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Reis Soares N, Costa ZP, Marques JPR, Garsmeur O, Sampaio Carneiro M, Monteiro Vitorello CB, D'Hont A, Vieira MLC. First investigation into the genetic control of meiosis in sugarcane. Plant J 2024. [PMID: 38523577 DOI: 10.1111/tpj.16731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/28/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024]
Abstract
The sugarcane (Saccharum spp.) genome is one of the most complex of all. Modern varieties are highly polyploid and aneuploid as a result of hybridization between Saccharum officinarum and S. spontaneum. Little research has been done on meiotic control in polyploid species, with the exception of the wheat Ph1 locus harboring the ZIP4 gene (TaZIP4-B2) which promotes pairing between homologous chromosomes while suppressing crossover between homeologs. In sugarcane, despite its interspecific origin, bivalent association is favored, and multivalents, if any, are resolved at the end of prophase I. Thus, our aim herein was to investigate the purported genetic control of meiosis in the parental species and in sugarcane itself. We investigated the ZIP4 gene and immunolocalized meiotic proteins, namely synaptonemal complex proteins Zyp1 and Asy1. The sugarcane ZIP4 gene is located on chromosome 2 and expressed more abundantly in flowers, a similar profile to that found for TaZIP4-B2. ZIP4 expression is higher in S. spontaneum a neoautopolyploid, with lower expression in S. officinarum, a stable octoploid species. The sugarcane Zip4 protein contains a TPR domain, essential for scaffolding. Its 3D structure was also predicted, and it was found to be very similar to that of TaZIP4-B2, reflecting their functional relatedness. Immunolocalization of the Asy1 and Zyp1 proteins revealed that S. officinarum completes synapsis. However, in S. spontaneum and SP80-3280 (a modern variety), no nuclei with complete synapsis were observed. Importantly, our results have implications for sugarcane cytogenetics, genetic mapping, and genomics.
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Affiliation(s)
- Nina Reis Soares
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
| | - João Paulo Rodrigues Marques
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, SP, 13635-900, Pirassununga, São Paulo, Brazil
| | - Olivier Garsmeur
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, 13604-900, Araras, São Paulo, Brazil
| | - Cláudia Barros Monteiro Vitorello
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
| | - Angélique D'Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, São Paulo, Brazil
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2
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Chen L, Weir JR. The molecular machinery of meiotic recombination. Biochem Soc Trans 2024; 52:379-393. [PMID: 38348856 PMCID: PMC10903461 DOI: 10.1042/bst20230712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Meiotic recombination, a cornerstone of eukaryotic diversity and individual genetic identity, is essential for the creation of physical linkages between homologous chromosomes, facilitating their faithful segregation during meiosis I. This process requires that germ cells generate controlled DNA lesions within their own genome that are subsequently repaired in a specialised manner. Repair of these DNA breaks involves the modulation of existing homologous recombination repair pathways to generate crossovers between homologous chromosomes. Decades of genetic and cytological studies have identified a multitude of factors that are involved in meiotic recombination. Recent work has started to provide additional mechanistic insights into how these factors interact with one another, with DNA, and provide the molecular outcomes required for a successful meiosis. Here, we provide a review of the recent developments with a focus on protein structures and protein-protein interactions.
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Affiliation(s)
- Linda Chen
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - John R Weir
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
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3
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Blundon JM, Cesar BI, Bae JW, Čavka I, Haversat J, Ries J, Köhler S, Kim Y. Skp1 proteins are structural components of the synaptonemal complex in C. elegans. Sci Adv 2024; 10:eadl4876. [PMID: 38354250 PMCID: PMC10866564 DOI: 10.1126/sciadv.adl4876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The synaptonemal complex (SC) is a zipper-like protein assembly that links homologous chromosomes to regulate recombination and segregation during meiosis. The SC has been notoriously refractory to in vitro reconstitution, thus leaving its molecular organization largely unknown. Here, we report a moonlighting function of two paralogous S-phase kinase-associated protein 1 (Skp1)-related proteins (SKR-1 and SKR-2), well-known adaptors of the Skp1-Cul1-F-box (SCF) ubiquitin ligase, as the key missing components of the SC in Caenorhabditis elegans. SKR proteins repurpose their SCF-forming interfaces to dimerize and interact with meiosis-specific SC proteins, thereby driving synapsis independent of SCF activity. SKR-1 enables the formation of the long-sought-after soluble complex with previously identified SC proteins in vitro, which we propose it to represent a complete SC building block. Our findings demonstrate how a conserved cell cycle regulator has been co-opted to interact with rapidly evolving meiotic proteins to construct the SC and provide a foundation for understanding its structure and assembly mechanisms.
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Affiliation(s)
- Joshua M. Blundon
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Brenda I. Cesar
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jung Woo Bae
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ivana Čavka
- The European Molecular Biology Laboratory, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Jocelyn Haversat
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jonas Ries
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Simone Köhler
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yumi Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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4
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Versini R, Sritharan S, Aykac Fas B, Tubiana T, Aimeur SZ, Henri J, Erard M, Nüsse O, Andreani J, Baaden M, Fuchs P, Galochkina T, Chatzigoulas A, Cournia Z, Santuz H, Sacquin-Mora S, Taly A. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model 2024; 64:26-41. [PMID: 38124369 DOI: 10.1021/acs.jcim.3c01361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
AlphaFold2 (AF2) and RoseTTaFold (RF) have revolutionized structural biology, serving as highly reliable and effective methods for predicting protein structures. This article explores their impact and limitations, focusing on their integration into experimental pipelines and their application in diverse protein classes, including membrane proteins, intrinsically disordered proteins (IDPs), and oligomers. In experimental pipelines, AF2 models help X-ray crystallography in resolving the phase problem, while complementarity with mass spectrometry and NMR data enhances structure determination and protein flexibility prediction. Predicting the structure of membrane proteins remains challenging for both AF2 and RF due to difficulties in capturing conformational ensembles and interactions with the membrane. Improvements in incorporating membrane-specific features and predicting the structural effect of mutations are crucial. For intrinsically disordered proteins, AF2's confidence score (pLDDT) serves as a competitive disorder predictor, but integrative approaches including molecular dynamics (MD) simulations or hydrophobic cluster analyses are advocated for accurate dynamics representation. AF2 and RF show promising results for oligomeric models, outperforming traditional docking methods, with AlphaFold-Multimer showing improved performance. However, some caveats remain in particular for membrane proteins. Real-life examples demonstrate AF2's predictive capabilities in unknown protein structures, but models should be evaluated for their agreement with experimental data. Furthermore, AF2 models can be used complementarily with MD simulations. In this Perspective, we propose a "wish list" for improving deep-learning-based protein folding prediction models, including using experimental data as constraints and modifying models with binding partners or post-translational modifications. Additionally, a meta-tool for ranking and suggesting composite models is suggested, driving future advancements in this rapidly evolving field.
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Affiliation(s)
- Raphaelle Versini
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Sujith Sritharan
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Burcu Aykac Fas
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sana Zineb Aimeur
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Julien Henri
- Sorbonne Université, CNRS, Laboratoire de Biologie, Computationnelle et Quantitative UMR 7238, Institut de Biologie Paris-Seine, 4 Place Jussieu, F-75005 Paris, France
| | - Marie Erard
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Oliver Nüsse
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Patrick Fuchs
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Université de Paris, UFR Sciences du Vivant, 75013 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Alexios Chatzigoulas
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
- Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Hubert Santuz
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France
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Vrielynck N, Peuch M, Durand S, Lian Q, Chambon A, Hurel A, Guérin J, Guérois R, Mercier R, Grelon M, Mézard C. SCEP1 and SCEP2 are two new components of the synaptonemal complex central element. Nat Plants 2023; 9:2016-2030. [PMID: 37973938 DOI: 10.1038/s41477-023-01558-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
The synaptonemal complex (SC) is a proteinaceous structure that forms between homologous chromosomes during meiosis prophase. The SC is widely conserved across species, but its structure and roles during meiotic recombination are still debated. While the SC central region is made up of transverse filaments and central element proteins in mammals and fungi, few central element proteins have been identified in other species. Here we report the identification of two coiled-coil proteins, SCEP1 and SCEP2, that form a complex and localize at the centre of the Arabidopsis thaliana SC. In scep1 and scep2 mutants, chromosomes are aligned but not synapsed (the ZYP1 transverse filament protein is not loaded), crossovers are increased compared with the wild type, interference is lost and heterochiasmy is strongly reduced. We thus report the identification of two plant SC central elements, and homologues of these are found in all major angiosperm clades.
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Affiliation(s)
- Nathalie Vrielynck
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Marion Peuch
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Stéphanie Durand
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aurélie Chambon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Aurélie Hurel
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Julie Guérin
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France
| | - Raphaël Guérois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Raphaël Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mathilde Grelon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France.
| | - Christine Mézard
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin, Versailles, France.
- Université Paris-Saclay, INRAE, AgroParisTech, CNRS, Institut Jean-Pierre Bourgin, Versailles, France.
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6
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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7
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Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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Draeger TN, Rey MD, Hayta S, Smedley M, Alabdullah AK, Moore G, Martín AC. ZIP4 is required for normal progression of synapsis and for over 95% of crossovers in wheat meiosis. Front Plant Sci 2023; 14:1189998. [PMID: 37324713 PMCID: PMC10266424 DOI: 10.3389/fpls.2023.1189998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
Tetraploid (AABB) and hexaploid (AABBDD) wheat have multiple sets of similar chromosomes, with successful meiosis and preservation of fertility relying on synapsis and crossover (CO) formation only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic gene TaZIP4-B2 (Ph1) on chromosome 5B, promotes CO formation between homologous chromosomes, whilst suppressing COs between homeologous (related) chromosomes. In other species, ZIP4 mutations eliminate approximately 85% of COs, consistent with loss of the class I CO pathway. Tetraploid wheat has three ZIP4 copies: TtZIP4-A1 on chromosome 3A, TtZIP4-B1 on 3B and TtZIP4-B2 on 5B. Here, we have developed single, double and triple zip4 TILLING mutants and a CRISPR Ttzip4-B2 mutant, to determine the effect of ZIP4 genes on synapsis and CO formation in the tetraploid wheat cultivar 'Kronos'. We show that disruption of two ZIP4 gene copies in Ttzip4-A1B1 double mutants, results in a 76-78% reduction in COs when compared to wild-type plants. Moreover, when all three copies are disrupted in Ttzip4-A1B1B2 triple mutants, COs are reduced by over 95%, suggesting that the TtZIP4-B2 copy may also affect class II COs. If this is the case, the class I and class II CO pathways may be interlinked in wheat. When ZIP4 duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy, TaZIP4-B2, could have acquired an additional function to stabilize both CO pathways. In tetraploid plants deficient in all three ZIP4 copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3 Mb deletion mutant, ph1b, encompassing the TaZIP4-B2 gene on chromosome 5B. These findings confirm the requirement of ZIP4-B2 for efficient synapsis, and suggest that TtZIP4 genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus, ZIP4-B2 in wheat accounts for the two major phenotypes reported for Ph1, promotion of homologous synapsis and suppression of homeologous COs.
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Affiliation(s)
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Córdoba, Córdoba, Spain
| | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Azahara C. Martín
- Department of Plant Genetic Improvement, Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
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9
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Almanzar DE, Gordon SG, Bristow C, Hamrick A, von Diezmann L, Liu H, Rog O. Meiotic DNA exchanges in C. elegans are promoted by proximity to the synaptonemal complex. Life Sci Alliance 2023; 6:e202301906. [PMID: 36697255 PMCID: PMC9877436 DOI: 10.26508/lsa.202301906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
During meiosis, programmed double-strand DNA breaks are repaired to form exchanges between the parental chromosomes called crossovers. Chromosomes lacking a crossover fail to segregate accurately into the gametes, leading to aneuploidy. In addition to engaging the homolog, crossover formation requires the promotion of exchanges, rather than non-exchanges, as repair products. However, the mechanism underlying this meiosis-specific preference is not fully understood. Here, we study the regulation of meiotic sister chromatid exchanges in Caenorhabditis elegans by direct visualization. We find that a conserved chromosomal interface that promotes exchanges between the parental chromosomes, the synaptonemal complex, can also promote exchanges between the sister chromatids. In both cases, exchanges depend on the recruitment of the same set of pro-exchange factors to repair sites. Surprisingly, although the synaptonemal complex usually assembles between the two DNA molecules undergoing an exchange, its activity does not rely on a specific chromosome conformation. This suggests that the synaptonemal complex regulates exchanges-both crossovers and sister exchanges-by establishing a nuclear domain conducive to nearby recruitment of exchange-promoting factors.
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Affiliation(s)
- David E Almanzar
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Spencer G Gordon
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Chloe Bristow
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Antonia Hamrick
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Lexy von Diezmann
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Hanwenheng Liu
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT, USA
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10
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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11
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Pollard MG, Rockmill B, Oke A, Anderson CM, Fung JC. Kinetic analysis of synaptonemal complex dynamics during meiosis of yeast Saccharomyces cerevisiae reveals biphasic growth and abortive disassembly. Front Cell Dev Biol 2023; 11:1098468. [PMID: 36814598 PMCID: PMC9939684 DOI: 10.3389/fcell.2023.1098468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
The synaptonemal complex (SC) is a dynamic structure formed between chromosomes during meiosis which stabilizes and supports many essential meiotic processes such as pairing and recombination. In budding yeast, Zip1 is a functionally conserved element of the SC that is important for synapsis. Here, we directly measure the kinetics of Zip1-GFP assembly and disassembly in live cells of the yeast S. cerevisiae. The imaging of SC assembly in yeast is challenging due to the large number of chromosomes packed into a small nucleus. We employ a zip3Δ mutant in which only a few chromosomes undergo synapsis at any given time, initiating from a single site on each chromosome, thus allowing the assembly and disassembly kinetics of single SCs to be accurately monitored in living cells. SC assembly occurs with both monophasic and biphasic kinetics, in contrast to the strictly monophasic assembly seen in C. elegans. In wild-type cells, once maximal synapsis is achieved, programmed final disassembly rapidly follows, as Zip1 protein is actively degraded. In zip3Δ, this period is extended and final disassembly is prolonged. Besides final disassembly, we found novel disassembly events involving mostly short SCs that disappeared in advance of programmed final disassembly, which we termed "abortive disassembly." Abortive disassembly is distinct from final disassembly in that it occurs when Zip1 protein levels are still high, and exhibits a much slower rate of disassembly, suggesting a different mechanism for removal in the two types of disassembly. We speculate that abortive disassembly events represent defective or stalled SCs, possibly representing SC formation between non-homologs, that is then targeted for dissolution. These results reveal novel aspects of SC assembly and disassembly, potentially providing evidence of additional regulatory pathways controlling not just the assembly, but also the disassembly, of this complex cellular structure.
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Affiliation(s)
| | | | | | | | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
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Song J, Sha Y, Liu X, Zeng X, Zhao X. Novel mutations of TEX11 are associated with non-obstructive azoospermia. Front Endocrinol (Lausanne) 2023; 14:1159723. [PMID: 37124723 PMCID: PMC10140331 DOI: 10.3389/fendo.2023.1159723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
Non-obstructive azoospermia (NOA) affects 10% of infertile men worldwide, and genetic studies revealed that there are plenty of monogenic mutations that responsible for a part of idiopathic NOA cases. Testis-expressed gene 11 (TEX11) is an X-linked meiosis-specific gene, many pathogenic variants in TEX11 have been detected in NOA patients, and the deficiency of this gene can cause abnormal meiotic recombination and chromosomal synapsis. However, many NOA-affected cases caused by TEX11 mutation remain largely unknown. This study reported three novel TEX11 mutations (exon 5, c.313C>T: p.R105*), (exon 7, c.427A>C: p.K143Q) and (exon 29, c.2575G>A: p.G859R). Mutations were screened using whole-exome sequencing (WES) and further verified by amplifying and sequencing the specific exon. Histological analysis of testicular biopsy specimens revealed a thicker basement membrane of the seminiferous tubules and poorly developed spermatocytes, and no post-meiotic round spermatids or mature spermatozoa were observed in the seminiferous tubules of patients with TEX11 mutation. Conclusion This study presents three novel variants of TEX11 as potential infertility alleles that have not been previously reported. It expanded the variant spectrum of patients with NOA, which also emphasizes the necessity of this gene screening for the clinical auxiliary diagnosis of patients with azoospermia.
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Affiliation(s)
- Jian Song
- Affiliated Hospital of Nantong University, School of Medicine, Nantong University, Nantong, China
- School of Medicine, Nantong University, Nantong, China
| | - Yanwei Sha
- Department of Andrology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Xiaojun Liu
- School of Medicine, Nantong University, Nantong, China
| | - Xuhui Zeng
- School of Medicine, Nantong University, Nantong, China
- *Correspondence: Xuhui Zeng, ; Xiuling Zhao,
| | - Xiuling Zhao
- School of Medicine, Nantong University, Nantong, China
- *Correspondence: Xuhui Zeng, ; Xiuling Zhao,
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Nibau C, Gonzalo A, Evans A, Sweet‐Jones W, Phillips D, Lloyd A. Meiosis in allopolyploid Arabidopsis suecica. Plant J 2022; 111:1110-1122. [PMID: 35759495 PMCID: PMC9545853 DOI: 10.1111/tpj.15879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 06/01/2023]
Abstract
Polyploidy is a major force shaping eukaryote evolution but poses challenges for meiotic chromosome segregation. As a result, first-generation polyploids often suffer from more meiotic errors and lower fertility than established wild polyploid populations. How established polyploids adapt their meiotic behaviour to ensure genome stability and accurate chromosome segregation remains an active research question. We present here a cytological description of meiosis in the model allopolyploid species Arabidopsis suecica (2n = 4x = 26). In large part meiosis in A. suecica is diploid-like, with normal synaptic progression and no evidence of synaptic partner exchanges. Some abnormalities were seen at low frequency, including univalents at metaphase I, anaphase bridges and aneuploidy at metaphase II; however, we saw no evidence of crossover formation occurring between non-homologous chromosomes. The crossover number in A. suecica is similar to the combined number reported from its diploid parents Arabidopsis thaliana (2n = 2x = 10) and Arabidopsis arenosa (2n = 2x = 16), with an average of approximately 1.75 crossovers per chromosome pair. This contrasts with naturally evolved autotetraploid A. arenosa, where accurate chromosome segregation is achieved by restricting crossovers to approximately 1 per chromosome pair. Although an autotetraploid donor is hypothesized to have contributed the A. arenosa subgenome to A. suecica, A. suecica harbours diploid A. arenosa variants of key meiotic genes. These multiple lines of evidence suggest that meiosis in the recently evolved allopolyploid A. suecica is essentially diploid like, with meiotic adaptation following a very different trajectory to that described for autotetraploid A. arenosa.
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Affiliation(s)
- Candida Nibau
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - Adrián Gonzalo
- John Innes CentreColney LaneNorwichNR4 7UHUK
- Department of Biology, Institute of Molecular Plant BiologySwiss Federal Institute of Technology (ETH) ZürichZürich8092Switzerland
| | - Aled Evans
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - William Sweet‐Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - Dylan Phillips
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
| | - Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS)Aberystwyth UniversityPenglaisAberystwythCeredigionSY23 3DAUK
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Higgins JD, Osman K, Desjardins SD, Henderson IR, Edwards KJ, Franklin FCH. Unravelling mechanisms that govern meiotic crossover formation in wheat. Biochem Soc Trans 2022:BST20220405. [PMID: 35901450 DOI: 10.1042/BST20220405] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Wheat is a major cereal crop that possesses a large allopolyploid genome formed through hybridisation of tetraploid and diploid progenitors. During meiosis, crossovers (COs) are constrained in number to 1–3 per chromosome pair that are predominantly located towards the chromosome ends. This reduces the probability of advantageous traits recombining onto the same chromosome, thus limiting breeding. Therefore, understanding the underlying factors controlling meiotic recombination may provide strategies to unlock the genetic potential in wheat. In this mini-review, we will discuss the factors associated with restricted CO formation in wheat, such as timing of meiotic events, chromatin organisation, pre-meiotic DNA replication and dosage of CO genes, as a means to modulate recombination.
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Abstract
In this Outlook, Grey and de Massy discuss a study by Pyatnitskaya et al. in this issue of Genes & Development that highlights the central role of the Saccharomyces cerevisiae ZMM protein Zip4 in how crossover formation and synapsis initiation are linked. During meiosis, a molecular program induces DNA double-strand breaks (DSBs) and their repair by homologous recombination. DSBs can be repaired with or without crossovers. ZMM proteins promote the repair toward crossover. The sites of DSB repair are also sites where the axes of homologous chromosomes are juxtaposed and stabilized, and where a structure called the synaptonemal complex initiates, providing further regulation of both DSB formation and repair. How crossover formation and synapsis initiation are linked has remained unknown. The study by Pyatnitskaya and colleagues (pp. 53–69) in this issue of Genes & Development highlights the central role of the Saccharomyces cerevisiae ZMM protein Zip4 in this process.
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Affiliation(s)
- Corinne Grey
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Université Montpellier, Montpellier 34396, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Université Montpellier, Montpellier 34396, France
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