, HOP2 shows distinctive mechanistic signatures as a recombinase. Namely, HOP2-mediated strand exchange does not require ATP and, in contrast to DMC1, joint molecules formed by HOP2 are more sensitive to mismatches and are efficiently dissociated by RAD54. We propose that HOP2 may act as a recombinase with specific functions in meiosis.
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Affiliation(s)
- Roberto J Pezza
- Oklahoma Medical Research Foundation, Oklahoma City, 73104 OK, USA, Department of Cell Biology, Oklahoma University Health Science Center, Oklahoma City, 73126 OK, USA, Genetics and Biochemistry Branch, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, 20892 MD, USA, Institute of Molecular Genetics of the Russian Academy of Sciences, 123182 Moscow, Russia, Biomedical Research Center, National Institute of Aging, Baltimore, 21224 MA, USA and Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, 19102 PA, USA
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15
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Zhao W, Saro D, Hammel M, Kwon Y, Xu Y, Rambo RP, Williams GJ, Chi P, Lu L, Pezza RJ, Camerini-Otero RD, Tainer JA, Wang HW, Sung P. Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res 2013; 42:906-17. [PMID: 24150939 PMCID: PMC3902922 DOI: 10.1093/nar/gkt924] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Hop2–Mnd1 complex functions with the DMC1 recombinase in meiotic recombination. Hop2–Mnd1 stabilizes the DMC1-single-stranded DNA (ssDNA) filament and promotes the capture of the double-stranded DNA partner by the recombinase filament to assemble the synaptic complex. Herein, we define the action mechanism of Hop2–Mnd1 in DMC1-mediated recombination. Small angle X-ray scattering analysis and electron microscopy reveal that the heterodimeric Hop2–Mnd1 is a V-shaped molecule. We show that the protein complex harbors three distinct DNA binding sites, and determine their functional relevance. Specifically, the N-terminal double-stranded DNA binding functions of Hop2 and Mnd1 co-operate to mediate synaptic complex assembly, whereas ssDNA binding by the Hop2 C-terminus helps stabilize the DMC1-ssDNA filament. A model of the Hop2-Mnd1-DMC1-ssDNA ensemble is proposed to explain how it mediates homologous DNA pairing in meiotic recombination.
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Affiliation(s)
- Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA, Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA and 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
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16
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Singh DK, Andreuzza S, Panoli AP, Siddiqi I. AtCTF7 is required for establishment of sister chromatid cohesion and association of cohesin with chromatin during meiosis in Arabidopsis. BMC PLANT BIOLOGY 2013; 13:117. [PMID: 23941555 PMCID: PMC3751900 DOI: 10.1186/1471-2229-13-117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/05/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND The establishment of sister chromatid cohesion followed by its controlled release at the metaphase to anaphase transition is necessary for faithful segregation of chromosomes in mitosis and meiosis. Cohesion is established by the action of Ctf7/Eco1 on the cohesin complex during DNA replication following loading of cohesin onto chromatin by the Scc2-Scc4 complex. Ctf7 is also required for sister chromatid cohesion during repair of DNA double strand breaks. Ctf7 contains an acetyltransferase domain and a zinc finger motif and acetylates conserved lysine residues in the Smc3 subunit of cohesin. In Arabidopsis CTF7 is encoded by a single gene and mutations in AtCTF7 cause embryo lethality indicating that the gene is essential. RESULTS To study the function of Ctf7 in plants and to determine its role in sister chromatid cohesion, we constructed a conditional allele of AtCTF7 in Arabidopsis using an inducible RNA interference (RNAi) strategy, so as to avoid the embryo lethality caused by mutations in AtCTF7. We found that induction of RNAi against AtCTF7 caused severe inhibition and defects in growth during vegetative and reproductive stages as well as sterility. AtCTF7-RNAi plants displayed chromosome fragmentation and loss of sister chromatid cohesion during meiosis. Immunostaining for the cohesion subunit AtSCC3 showed a marked reduction in association of cohesin with chromatin during meiosis in AtCTF7-RNAi plants. CONCLUSIONS We find that AtCTF7 is essential for sister chromatid cohesion during meiosis in Arabidopsis and is required for association of cohesin with chromatin in prophase of meiosis.
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Affiliation(s)
- Dipesh K Singh
- Centre for Cellular & Molecular Biology (CSIR), Uppal Road, Hyderabad 500007, India
| | - Sebastien Andreuzza
- Centre for Cellular & Molecular Biology (CSIR), Uppal Road, Hyderabad 500007, India
| | - Aneesh P Panoli
- Centre for Cellular & Molecular Biology (CSIR), Uppal Road, Hyderabad 500007, India
| | - Imran Siddiqi
- Centre for Cellular & Molecular Biology (CSIR), Uppal Road, Hyderabad 500007, India
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17
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Da Ines O, Abe K, Goubely C, Gallego ME, White CI. Differing requirements for RAD51 and DMC1 in meiotic pairing of centromeres and chromosome arms in Arabidopsis thaliana. PLoS Genet 2012; 8:e1002636. [PMID: 22532804 PMCID: PMC3330102 DOI: 10.1371/journal.pgen.1002636] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 02/21/2012] [Indexed: 11/18/2022] Open
Abstract
During meiosis homologous chromosomes pair, recombine, and synapse, thus ensuring accurate chromosome segregation and the halving of ploidy necessary for gametogenesis. The processes permitting a chromosome to pair only with its homologue are not fully understood, but successful pairing of homologous chromosomes is tightly linked to recombination. In Arabidopsis thaliana, meiotic prophase of rad51, xrcc3, and rad51C mutants appears normal up to the zygotene/pachytene stage, after which the genome fragments, leading to sterility. To better understand the relationship between recombination and chromosome pairing, we have analysed meiotic chromosome pairing in these and in dmc1 mutant lines. Our data show a differing requirement for these proteins in pairing of centromeric regions and chromosome arms. No homologous pairing of mid-arm or distal regions was observed in rad51, xrcc3, and rad51C mutants. However, homologous centromeres do pair in these mutants and we show that this does depend upon recombination, principally on DMC1. This centromere pairing extends well beyond the heterochromatic centromere region and, surprisingly, does not require XRCC3 and RAD51C. In addition to clarifying and bringing the roles of centromeres in meiotic synapsis to the fore, this analysis thus separates the roles in meiotic synapsis of DMC1 and RAD51 and the meiotic RAD51 paralogs, XRCC3 and RAD51C, with respect to different chromosome domains. Meiosis is a specialised cell division that acts to halve the chromosome complement, or ploidy, in the production of gametes for sexual reproduction in eukaryotes. To ensure that each gamete has a full complement of the genetic material, homologous chromosomes must pair and then separate in a coordinated manner during meiosis, and this is mediated by recombination in the majority of studied eukaryotes. To better understand the relationship between recombination and meiotic homologue pairing, we have analysed meiotic chromosome pairing in plant mutants lacking key recombination proteins. This work provides new insights into the homologous chromosome pairing mechanisms occurring in meiotic prophase of Arabidopsis thaliana: heterochromatic centromeres and 5S rDNA regions pair early, and their pairing has different requirements for recombination proteins than does that of the chromosome arms. These data raise a number of questions concerning the specificities and roles of recombination at different chromosome and/or chromatin regions in the synapsis of homologous chromosomes at meiosis.
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Affiliation(s)
| | | | | | | | - Charles I. White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Aubière, France
- * E-mail:
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18
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Seeliger K, Dukowic-Schulze S, Wurz-Wildersinn R, Pacher M, Puchta H. BRCA2 is a mediator of RAD51- and DMC1-facilitated homologous recombination in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2012; 193:364-75. [PMID: 22077663 DOI: 10.1111/j.1469-8137.2011.03947.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• Mutations in the breast cancer susceptibility gene 2 (BRCA2) are correlated with hereditary breast cancer in humans. Studies have revealed that mammalian BRCA2 plays crucial roles in DNA repair. Therefore, we wished to define the role of the BRCA2 homologs in Arabidopsis in detail. • As Arabidopsis contains two functional BRCA2 homologs, an Atbrca2 double mutant was generated and analyzed with respect to hypersensitivity to genotoxic agents and recombination frequencies. Cytological studies addressing male and female meiosis were also conducted, and immunolocalization was performed in male meiotic prophase I. • The Atbrca2 double mutant showed hypersensitivity to the cross-linking agent mitomycin C and displayed a dramatic reduction in somatic homologous recombination frequency, especially after double-strand break induction. The loss of AtBRCA2 also led to severe defects in male meiosis and development of the female gametophyte and impeded proper localization of the synaptonemal complex protein AtZYP1 and the recombinases AtRAD51 and AtDMC1. • The results demonstrate that AtBRCA2 is important for both somatic and meiotic homologous recombination. We further show that AtBRCA2 is required for proper meiotic synapsis and mediates the recruitment of AtRAD51 and AtDMC1. Our results suggest that BRCA2 controls single-strand invasion steps during homologous recombination in plants.
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Affiliation(s)
- Katharina Seeliger
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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19
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Osman K, Higgins JD, Sanchez-Moran E, Armstrong SJ, Franklin FCH. Pathways to meiotic recombination in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2011; 190:523-44. [PMID: 21366595 DOI: 10.1111/j.1469-8137.2011.03665.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Meiosis is a central feature of sexual reproduction. Studies in plants have made and continue to make an important contribution to fundamental research aimed at the understanding of this complex process. Moreover, homologous recombination during meiosis provides the basis for plant breeders to create new varieties of crops. The increasing global demand for food, combined with the challenges from climate change, will require sustained efforts in crop improvement. An understanding of the factors that control meiotic recombination has the potential to make an important contribution to this challenge by providing the breeder with the means to make fuller use of the genetic variability that is available within crop species. Cytogenetic studies in plants have provided considerable insights into chromosome organization and behaviour during meiosis. More recently, studies, predominantly in Arabidopsis thaliana, are providing important insights into the genes and proteins that are required for crossover formation during plant meiosis. As a result, substantial progress in the understanding of the molecular mechanisms that underpin meiosis in plants has begun to emerge. This article summarizes current progress in the understanding of meiotic recombination and its control in Arabidopsis. We also assess the relationship between meiotic recombination in Arabidopsis and other eukaryotes, highlighting areas of close similarity and apparent differences.
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Affiliation(s)
- Kim Osman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
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20
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Chang F, Wang Y, Wang S, Ma H. Molecular control of microsporogenesis in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:66-73. [PMID: 21145279 DOI: 10.1016/j.pbi.2010.11.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Revised: 09/17/2010] [Accepted: 11/11/2010] [Indexed: 05/20/2023]
Abstract
Microsporogenesis is essential for male fertility and requires both the formation of somatic and reproductive cells in the anther and meiotic segregation of homologous chromosomes. Molecular genetic studies have uncovered signaling molecules and transcription factors that play crucial roles in determining the anther cell types and in controlling gene expression for microsporogenesis. At the same time, key components of in meiotic recombination pathways have been discovered, enriching our knowledge about plant reproductive development.
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Affiliation(s)
- Fang Chang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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21
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Chen C, Farmer AD, Langley RJ, Mudge J, Crow JA, May GD, Huntley J, Smith AG, Retzel EF. Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes. BMC PLANT BIOLOGY 2010; 10:280. [PMID: 21167045 PMCID: PMC3018465 DOI: 10.1186/1471-2229-10-280] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/17/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., Saccharomyces cerevisiae and Drosophila melanogaster), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes. RESULTS A high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes. CONCLUSION These findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.
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Affiliation(s)
- Changbin Chen
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN 55108, USA
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - Raymond J Langley
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
- Immunology, Lovelace Respiratory Research Institute, 2425 Ridgecrest Drive SE, Albuquerque, NM 87108, USA
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - John A Crow
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - Gregory D May
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
| | - James Huntley
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
- Illumina Inc., Hayward, California 94545, USA
| | - Alan G Smith
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN 55108, USA
| | - Ernest F Retzel
- National Center for Genome Resources, 2935 Rodeo Park Drive E., Santa Fe, NM 87505, USA
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22
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Harrison CJ, Alvey E, Henderson IR. Meiosis in flowering plants and other green organisms. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2863-75. [PMID: 20576791 DOI: 10.1093/jxb/erq191] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sexual eukaryotes generate gametes using a specialized cell division called meiosis that serves both to halve the number of chromosomes and to reshuffle genetic variation present in the parent. The nature and mechanism of the meiotic cell division in plants and its effect on genetic variation are reviewed here. As flowers are the site of meiosis and fertilization in angiosperms, meiotic control will be considered within this developmental context. Finally, we review what is known about the control of meiosis in green algae and non-flowering land plants and discuss evolutionary transitions relating to meiosis that have occurred in the lineages giving rise to the angiosperms.
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Affiliation(s)
- C Jill Harrison
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
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23
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Sebastian J, Ravi M, Andreuzza S, Panoli AP, Marimuthu MPA, Siddiqi I. The plant adherin AtSCC2 is required for embryogenesis and sister-chromatid cohesion during meiosis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:1-13. [PMID: 19228337 DOI: 10.1111/j.1365-313x.2009.03845.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Adherin plays an important role in loading the cohesin complex onto chromosomes, and is essential for the establishment of sister-chromatid cohesion. We have identified and analyzed the Arabidopsis adherin homolog AtSCC2. Interestingly, the sequence analysis of AtSCC2 and of other putative plant adherin homologs revealed the presence of a PHD finger, which is not found in their fungal and animal counterparts. AtSCC2 is identical to EMB2773, and mutants show early embryo lethality and formation of giant endosperm nuclei. A role for AtSCC2 in sister-chromatid cohesion was established by using conditional RNAi and examining meiotic chromosome organization. AtSCC2-RNAi lines showed sterility, arising from the following defects in meiotic chromosome organization: failure of homologous pairing, loss of sister-chromatid cohesion, mixed segregation of chromosomes and chromosome fragmentation. The mutant phenotype, which included defects in chromosome organization and cohesion in prophase I, is distinct from that of the Arabidopsis cohesin mutant Atrec8, which retains centromere cohesion up to anaphase I. Immunostaining experiments revealed the aberrant distribution of the cohesin subunit AtSCC3 on chromosomes, and defects in chromosomal axis formation, in the meiocytes of AtSCC2-RNAi lines. These results demonstrate a role for AtSCC2 in sister-chromatid cohesion and centromere organization, and show that the machinery responsible for the establishment of cohesion is conserved in plants.
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Affiliation(s)
- Jose Sebastian
- Centre for Cellular & Molecular Biology, Uppal Road, Hyderabad 500007, India
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24
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Chelysheva L, Vezon D, Belcram K, Gendrot G, Grelon M. The Arabidopsis BLAP75/Rmi1 homologue plays crucial roles in meiotic double-strand break repair. PLoS Genet 2008; 4:e1000309. [PMID: 19096505 PMCID: PMC2588655 DOI: 10.1371/journal.pgen.1000309] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 11/14/2008] [Indexed: 11/19/2022] Open
Abstract
In human cells and in Saccharomyces cerevisiae, BLAP75/Rmi1 acts together with BLM/Sgs1 and TopoIIIalpha/Top3 to maintain genome stability by limiting crossover (CO) formation in favour of NCO events, probably through the dissolution of double Holliday junction intermediates (dHJ). So far, very limited data is available on the involvement of these complexes in meiotic DNA repair. In this paper, we present the first meiotic study of a member of the BLAP75 family through characterisation of the Arabidopsis thaliana homologue. In A. thaliana blap75 mutants, meiotic recombination is initiated, and recombination progresses until the formation of bivalent-like structures, even in the absence of ZMM proteins. However, chromosome fragmentation can be detected as soon as metaphase I and is drastic at anaphase I, while no second meiotic division is observed. Using genetic and imunolocalisation studies, we showed that these defects reflect a role of A. thaliana BLAP75 in meiotic double-strand break (DSB) repair -- that it acts after the invasion step mediated by RAD51 and associated proteins and that it is necessary to repair meiotic DSBs onto sister chromatids as well as onto the homologous chromosome. In conclusion, our results show for the first time that BLAP75/Rmi1 is a key protein of the meiotic homologous recombination machinery. In A. thaliana, we found that this protein is dispensable for homologous chromosome recognition and synapsis but necessary for the repair of meiotic DSBs. Furthermore, in the absence of BLAP75, bivalent formation can happen even in the absence of ZMM proteins, showing that in blap75 mutants, recombination intermediates exist that are stable enough to form bivalent structures, even when ZMM are absent.
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Affiliation(s)
- Liudmila Chelysheva
- INRA de Versailles, Institut Jean-Pierre Bourgin, Station de Génétique et d'Amélioration des Plantes UR-254, Versailles, France
| | - Daniel Vezon
- INRA de Versailles, Institut Jean-Pierre Bourgin, Station de Génétique et d'Amélioration des Plantes UR-254, Versailles, France
| | - Katia Belcram
- INRA de Versailles, Institut Jean-Pierre Bourgin, Station de Génétique et d'Amélioration des Plantes UR-254, Versailles, France
| | - Ghislaine Gendrot
- INRA de Versailles, Institut Jean-Pierre Bourgin, Station de Génétique et d'Amélioration des Plantes UR-254, Versailles, France
| | - Mathilde Grelon
- INRA de Versailles, Institut Jean-Pierre Bourgin, Station de Génétique et d'Amélioration des Plantes UR-254, Versailles, France
- * E-mail:
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25
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Abstract
Accurate segregation of chromosomes during meiosis requires physical links between homologs. These links are usually established through chromosome pairing, synapsis, and recombination, which occur during meiotic prophase. How chromosomes pair with their homologous partners is one of the outstanding mysteries of meiosis. Surprisingly, experimental evidence indicates that different organisms have found more than one way to accomplish this feat. Whereas some species depend on recombination machinery to achieve homologous pairing, others are able to pair and synapse their homologs in the absence of recombination. To ensure specific pairing between homologous chromosomes, both recombination-dependent and recombination-independent mechanisms must strike the proper balance between forces that promote chromosome interactions and activities that temper the promiscuity of those interactions. The initiation of synapsis is likely to be a tightly regulated step in a process that must be mechanically coupled to homolog pairing.
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Affiliation(s)
- Needhi Bhalla
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA.
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26
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d'Erfurth I, Jolivet S, Froger N, Catrice O, Novatchkova M, Simon M, Jenczewski E, Mercier R. Mutations in AtPS1 (Arabidopsis thaliana parallel spindle 1) lead to the production of diploid pollen grains. PLoS Genet 2008; 4:e1000274. [PMID: 19043546 PMCID: PMC2581889 DOI: 10.1371/journal.pgen.1000274] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 10/20/2008] [Indexed: 11/25/2022] Open
Abstract
Polyploidy has had a considerable impact on the evolution of many eukaryotes, especially angiosperms. Indeed, most--if not all-angiosperms have experienced at least one round of polyploidy during the course of their evolution, and many important crop plants are current polyploids. The occurrence of 2n gametes (diplogametes) in diploid populations is widely recognised as the major source of polyploid formation. However, limited information is available on the genetic control of diplogamete production. Here, we describe the isolation and characterisation of the first gene, AtPS1 (Arabidopsis thaliana Parallel Spindle 1), implicated in the formation of a high frequency of diplogametes in plants. Atps1 mutants produce diploid male spores, diploid pollen grains, and spontaneous triploid plants in the next generation. Female meiosis is not affected in the mutant. We demonstrated that abnormal spindle orientation at male meiosis II leads to diplogamete formation. Most of the parent's heterozygosity is therefore conserved in the Atps1 diploid gametes, which is a key issue for plant breeding. The AtPS1 protein is conserved throughout the plant kingdom and carries domains suggestive of a regulatory function. The isolation of a gene involved in diplogamete production opens the way for new strategies in plant breeding programmes and progress in evolutionary studies.
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Affiliation(s)
- Isabelle d'Erfurth
- French National Institute for Agricultural Research (INRA), UR254, Versailles, France
| | - Sylvie Jolivet
- French National Institute for Agricultural Research (INRA), UR254, Versailles, France
| | - Nicole Froger
- French National Institute for Agricultural Research (INRA), UR254, Versailles, France
| | - Olivier Catrice
- National Center for Scientific Research (CNRS), UPR2355, Gif sur Yvette, France
| | | | - Mathieu Simon
- French National Institute for Agricultural Research (INRA), UR254, Versailles, France
| | - Eric Jenczewski
- French National Institute for Agricultural Research (INRA), UR254, Versailles, France
| | - Raphaël Mercier
- French National Institute for Agricultural Research (INRA), UR254, Versailles, France
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27
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Bozza C, Pawlowski W. The cytogenetics of homologous chromosome pairing in meiosis in plants. Cytogenet Genome Res 2008; 120:313-9. [DOI: 10.1159/000121080] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2007] [Indexed: 11/19/2022] Open
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28
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Pezza RJ, Voloshin ON, Vanevski F, Camerini-Otero RD. Hop2/Mnd1 acts on two critical steps in Dmc1-promoted homologous pairing. Genes Dev 2007; 21:1758-66. [PMID: 17639081 PMCID: PMC1920170 DOI: 10.1101/gad.1562907] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Meiotic recombination between homologous chromosomes ensures their proper segregation at the first division of meiosis and is the main force shaping genetic variation of genomes. The HOP2 and MND1 genes are essential for this recombination: Their disruption results in severe defects in homologous chromosome synapsis and an early-stage failure in meiotic recombination. The mouse Hop2 and Mnd1 proteins form a stable heterodimer (Hop2/Mnd1) that greatly enhances Dmc1-mediated strand invasion. In order to elucidate the mechanism by which Hop2/Mnd1 stimulates Dmc1, we identify several intermediate steps in the homologous pairing reaction promoted by Dmc1. We show that Hop2/Mnd1 greatly stimulates Dmc1 to promote synaptic complex formation on long duplex DNAs, a step previously revealed only for bacterial homologous recombinases. This synaptic alignment is a consequence of the ability of Hop2/Mnd1 to (1) stabilize Dmc1-single-stranded DNA (ssDNA) nucleoprotein complexes, and (2) facilitate the conjoining of DNA molecules through the capture of double-stranded DNA by the Dmc1-ssDNA nucleoprotein filament. To our knowledge, Hop2/Mnd1 is the first homologous recombinase accessory protein that acts on these two separate and critical steps in mammalian meiotic recombination.
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Affiliation(s)
- Roberto J. Pezza
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Oleg N. Voloshin
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Filip Vanevski
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - R. Daniel Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
- Corresponding author.E-MAIL ; FAX (301) 496-9878
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