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Tang S, Koo J, Pourhosseinzadeh M, Nguyen E, Liu N, Ma C, Lu H, Lee M, Hunter N. Synaptonemal complex protects double-Holliday junctions during meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.14.613089. [PMID: 39314413 PMCID: PMC11419148 DOI: 10.1101/2024.09.14.613089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Chromosomal linkages formed through crossover recombination are essential for accurate segregation of homologous chromosomes during meiosis1. DNA events of recombination are spatially and functionally linked to structural components of meiotic chromosomes2. Imperatively, biased resolution of double-Holliday junction (dHJ) intermediates into crossovers3,4 occurs within the synaptonemal complex (SC), the meiosis-specific structure that mediates homolog synapsis during the pachytene stage5,6. However, the SC's role in crossing over remains unclear. Here we show that SC promotes crossover-specific resolution by protecting dHJs from unscheduled and aberrant resolution. When key SC components are conditionally inactivated during pachytene, dHJs are resolved into noncrossover products by Sgs1-Top3-Rmi1 (STR), the yeast ortholog of the human BLM complex7. Cohesin, the core component of SC lateral elements, plays a primary role in chromatin organization and is required to maintain both SCs and crossover recombination complexes (CRCs) during pachytene. SC central region component Zip1 is required to maintain CRCs even when dHJs are stabilized by inactivating STR. Reciprocally, SC stability requires continuous presence of CRCs, an unanticipated interdependence with important implications for SC dynamics. In conclusion, through hierarchical and interdependent functions of its key components, the SC enables crossover-specific dHJ resolution and thereby ensures the linkage and segregation of homologous chromosomes.
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Affiliation(s)
- Shangming Tang
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer Koo
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Mohammad Pourhosseinzadeh
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Emerald Nguyen
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Natalie Liu
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Christopher Ma
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Hanyu Lu
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Monica Lee
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
- Department of Molecular & Cellular Biology, University of California, Davis, Davis, CA, USA
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2
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Dumont A, Mendiboure N, Savocco J, Anani L, Moreau P, Thierry A, Modolo L, Jost D, Piazza A. Mechanism of homology search expansion during recombinational DNA break repair in Saccharomyces cerevisiae. Mol Cell 2024; 84:3237-3253.e6. [PMID: 39178861 DOI: 10.1016/j.molcel.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/26/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
Homology search is a central step of DNA double-strand break (DSB) repair by homologous recombination (HR). How it operates in cells remains elusive. We developed a Hi-C-based methodology to map single-stranded DNA (ssDNA) contacts genome-wide in S. cerevisiae, which revealed two main homology search phases. Initial search conducted by short Rad51-ssDNA nucleoprotein filaments (NPFs) is confined in cis by cohesin-mediated chromatin loop folding. Progressive growth of stiff NPFs enables exploration of distant genomic sites. Long-range resection drives this transition from local to genome-wide search by increasing the probability of assembling extensive NPFs. DSB end-tethering promotes coordinated search by opposite NPFs. Finally, an autonomous genetic element on chromosome III engages the NPF, which stimulates homology search in its vicinity. This work reveals the mechanism of the progressive expansion of homology search that is orchestrated by chromatin organizers, long-range resection, end-tethering, and specialized genetic elements and that exploits the stiff NPF structure conferred by Rad51 oligomerization.
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Affiliation(s)
- Agnès Dumont
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Nicolas Mendiboure
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Jérôme Savocco
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Loqmen Anani
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Pierrick Moreau
- Unité Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525, 75015 Paris, France
| | - Agnès Thierry
- Unité Régulation spatiale des génomes, Institut Pasteur, CNRS UMR3525, 75015 Paris, France
| | - Laurent Modolo
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France
| | - Aurèle Piazza
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR5239, Laboratoire de Biologie et Modélisation de la Cellule, 46 Allée d'Italie, 69007 Lyon, France.
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3
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Dutta A, Dutreux F, Garin M, Caradec C, Friedrich A, Brach G, Thiele P, Gaudin M, Llorente B, Schacherer J. Multiple independent losses of crossover interference during yeast evolutionary history. PLoS Genet 2024; 20:e1011426. [PMID: 39325820 PMCID: PMC11460703 DOI: 10.1371/journal.pgen.1011426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/08/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Meiotic recombination is essential for the accurate chromosome segregation and the generation of genetic diversity through crossover and gene conversion events. Although this process has been studied extensively in a few selected model species, understanding how its properties vary across species remains limited. For instance, the ancestral ZMM pathway that generates interference-dependent crossovers has undergone multiple losses throughout evolution, suggesting variations in the regulation of crossover formation. In this context, we first characterized the meiotic recombination landscape and properties of the Kluyveromyces lactis budding yeast. We then conducted a comprehensive analysis of 29,151 recombination events (19, 212 COs and 9, 939 NCOs) spanning 577 meioses in the five budding yeast species Saccharomyces cerevisiae, Saccharomyces paradoxus, Lachancea kluyveri, Lachancea waltii and K. lactis. Eventually, we found that the Saccharomyces yeasts displayed higher recombination rates compared to the non-Saccharomyces yeasts. In addition, bona fide crossover interference and associated crossover homeostasis were detected in the Saccharomyces species only, adding L. kluyveri and K. lactis to the list of budding yeast species that lost crossover interference. Finally, recombination hotspots, although highly conserved within the Saccharomyces yeasts are not conserved beyond the Saccharomyces genus. Overall, these results highlight great variability in the recombination landscape and properties through budding yeasts evolution.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Marion Garin
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Gauthier Brach
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Pia Thiele
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
| | - Maxime Gaudin
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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4
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Crickard JB, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. Genetics 2024; 227:iyae066. [PMID: 38657110 PMCID: PMC11228845 DOI: 10.1093/genetics/iyae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80% of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates to perform its role in crossover resolution. We performed a gene dosage screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3. Specifically, we looked for genes whose lowered dosage reduced meiotic crossing over using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. To our surprise we identified genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and in vivo. Partial complementation of Mlh3 crossover functions was observed when MLH3 was expressed under the control of the CLB1 promoter (NDT80 regulon), suggesting that Mlh3 function can be provided late in meiotic prophase at some functional cost. A model for how Dmc1 could facilitate Mlh1-Mlh3's role in crossover resolution is presented.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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5
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Condezo YB, Sainz-Urruela R, Gomez-H L, Salas-Lloret D, Felipe-Medina N, Bradley R, Wolff ID, Tanis S, Barbero JL, Sánchez-Martín M, de Rooij D, Hendriks IA, Nielsen ML, Gonzalez-Prieto R, Cohen PE, Pendas AM, Llano E. RNF212B E3 ligase is essential for crossover designation and maturation during male and female meiosis in the mouse. Proc Natl Acad Sci U S A 2024; 121:e2320995121. [PMID: 38865271 PMCID: PMC11194559 DOI: 10.1073/pnas.2320995121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/15/2024] [Indexed: 06/14/2024] Open
Abstract
Meiosis, a reductional cell division, relies on precise initiation, maturation, and resolution of crossovers (COs) during prophase I to ensure the accurate segregation of homologous chromosomes during metaphase I. This process is regulated by the interplay of RING-E3 ligases such as RNF212 and HEI10 in mammals. In this study, we functionally characterized a recently identified RING-E3 ligase, RNF212B. RNF212B colocalizes and interacts with RNF212, forming foci along chromosomes from zygonema onward in a synapsis-dependent and DSB-independent manner. These consolidate into larger foci at maturing COs, colocalizing with HEI10, CNTD1, and MLH1 by late pachynema. Genetically, RNF212B foci formation depends on Rnf212 but not on Msh4, Hei10, and Cntd1, while the unloading of RNF212B at the end of pachynema is dependent on Hei10 and Cntd1. Mice lacking RNF212B, or expressing an inactive RNF212B protein, exhibit modest synapsis defects, a reduction in the localization of pro-CO factors (MSH4, TEX11, RPA, MZIP2) and absence of late CO-intermediates (MLH1). This loss of most COs by diakinesis results in mostly univalent chromosomes. Double mutants for Rnf212b and Rnf212 exhibit an identical phenotype to that of Rnf212b single mutants, while double heterozygous demonstrate a dosage-dependent reduction in CO number, indicating a functional interplay between paralogs. SUMOylome analysis of testes from Rnf212b mutants and pull-down analysis of Sumo- and Ubiquitin-tagged HeLa cells, suggest that RNF212B is an E3-ligase with Ubiquitin activity, serving as a crucial factor for CO maturation. Thus, RNF212 and RNF212B play vital, yet overlapping roles, in ensuring CO homeostasis through their distinct E3 ligase activities.
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Affiliation(s)
- Yazmine B. Condezo
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (onsejo Superior de Investigaciones Científicas-Universidad de Salamanca), 37007Salamanca, Spain
| | - Raquel Sainz-Urruela
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (onsejo Superior de Investigaciones Científicas-Universidad de Salamanca), 37007Salamanca, Spain
| | - Laura Gomez-H
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (onsejo Superior de Investigaciones Científicas-Universidad de Salamanca), 37007Salamanca, Spain
- Department of Totipotency, Max Planck Institute of Biochemistry, 82152Martinsried, Germany
| | - Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Natalia Felipe-Medina
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (onsejo Superior de Investigaciones Científicas-Universidad de Salamanca), 37007Salamanca, Spain
| | - Rachel Bradley
- Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Ian D. Wolff
- Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Stephanie Tanis
- Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Jose Luis Barbero
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, 28040Madrid, Spain
| | | | - Dirk de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht3584CM, The Netherlands
| | - Ivo A. Hendriks
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200Copenhagen, Denmark
| | - Michael L. Nielsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200Copenhagen, Denmark
| | - Román Gonzalez-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Andalusian Center for Molecular Biology and Regenerative MedicineCentro Andaluz de Biología Molecular y Medicina Regenerativa, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad-Pablo de Olavide, 41092Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41012Sevilla, Spain
| | - Paula E. Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY14853
| | - Alberto M. Pendas
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (onsejo Superior de Investigaciones Científicas-Universidad de Salamanca), 37007Salamanca, Spain
| | - Elena Llano
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (onsejo Superior de Investigaciones Científicas-Universidad de Salamanca), 37007Salamanca, Spain
- Departamento de Fisiología, Universidad de Salamanca, 37007Salamanca, Spain
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6
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Arter M, Keeney S. Divergence and conservation of the meiotic recombination machinery. Nat Rev Genet 2024; 25:309-325. [PMID: 38036793 DOI: 10.1038/s41576-023-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 12/02/2023]
Abstract
Sexually reproducing eukaryotes use recombination between homologous chromosomes to promote chromosome segregation during meiosis. Meiotic recombination is almost universally conserved in its broad strokes, but specific molecular details often differ considerably between taxa, and the proteins that constitute the recombination machinery show substantial sequence variability. The extent of this variation is becoming increasingly clear because of recent increases in genomic resources and advances in protein structure prediction. We discuss the tension between functional conservation and rapid evolutionary change with a focus on the proteins that are required for the formation and repair of meiotic DNA double-strand breaks. We highlight phylogenetic relationships on different time scales and propose that this remarkable evolutionary plasticity is a fundamental property of meiotic recombination that shapes our understanding of molecular mechanisms in reproductive biology.
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Affiliation(s)
- Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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7
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Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Tuncay H, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. Nat Commun 2024; 15:2941. [PMID: 38580643 PMCID: PMC10997794 DOI: 10.1038/s41467-024-47020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
Programmed DNA double-strand break (DSB) formation is a crucial feature of meiosis in most organisms. DSBs initiate recombination-mediated linking of homologous chromosomes, which enables correct chromosome segregation in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We uncover in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms. Both IHO1 phosphorylation and formation of axial IHO1 platforms are diminished by chemical inhibition of DBF4-dependent kinase (DDK), suggesting that DDK contributes to the control of the axial DSB-machinery. Furthermore, we show that axial IHO1 platforms are based on an interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.
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Affiliation(s)
- Ihsan Dereli
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Vladyslav Telychko
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Frantzeskos Papanikos
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Kavya Raveendran
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Jiaqi Xu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Michiel Boekhout
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Marcello Stanzione
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Benjamin Neuditschko
- Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria
| | - Naga Sailaja Imjeti
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Elizaveta Selezneva
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hasibe Tuncay
- Department of Developmental Biology, University of Hamburg, 22609, Hamburg, Germany
| | - Sevgican Demir
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Teresa Giannattasio
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Marc Gentzel
- Core Facility Mass Spectrometry & Proteomics, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Anastasiia Bondarieva
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Michelle Stevense
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Marco Barchi
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
- Saint Camillus International University of Health Sciences, Rome, Italy
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, 22609, Hamburg, Germany
| | - John R Weir
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Franz Herzog
- Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Attila Tóth
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany.
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8
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Jones G, Kleckner N, Zickler D. Meiosis through three centuries. Chromosoma 2024; 133:93-115. [PMID: 38730132 PMCID: PMC11180163 DOI: 10.1007/s00412-024-00822-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Meiosis is the specialized cellular program that underlies gamete formation for sexual reproduction. It is therefore not only interesting but also a fundamentally important subject for investigation. An especially attractive feature of this program is that many of the processes of special interest involve organized chromosomes, thus providing the possibility to see chromosomes "in action". Analysis of meiosis has also proven to be useful in discovering and understanding processes that are universal to all chromosomal programs. Here we provide an overview of the different historical moments when the gap between observation and understanding of mechanisms and/or roles for the new discovered molecules was bridged. This review reflects also the synergy of thinking and discussion among our three laboratories during the past several decades.
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Affiliation(s)
- Gareth Jones
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de La Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198, Gif-Sur-Yvette, France
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9
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Zhou X, Fang K, Liu Y, Li W, Tan Y, Zhang J, Yu X, Wang G, Zhang Y, Shang Y, Zhang L, Chen CD, Wang S. ZFP541 and KCTD19 regulate chromatin organization and transcription programs for male meiotic progression. Cell Prolif 2024; 57:e13567. [PMID: 37921559 PMCID: PMC10984108 DOI: 10.1111/cpr.13567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
The successful progression of meiosis prophase I requires integrating information from the structural and molecular levels. In this study, we show that ZFP541 and KCTD19 work in the same genetic pathway to regulate the progression of male meiosis and thus fertility. The Zfp541 and/or Kctd19 knockout male mice show various structural and recombination defects including detached chromosome ends, aberrant localization of chromosome axis components and recombination proteins, and globally altered histone modifications. Further analyses on RNA-seq, ChIP-seq, and ATAC-seq data provide molecular evidence for the above defects and reveal that ZFP541/KCTD19 activates the expression of many genes by repressing several major transcription repressors. More importantly, we reveal an unexpected role of ZFP541/KCTD19 in directly modulating chromatin organization. These results suggest that ZFP541/KCTD19 simultaneously regulates the transcription cascade and chromatin organization to ensure the coordinated progression of multiple events at chromosome structural and biochemical levels during meiosis prophase I.
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Affiliation(s)
- Xu Zhou
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Kailun Fang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell Biology, Chinese Academy of SciencesShanghaiChina
| | - Yanlei Liu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Weidong Li
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Yingjin Tan
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Jiaming Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Xiaoxia Yu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Guoqiang Wang
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Yanan Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
| | - Yongliang Shang
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
| | - Liangran Zhang
- Advanced Medical Research InstituteShandong UniversityJinanShandongChina
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life SciencesShandong Normal UniversityJinanShandongChina
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell Biology, Chinese Academy of SciencesShanghaiChina
| | - Shunxin Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproductive MedicineShandong UniversityJinanShandongChina
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive GeneticsShandong UniversityJinanShandongChina
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive HealthShandong Technology Innovation Center for Reproductive HealthJinanShandongChina
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10
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Dash S, Joshi S, Pankajam AV, Shinohara A, Nishant KT. Heterozygosity alters Msh5 binding to meiotic chromosomes in the baker's yeast. Genetics 2024; 226:iyad214. [PMID: 38124392 DOI: 10.1093/genetics/iyad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Meiotic crossovers are initiated from programmed DNA double-strand breaks. The Msh4-Msh5 heterodimer is an evolutionarily conserved mismatch repair-related protein complex that promotes meiotic crossovers by stabilizing strand invasion intermediates and joint molecule structures such as Holliday junctions. In vivo studies using homozygous strains of the baker's yeast Saccharomyces cerevisiae (SK1) show that the Msh4-Msh5 complex associates with double-strand break hotspots, chromosome axes, and centromeres. Many organisms have heterozygous genomes that can affect the stability of strand invasion intermediates through heteroduplex rejection of mismatch-containing sequences. To examine Msh4-Msh5 function in a heterozygous context, we performed chromatin immunoprecipitation and sequencing (ChIP-seq) analysis in a rapidly sporulating hybrid S. cerevisiae strain (S288c-sp/YJM789, containing sporulation-enhancing QTLs from SK1), using SNP information to distinguish reads from homologous chromosomes. Overall, Msh5 localization in this hybrid strain was similar to that determined in the homozygous strain (SK1). However, relative Msh5 levels were reduced in regions of high heterozygosity, suggesting that high mismatch densities reduce levels of recombination intermediates to which Msh4-Msh5 binds. Msh5 peaks were also wider in the hybrid background compared to the homozygous strain (SK1). We determined regions containing heteroduplex DNA by detecting chimeric sequence reads with SNPs from both parents. Msh5-bound double-strand break hotspots overlap with regions that have chimeric DNA, consistent with Msh5 binding to heteroduplex-containing recombination intermediates.
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Affiliation(s)
- Suman Dash
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Sameer Joshi
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Ajith V Pankajam
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
- Center for High-Performance Computing, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695551, India
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11
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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] [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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12
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Ito M, Fujita Y, Shinohara A. Positive and negative regulators of RAD51/DMC1 in homologous recombination and DNA replication. DNA Repair (Amst) 2024; 134:103613. [PMID: 38142595 DOI: 10.1016/j.dnarep.2023.103613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
RAD51 recombinase plays a central role in homologous recombination (HR) by forming a nucleoprotein filament on single-stranded DNA (ssDNA) to catalyze homology search and strand exchange between the ssDNA and a homologous double-stranded DNA (dsDNA). The catalytic activity of RAD51 assembled on ssDNA is critical for the DNA-homology-mediated repair of DNA double-strand breaks in somatic and meiotic cells and restarting stalled replication forks during DNA replication. The RAD51-ssDNA complex also plays a structural role in protecting the regressed/reversed replication fork. Two types of regulators control RAD51 filament formation, stability, and dynamics, namely positive regulators, including mediators, and negative regulators, so-called remodelers. The appropriate balance of action by the two regulators assures genome stability. This review describes the roles of positive and negative RAD51 regulators in HR and DNA replication and its meiosis-specific homolog DMC1 in meiotic recombination. We also provide future study directions for a comprehensive understanding of RAD51/DMC1-mediated regulation in maintaining and inheriting genome integrity.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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13
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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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14
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Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Erbasi HT, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568863. [PMID: 38077023 PMCID: PMC10705248 DOI: 10.1101/2023.11.27.568863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Programmed DNA double-strand break (DSB) formation is a unique meiotic feature that initiates recombination-mediated linking of homologous chromosomes, thereby enabling chromosome number halving in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We discovered in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms, which are based on a DBF4-dependent kinase (DDK)-modulated interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.
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15
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Brooks Crickard J, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566911. [PMID: 38014100 PMCID: PMC10680668 DOI: 10.1101/2023.11.13.566911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates and whether it interacts with other meiotic factors prior to its role in crossover resolution. We performed a haploinsufficiency screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3 using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. We identified several genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and at times in meiotic prophase when Dmc1 acts as a recombinase. Interestingly, restricting MLH3 expression to roughly the time of crossover resolution resulted in a mlh3 null-like phenotype for crossing over. Our data are consistent with a model in which Dmc1 nucleates a polymer of Mlh1-Mlh3 to promote crossing over.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
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16
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Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
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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17
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Fukui K, Yamamoto T, Murakawa T, Baba S, Kumasaka T, Yano T. Catalytic mechanism of the zinc-dependent MutL endonuclease reaction. Life Sci Alliance 2023; 6:e202302001. [PMID: 37487639 PMCID: PMC10366529 DOI: 10.26508/lsa.202302001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023] Open
Abstract
DNA mismatch repair endonuclease MutL binds two zinc ions. However, the endonuclease activity of MutL is drastically enhanced by other divalent metals such as manganese, implying that MutL binds another catalytic metal at some site other than the zinc-binding sites. Here, we solved the crystal structure of the endonuclease domain of Aquifex aeolicus MutL in the manganese- or cadmium-bound form, revealing that these metals compete with zinc at the same sites. Mass spectrometry revealed that the MutL yielded 5'-phosphate and 3'-OH products, which is characteristic of the two-metal-ion mechanism. Crystallographic analyses also showed that the position and flexibility of a highly conserved Arg of A. aeolicus MutL altered depending on the presence of zinc/manganese or the specific inhibitor cadmium. Site-directed mutagenesis revealed that the Arg was critical for the catalysis. We propose that zinc ion and its binding sites are physiologically of catalytic importance and that the two-metal-ion mechanism works in the reaction, where the Arg plays a catalytic role. Our results also provide a mechanistic insight into the inhibitory effect of a mutagen/carcinogen, cadmium, on MutL.
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Affiliation(s)
- Kenji Fukui
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Tatsuya Yamamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Takeshi Murakawa
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
| | - Seiki Baba
- Structural Biology Division, Japan Synchrotron Radiation Research Institute (JASRI), Hyogo, Japan
| | - Takashi Kumasaka
- Structural Biology Division, Japan Synchrotron Radiation Research Institute (JASRI), Hyogo, Japan
| | - Takato Yano
- Department of Biochemistry, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki, Japan
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18
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Shao Q, Zhang Y, Liu Y, Shang Y, Li S, Liu L, Wang G, Zhou X, Wang P, Gao J, Zhou J, Zhang L, Wang S. ATF7IP2, a meiosis-specific partner of SETDB1, is required for proper chromosome remodeling and crossover formation during spermatogenesis. Cell Rep 2023; 42:112953. [PMID: 37542719 DOI: 10.1016/j.celrep.2023.112953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/25/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023] Open
Abstract
Meiotic crossovers are required for the faithful segregation of homologous chromosomes and to promote genetic diversity. However, it is unclear how crossover formation is regulated, especially on the XY chromosomes, which show a homolog only at the tiny pseudoautosomal region. Here, we show that ATF7IP2 is a meiosis-specific ortholog of ATF7IP and a partner of SETDB1. In the absence of ATF7IP2, autosomes show increased axis length and more crossovers; however, many XY chromosomes lose the obligatory crossover, although the overall XY axis length is also increased. Additionally, meiotic DNA double-strand break formation/repair may also be affected by altered histone modifications. Ultimately, spermatogenesis is blocked, and male mice are infertile. These findings suggest that ATF7IP2 constraints autosomal axis length and crossovers on autosomes; meanwhile, it also modulates XY chromosomes to establish meiotic sex chromosome inactivation for cell-cycle progression and to ensure XY crossover formation during spermatogenesis.
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Affiliation(s)
- Qiqi Shao
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Yanan Zhang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Yanlei Liu
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Yongliang Shang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Si Li
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Lin Liu
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Guoqiang Wang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Xu Zhou
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China
| | - Ping Wang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China
| | - Jinmin Gao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China
| | - Liangran Zhang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250012, China; Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan 250014, Shandong, China.
| | - Shunxin Wang
- Center for Reproductive Medicine, State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong 250012, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong 250012, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, Shandong 250012, China.
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19
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Premkumar T, Paniker L, Kang R, Biot M, Humphrey E, Destain H, Ferranti I, Okulate I, Nguyen H, Kilaru V, Frasca M, Chakraborty P, Cole F. Genetic dissection of crossover mutants defines discrete intermediates in mouse meiosis. Mol Cell 2023; 83:2941-2958.e7. [PMID: 37595556 PMCID: PMC10469168 DOI: 10.1016/j.molcel.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/28/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
Crossovers (COs), the exchange of homolog arms, are required for accurate chromosome segregation during meiosis. Studies in yeast have described the single-end invasion (SEI) intermediate: a stabilized 3' end annealed with the homolog as the first detectible CO precursor. SEIs are thought to differentiate into double Holliday junctions (dHJs) that are resolved by MutLgamma (MLH1/MLH3) into COs. Currently, we lack knowledge of early steps of mammalian CO recombination or how intermediates are differentiated in any organism. Using comprehensive analysis of recombination in thirteen different genetic conditions with varying levels of compromised CO resolution, we infer CO precursors include asymmetric SEI-like intermediates and dHJs in mouse. In contrast to yeast, MLH3 is structurally required to differentiate CO precursors into dHJs. We verify conservation of aspects of meiotic recombination and show unique features in mouse, providing mechanistic insight into CO formation.
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Affiliation(s)
- Tolkappiyan Premkumar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Program in Genetics and Epigenetics, Houston, TX, USA
| | - Lakshmi Paniker
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rhea Kang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Program in Genetics and Epigenetics, Houston, TX, USA
| | - Mathilde Biot
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ericka Humphrey
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Honorine Destain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Isabella Ferranti
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Iyinyeoluwa Okulate
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Holly Nguyen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vindhya Kilaru
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa Frasca
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Program in Genetics and Epigenetics, Houston, TX, USA
| | - Parijat Chakraborty
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francesca Cole
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Program in Genetics and Epigenetics, Houston, TX, USA.
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20
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. Genes Dev 2023; 37:621-639. [PMID: 37541760 PMCID: PMC10499017 DOI: 10.1101/gad.350618.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR subpathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology and results in sequence insertion without additional breaks or SVs. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Yasmina Djeghmoum
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Ruth A Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA;
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA
| | - Aurèle Piazza
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France;
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21
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Shinohara M, Shinohara A. The Msh5 complex shows homeostatic localization in response to DNA double-strand breaks in yeast meiosis. Front Cell Dev Biol 2023; 11:1170689. [PMID: 37274743 PMCID: PMC10232913 DOI: 10.3389/fcell.2023.1170689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023] Open
Abstract
Meiotic crossing over is essential for the segregation of homologous chromosomes. The formation and distribution of meiotic crossovers (COs), which are initiated by the formation of double-strand break (DSB), are tightly regulated to ensure at least one CO per bivalent. One type of CO control, CO homeostasis, maintains a consistent level of COs despite fluctuations in DSB numbers. Here, we analyzed the localization of proteins involved in meiotic recombination in budding yeast xrs2 hypomorphic mutants which show different levels of DSBs. The number of cytological foci with recombinases, Rad51 and Dmc1, which mark single-stranded DNAs at DSB sites is proportional to the DSB numbers. Among the pro-CO factor, ZMM/SIC proteins, the focus number of Zip3, Mer3, or Spo22/Zip4, was linearly proportional to reduced DSBs in the xrs2 mutant. In contrast, foci of Msh5, a component of the MutSγ complex, showed a non-linear response to reduced DSBs. We also confirmed the homeostatic response of COs by genetic analysis of meiotic recombination in the xrs2 mutants and found a chromosome-specific homeostatic response of COs. Our study suggests that the homeostatic response of the Msh5 assembly to reduced DSBs was genetically distinct from that of the Zip3 assembly for CO control.
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Affiliation(s)
- Miki Shinohara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Osaka, Japan
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22
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Gioia M, Payero L, Salim S, Fajish V. G, Farnaz AF, Pannafino G, Chen JJ, Ajith VP, Momoh S, Scotland M, Raghavan V, Manhart CM, Shinohara A, Nishant KT, Alani E. Exo1 protects DNA nicks from ligation to promote crossover formation during meiosis. PLoS Biol 2023; 21:e3002085. [PMID: 37079643 PMCID: PMC10153752 DOI: 10.1371/journal.pbio.3002085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/02/2023] [Accepted: 03/17/2023] [Indexed: 04/21/2023] Open
Abstract
In most sexually reproducing organisms crossing over between chromosome homologs during meiosis is essential to produce haploid gametes. Most crossovers that form in meiosis in budding yeast result from the biased resolution of double Holliday junction (dHJ) intermediates. This dHJ resolution step involves the actions of Rad2/XPG family nuclease Exo1 and the Mlh1-Mlh3 mismatch repair endonuclease. Here, we provide genetic evidence in baker's yeast that Exo1 promotes meiotic crossing over by protecting DNA nicks from ligation. We found that structural elements in Exo1 that interact with DNA, such as those required for the bending of DNA during nick/flap recognition, are critical for its role in crossing over. Consistent with these observations, meiotic expression of the Rad2/XPG family member Rad27 partially rescued the crossover defect in exo1 null mutants, and meiotic overexpression of Cdc9 ligase reduced the crossover levels of exo1 DNA-binding mutants to levels that approached the exo1 null. In addition, our work identified a role for Exo1 in crossover interference. Together, these studies provide experimental evidence for Exo1-protected nicks being critical for the formation of meiotic crossovers and their distribution.
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Affiliation(s)
- Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sagar Salim
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Ghanim Fajish V.
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Amamah F. Farnaz
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - V. P. Ajith
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Sherikat Momoh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michelle Scotland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Vandana Raghavan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Carol M. Manhart
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - K. T. Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
- Center for High-Performance Computing, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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23
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532751. [PMID: 36993162 PMCID: PMC10055120 DOI: 10.1101/2023.03.15.532751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Yasmina Djeghmoum
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
| | - Ruth A. Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Aurèle Piazza
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
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24
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Ziolkowski PA. Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism. PLANT REPRODUCTION 2023; 36:43-54. [PMID: 35819509 PMCID: PMC9958190 DOI: 10.1007/s00497-022-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 06/06/2023]
Abstract
At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and perform separate functions, which directly translate into their roles in meiosis. The formation of one crossover per chromosome pair is required for proper chromosome segregation. This "obligate" crossover is ensured by the major crossover pathway in plants, and in many other eukaryotes, known as the ZMM pathway. The secondary pathways play important roles also in somatic cells and function mainly as repair mechanisms for DNA double-strand breaks (DSBs) not used for crossover formation. One of the consequences of the functional differences between ZMM and other DSB repair pathways is their distinct sensitivities to polymorphisms between homologous chromosomes. From a population genetics perspective, these differences may affect the maintenance of genetic variability. This might be of special importance when considering that a significant portion of plants uses inbreeding as a predominant reproductive strategy, which results in loss of interhomolog polymorphism. While we are still far from fully understanding the relationship between meiotic recombination pathways and genetic variation in populations, recent studies of crossovers in plants offer a new perspective.
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Affiliation(s)
- Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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25
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Trost H, Merkell A, Lopezcolorado FW, Stark J. Resolution of sequence divergence for repeat-mediated deletions shows a polarity that is mediated by MLH1. Nucleic Acids Res 2023; 51:650-667. [PMID: 36620890 PMCID: PMC9881173 DOI: 10.1093/nar/gkac1240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Repeat-mediated deletions (RMDs) are a type of chromosomal rearrangement between two homologous sequences that causes loss of the sequence between the repeats, along with one of the repeats. Sequence divergence between repeats suppresses RMDs; the mechanisms of such suppression and of resolution of the sequence divergence remains poorly understood. We identified RMD regulators using a set of reporter assays in mouse cells that test two key parameters: repeat sequence divergence and the distances between one repeat and the initiating chromosomal break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in the same pathway as MSH2 and MSH6, and which is dependent on residues in MLH1 and its binding partner PMS2 that are important for nuclease activity. Additionally, we found that the resolution of sequence divergence in the RMD product has a specific polarity, where divergent bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the domain of MLH1 that forms part of the MLH1-PMS2 endonuclease is important for polarity of resolution of sequence divergence. We also identified distinctions between MLH1 versus TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional resolution of sequence divergence in the RMD product.
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Affiliation(s)
- Hannah Trost
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Arianna Merkell
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- To whom correspondence should be addressed. Tel: +1 626 218-6346; Fax: +1 626 218 8892;
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26
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Dutreux F, Dutta A, Peltier E, Bibi-Triki S, Friedrich A, Llorente B, Schacherer J. Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii. PLoS Genet 2023; 19:e1010592. [PMID: 36608114 PMCID: PMC9851511 DOI: 10.1371/journal.pgen.1010592] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/19/2023] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Meiotic recombination is a driving force for genome evolution, deeply characterized in a few model species, notably in the budding yeast Saccharomyces cerevisiae. Interestingly, Zip2, Zip3, Zip4, Spo16, Msh4, and Msh5, members of the so-called ZMM pathway that implements the interfering meiotic crossover pathway in S. cerevisiae, have been lost in Lachancea yeast species after the divergence of Lachancea kluyveri from the rest of the clade. In this context, after investigating meiosis in L. kluyveri, we determined the meiotic recombination landscape of Lachancea waltii. Attempts to generate diploid strains with fully hybrid genomes invariably resulted in strains with frequent whole-chromosome aneuploidy and multiple extended regions of loss of heterozygosity (LOH), which mechanistic origin is so far unclear. Despite the lack of multiple ZMM pro-crossover factors in L. waltii, numbers of crossovers and noncrossovers per meiosis were higher than in L. kluyveri but lower than in S. cerevisiae, for comparable genome sizes. Similar to L. kluyveri but opposite to S. cerevisiae, L. waltii exhibits an elevated frequency of zero-crossover bivalents. Lengths of gene conversion tracts for both crossovers and non-crossovers in L. waltii were comparable to those observed in S. cerevisiae and shorter than in L. kluyveri despite the lack of Mlh2, a factor limiting conversion tract size in S. cerevisiae. L. waltii recombination hotspots were not shared with either S. cerevisiae or L. kluyveri, showing that meiotic recombination hotspots can evolve at a rather limited evolutionary scale within budding yeasts. Finally, L. waltii crossover interference was reduced relative to S. cerevisiae, with interference being detected only in the 25 kb distance range. Detection of positive inference only at short distance scales in the absence of multiple ZMM factors required for interference-sensitive crossovers in other systems likely reflects interference between early recombination precursors such as DSBs.
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Affiliation(s)
- Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Emilien Peltier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France,* E-mail: (BL); (JS)
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France,Institut Universitaire de France (IUF), Paris, France,* E-mail: (BL); (JS)
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27
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Palacios-Blanco I, Martín-Castellanos C. Cyclins and CDKs in the regulation of meiosis-specific events. Front Cell Dev Biol 2022; 10:1069064. [PMID: 36523509 PMCID: PMC9745066 DOI: 10.3389/fcell.2022.1069064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/14/2022] [Indexed: 07/13/2024] Open
Abstract
How eukaryotic cells control their duplication is a fascinating example of how a biological system self-organizes specific activities to temporally order cellular events. During cell cycle progression, the cellular level of CDK (Cyclin-Dependent Kinase) activity temporally orders the different cell cycle phases, ensuring that DNA replication occurs prior to segregation into two daughter cells. CDK activity requires the binding of a regulatory subunit (cyclin) to the core kinase, and both CDKs and cyclins are well conserved throughout evolution from yeast to humans. As key regulators, they coordinate cell cycle progression with metabolism, DNA damage, and cell differentiation. In meiosis, the special cell division that ensures the transmission of genetic information from one generation to the next, cyclins and CDKs have acquired novel functions to coordinate meiosis-specific events such as chromosome architecture, recombination, and synapsis. Interestingly, meiosis-specific cyclins and CDKs are common in evolution, some cyclins seem to have evolved to acquire CDK-independent functions, and even some CDKs associate with a non-cyclin partner. We will review the functions of these key regulators in meiosis where variation has specially flourished.
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28
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Kazi S, Castañeda JM, Savolainen A, Xu Y, Liu N, Qiao H, Ramirez‐Solis R, Nozawa K, Yu Z, Matzuk MM, Prunskaite‐Hyyryläinen R. MRNIP interacts with sex body chromatin to support meiotic progression, spermatogenesis, and male fertility in mice. FASEB J 2022; 36:e22479. [PMID: 35920200 PMCID: PMC9544956 DOI: 10.1096/fj.202101168rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022]
Abstract
Meiosis has a principal role in sexual reproduction to generate haploid gametes in both sexes. During meiosis, the cell nucleus hosts a dynamic environment where some genes are transcriptionally activated, and some are inactivated at the same time. This becomes possible through subnuclear compartmentalization. The sex body, sequestering X and Y chromosomes during male meiosis and creating an environment for the meiotic sex chromosome inactivation (MSCI) is one of the best known and studied subnuclear compartments. Herein, we show that MRNIP forms droplet-like accumulations that fuse together to create a distinct subnuclear compartment that partially overlaps with the sex body chromatin during diplotene. We demonstrate that Mrnip-/- spermatocytes have impaired DNA double-strand break (DSB) repair, they display reduced sex body formation and defective MSCI. We show that Mrnip-/- undergoes critical meiocyte loss at the diplotene stage. Furthermore, we determine that DNA DSBs (induced by SPO11) and synapsis initiation (facilitated by SYCP1) precede Mrnip expression in testes. Altogether, our findings indicate that in addition to an emerging role in DNA DSB repair, MRNIP has an essential function in spermatogenesis during meiosis I by forming drop-like accumulations interacting with the sex body.
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Affiliation(s)
- Samina Kazi
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | | | - Audrey Savolainen
- Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Yiding Xu
- Department of Comparative BiosciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Ning Liu
- Department of Comparative BiosciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Huanyu Qiao
- Department of Comparative BiosciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | | | - Kaori Nozawa
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTexasUSA
| | - Zhifeng Yu
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTexasUSA
- Center for Drug DiscoveryBaylor College of MedicineHoustonTexasUSA
| | - Martin M. Matzuk
- Department of Pathology & ImmunologyBaylor College of MedicineHoustonTexasUSA
- Center for Drug DiscoveryBaylor College of MedicineHoustonTexasUSA
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29
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Shodhan A, Xaver M, Wheeler D, Lichten M. Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae. Genetics 2022; 222:iyac106. [PMID: 35876814 PMCID: PMC9434160 DOI: 10.1093/genetics/iyac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
The DNA double-strand breaks that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in Saccharomyces cerevisiae contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red1 are important for double-strand break formation; double-strand break levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with double-strand break levels. How axis protein levels influence double-strand break formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased double-strand breaks and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in double-strand breaks did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote double-strand break formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, crossovers that formed at an insert locus were only modestly reduced in the absence of MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local double-strand break levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.
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Affiliation(s)
- Anura Shodhan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Martin Xaver
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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30
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Wang S, Lee K, Gray S, Zhang Y, Tang C, Morrish R, Tosti E, van Oers J, Amin MR, Cohen P, MacCarthy T, Roa S, Scharff M, Edelmann W, Chahwan R. Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice. Nucleic Acids Res 2022; 50:8093-8106. [PMID: 35849338 PMCID: PMC9371890 DOI: 10.1093/nar/gkac616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022] Open
Abstract
DNA damage response pathways rely extensively on nuclease activity to process DNA intermediates. Exonuclease 1 (EXO1) is a pleiotropic evolutionary conserved DNA exonuclease involved in various DNA repair pathways, replication, antibody diversification, and meiosis. But, whether EXO1 facilitates these DNA metabolic processes through its enzymatic or scaffolding functions remains unclear. Here, we dissect the contribution of EXO1 enzymatic versus scaffolding activity by comparing Exo1DA/DA mice expressing a proven nuclease-dead mutant form of EXO1 to entirely EXO1-deficient Exo1-/- and EXO1 wild type Exo1+/+ mice. We show that Exo1DA/DA and Exo1-/- mice are compromised in canonical DNA repair processing, suggesting that the EXO1 enzymatic role is important for error-free DNA mismatch and double-strand break repair pathways. However, in non-canonical repair pathways, EXO1 appears to have a more nuanced function. Next-generation sequencing of heavy chain V region in B cells showed the mutation spectra of Exo1DA/DA mice to be intermediate between Exo1+/+ and Exo1-/- mice, suggesting that both catalytic and scaffolding roles of EXO1 are important for somatic hypermutation. Similarly, while overall class switch recombination in Exo1DA/DA and Exo1-/- mice was comparably defective, switch junction analysis suggests that EXO1 might fulfill an additional scaffolding function downstream of class switching. In contrast to Exo1-/- mice that are infertile, meiosis progressed normally in Exo1DA/DA and Exo1+/+ cohorts, indicating that a structural but not the nuclease function of EXO1 is critical for meiosis. However, both Exo1DA/DA and Exo1-/- mice displayed similar mortality and cancer predisposition profiles. Taken together, these data demonstrate that EXO1 has both scaffolding and enzymatic functions in distinct DNA repair processes and suggest a more composite and intricate role for EXO1 in DNA metabolic processes and disease.
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Affiliation(s)
- Shanzhi Wang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
- Current position: Department of Chemistry, University of Arkansas at Little Rock, Little Rock, AR 72204, USA
| | - Kyeryoung Lee
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Stephen Gray
- Department of Biomedical Sciences, Cornell University, NY 14853, USA
- Current position: School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Yongwei Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Rikke B Morrish
- Current position: School of Physics and Astronomy, University of Exeter, Exeter EX4 4QD, UK
| | - Elena Tosti
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Johanna van Oers
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Mohammad Ruhul Amin
- Department of Computer and Information Science, Fordham University, Bronx, NY, USA
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, NY 14853, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Sergio Roa
- Department of Biochemistry and Genetics, University of Navarra, 31008Pamplona, Spain
- Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Matthew D Scharff
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
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31
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Firlej M, Weir JR. Unwinding during stressful times: Mechanisms of helicases in meiotic recombination. Curr Top Dev Biol 2022; 151:191-215. [PMID: 36681470 DOI: 10.1016/bs.ctdb.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Successful meiosis I requires that homologous chromosomes be correctly linked before they are segregated. In most organisms this physical linkage is achieved through the generation of crossovers between the homologs. Meiotic recombination co-opts and modifies the canonical homologous recombination pathway to successfully generate crossovers One of the central components of this pathway are a number of conserved DNA helicases. Helicases couple nucleic acid binding to nucleotide hydrolysis and use this activity to modify DNA or protein-DNA substrates. During meiosis I it is necessary for the cell to modulate the canonical DNA repair pathways in order to facilitate the generation of interhomolog crossovers. Many of these meiotic modulations take place in pathways involving DNA helicases, or with a meiosis specific helicase. This short review explores what is currently understood about these helicases, their interaction partners, and the role of regulatory modifications during meiosis I. We focus in particular on the molecular structure and mechanisms of these helicases.
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Affiliation(s)
- Magdalena Firlej
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany
| | - John R Weir
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory of the Max Planck Society, Tuebingen, Germany.
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32
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Sriram N, Mukherjee S, Sah MK. Gene expression profiling and protein-protein interaction analysis reveals the dynamic role of MCM7 in Alzheimer's disorder and breast cancer. 3 Biotech 2022; 12:146. [PMID: 35698583 PMCID: PMC9187790 DOI: 10.1007/s13205-022-03207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/14/2022] [Indexed: 11/01/2022] Open
Abstract
The interrelation of cancer and Alzheimer's disorder (AD)-associated molecular mechanisms, reported last decade, paved the path for drug discoveries. In this direction, while chemotherapy is well established for breast cancer (BC), the detection and targeted therapy for AD is not advanced due to a lack of recognized peripheral biomarkers. The present study aimed to find diagnostic and prognostic molecular signature markers common to both BC and AD for possible drug targeting and repurposing. For these disorders, two corresponding microarray datasets (GSE42568, GSE33000) were used for identifying the differentially expressed genes (DEGs), resulting in recognition of CD209 and MCM7 as the two common players. While the CD209 gene was upregulated in both disorders and has been studied vastly, the MCM7 gene showed a strikingly reverse pattern of expression level, downregulated in the case of BC while upregulated in the case of AD. Thus, the MCM7 gene was further analyzed for expression, predictions, and validations of its structure and protein-protein interaction (PPI) for the possible development of new treatment methods for AD. The study concluded with indicative drug repurposing studies to check the effect of existing clinically approved drugs for BC for rectifying the expression levels of the mutated MCM7 gene in AD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03207-1.
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Affiliation(s)
- Navneeth Sriram
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
| | - Sunny Mukherjee
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
| | - Mahesh Kumar Sah
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
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33
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Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
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34
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Haversat J, Woglar A, Klatt K, Akerib CC, Roberts V, Chen SY, Arur S, Villeneuve AM, Kim Y. Robust designation of meiotic crossover sites by CDK-2 through phosphorylation of the MutSγ complex. Proc Natl Acad Sci U S A 2022; 119:e2117865119. [PMID: 35576467 PMCID: PMC9173770 DOI: 10.1073/pnas.2117865119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
Crossover formation is essential for proper segregation of homologous chromosomes during meiosis. Here, we show that Caenorhabditis elegans cyclin-dependent kinase 2 (CDK-2) partners with cyclin-like protein COSA-1 to promote crossover formation by promoting conversion of meiotic double-strand breaks into crossover–specific recombination intermediates. Further, we identify MutSγ component MSH-5 as a CDK-2 phosphorylation target. MSH-5 has a disordered C-terminal tail that contains 13 potential CDK phosphosites and is required to concentrate crossover–promoting proteins at recombination sites. Phosphorylation of the MSH-5 tail appears dispensable in a wild-type background, but when MutSγ activity is partially compromised, crossover formation and retention of COSA-1 at recombination sites are exquisitely sensitive to phosphosite loss. Our data support a model in which robustness of crossover designation reflects a positive feedback mechanism involving CDK-2–mediated phosphorylation and scaffold-like properties of the MSH5 C-terminal tail, features that combine to promote full recruitment and activity of crossover–promoting complexes.
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Affiliation(s)
- Jocelyn Haversat
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Alexander Woglar
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Kayla Klatt
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Chantal C. Akerib
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Victoria Roberts
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Shin-Yu Chen
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Swathi Arur
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Anne M. Villeneuve
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Yumi Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
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35
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Castellanos M, Verhey TB, Goldstein M, Chaconas G. The Putative Endonuclease Activity of MutL Is Required for the Segmental Gene Conversion Events That Drive Antigenic Variation of the Lyme Disease Spirochete. Front Microbiol 2022; 13:888494. [PMID: 35663861 PMCID: PMC9159922 DOI: 10.3389/fmicb.2022.888494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
The Lyme disease spirochete Borrelia burgdorferi, encodes an elaborate antigenic variation system that promotes the ongoing variation of a major surface lipoprotein, VlsE. Changes in VlsE are continual and always one step ahead of the host acquired immune system, which requires 1–2 weeks to generate specific antibodies. By the time this happens, new VlsE variants have arisen that escape immunosurveillance, providing an avenue for persistent infection. This antigenic variation system is driven by segmental gene conversion events that transfer information from a series of silent cassettes (vls2-16) to the expression locus, vlsE. The molecular details of this process remain elusive. Recombinational switching at vlsE is RecA-independent and the only required factor identified to date is the RuvAB branch migrase. In this work we have used next generation long-read sequencing to analyze the effect of several DNA replication/recombination/repair gene disruptions on the frequency of gene conversions at vlsE and report a requirement for the mismatch repair protein MutL. Site directed mutagenesis of mutL suggests that the putative MutL endonuclease activity is required for recombinational switching at vlsE. This is the first report of an unexpected essential role for MutL in a bacterial recombination system and expands the known function of this protein as well as our knowledge of the details of the novel recombinational switching mechanism for vlsE variation.
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Affiliation(s)
- Mildred Castellanos
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Theodore B. Verhey
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Madeleine Goldstein
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - George Chaconas
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- *Correspondence: George Chaconas,
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36
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Voelkel-Meiman K, Oke A, Feil A, Shames A, Fung J, MacQueen AJ. A role for synaptonemal complex in meiotic mismatch repair. Genetics 2022; 220:iyab230. [PMID: 35100397 PMCID: PMC9097268 DOI: 10.1093/genetics/iyab230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/17/2021] [Indexed: 11/14/2022] Open
Abstract
A large subset of meiotic recombination intermediates form within the physical context of synaptonemal complex (SC), but the functional relationship between SC structure and homologous recombination remains obscure. Our prior analysis of strains deficient for SC central element proteins demonstrated that tripartite SC is dispensable for interhomolog recombination in Saccharomyces cerevisiae. Here, we report that while dispensable for recombination per se, SC proteins promote efficient mismatch repair at interhomolog recombination sites. Failure to repair mismatches within heteroduplex-containing meiotic recombination intermediates leads to genotypically sectored colonies (postmeiotic segregation events). We discovered increased postmeiotic segregation at THR1 in cells lacking Ecm11 or Gmc2, or in the SC-deficient but recombination-proficient zip1[Δ21-163] mutant. High-throughput sequencing of octad meiotic products furthermore revealed a genome-wide increase in recombination events with unrepaired mismatches in ecm11 mutants relative to wildtype. Meiotic cells missing Ecm11 display longer gene conversion tracts, but tract length alone does not account for the higher frequency of unrepaired mismatches. Interestingly, the per-nucleotide mismatch frequency is elevated in ecm11 when analyzing all gene conversion tracts, but is similar between wildtype and ecm11 if considering only those events with unrepaired mismatches. Thus, in both wildtype and ecm11 strains a subset of recombination events is susceptible to a similar degree of inefficient mismatch repair, but in ecm11 mutants a larger fraction of events fall into this inefficient repair category. Finally, we observe elevated postmeiotic segregation at THR1 in mutants with a dual deficiency in MutSγ crossover recombination and SC assembly, but not in the mlh3 mutant, which lacks MutSγ crossovers but has abundant SC. We propose that SC structure promotes efficient mismatch repair of joint molecule recombination intermediates, and that absence of SC is the molecular basis for elevated postmeiotic segregation in both MutSγ crossover-proficient (ecm11, gmc2) and MutSγ crossover-deficient (msh4, zip3) strains.
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Affiliation(s)
- Karen Voelkel-Meiman
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arden Feil
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Alexander Shames
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Jennifer Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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37
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Xie C, Wang W, Tu C, Meng L, Lu G, Lin G, Lu LY, Tan YQ. OUP accepted manuscript. Hum Reprod Update 2022; 28:763-797. [PMID: 35613017 DOI: 10.1093/humupd/dmac024] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/18/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chunbo Xie
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Weili Wang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Chaofeng Tu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lanlan Meng
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Guangxiu Lu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ge Lin
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lin-Yu Lu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue-Qiu Tan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
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38
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Carreira R, Aguado FJ, Hurtado-Nieves V, Blanco MG. Canonical and novel non-canonical activities of the Holliday junction resolvase Yen1. Nucleic Acids Res 2021; 50:259-280. [PMID: 34928393 PMCID: PMC8754655 DOI: 10.1093/nar/gkab1225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/12/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
Yen1 and GEN1 are members of the Rad2/XPG family of nucleases that were identified as the first canonical nuclear Holliday junction (HJ) resolvases in budding yeast and humans due to their ability to introduce two symmetric, coordinated incisions on opposite strands of the HJ, yielding nicked DNA products that could be readily ligated. While GEN1 has been extensively characterized in vitro, much less is known about the biochemistry of Yen1. Here, we have performed the first in-depth characterization of purified Yen1. We confirmed that Yen1 resembles GEN1 in many aspects, including range of substrates targeted, position of most incisions they produce or the increase in the first incision rate by assembly of a dimer on a HJ, despite minor differences. However, we demonstrate that Yen1 is endowed with additional nuclease activities, like a nick-specific 5′-3′ exonuclease or HJ arm-chopping that could apparently blur its classification as a canonical HJ resolvase. Despite this, we show that Yen1 fulfils the requirements of a canonical HJ resolvase and hypothesize that its wider array of nuclease activities might contribute to its function in the removal of persistent recombination or replication intermediates.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Vanesa Hurtado-Nieves
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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39
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Qu W, Liu C, Xu YT, Xu YM, Luo MC. The formation and repair of DNA double-strand breaks in mammalian meiosis. Asian J Androl 2021; 23:572-579. [PMID: 34708719 PMCID: PMC8577251 DOI: 10.4103/aja202191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) are necessary for meiosis in mammals. A sufficient number of DSBs ensure the normal pairing/synapsis of homologous chromosomes. Abnormal DSB repair undermines meiosis, leading to sterility in mammals. The DSBs that initiate recombination are repaired as crossovers and noncrossovers, and crossovers are required for correct chromosome separation. Thus, the placement, timing, and frequency of crossover formation must be tightly controlled. Importantly, mutations in many genes related to the formation and repair of DSB result in infertility in humans. These mutations cause nonobstructive azoospermia in men, premature ovarian insufficiency and ovarian dysgenesis in women. Here, we have illustrated the formation and repair of DSB in mammals, summarized major factors influencing the formation of DSB and the theories of crossover regulation.
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Affiliation(s)
- Wei Qu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Cong Liu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ting Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Min Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Meng-Cheng Luo
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
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40
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Ahuja JS, Harvey CS, Wheeler DL, Lichten M. Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination. Mol Cell 2021; 81:4258-4270.e4. [PMID: 34453891 PMCID: PMC8541907 DOI: 10.1016/j.molcel.2021.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Currently favored models for meiotic recombination posit that both noncrossover and crossover recombination are initiated by DNA double-strand breaks but form by different mechanisms: noncrossovers by synthesis-dependent strand annealing and crossovers by formation and resolution of double Holliday junctions centered around the break. This dual mechanism hypothesis predicts different hybrid DNA patterns in noncrossover and crossover recombinants. We show that these predictions are not upheld, by mapping with unprecedented resolution parental strand contributions to recombinants at a model locus. Instead, break repair in both noncrossovers and crossovers involves synthesis-dependent strand annealing, often with multiple rounds of strand invasion. Crossover-specific double Holliday junction formation occurs via processes involving branch migration as an integral feature, one that can be separated from repair of the break itself. These findings reveal meiotic recombination to be a highly dynamic process and prompt a new view of the relationship between crossover and noncrossover recombination.
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Affiliation(s)
- Jasvinder S Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Catherine S Harvey
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David L Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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41
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Nandanan KG, Salim S, Pankajam AV, Shinohara M, Lin G, Chakraborty P, Farnaz A, Steinmetz LM, Shinohara A, Nishant KT. Regulation of Msh4-Msh5 association with meiotic chromosomes in budding yeast. Genetics 2021; 219:6317832. [PMID: 34849874 DOI: 10.1093/genetics/iyab102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/08/2021] [Indexed: 01/06/2023] Open
Abstract
In the baker's yeast Saccharomyces cerevisiae, most of the meiotic crossovers are generated through a pathway involving the highly conserved mismatch repair related Msh4-Msh5 complex. To understand the role of Msh4-Msh5 in meiotic crossing over, we determined its genome wide in vivo binding sites in meiotic cells. We show that Msh5 specifically associates with DSB hotspots, chromosome axes, and centromeres on chromosomes. A basal level of Msh5 association with these chromosomal features is observed even in the absence of DSB formation (spo11Δ mutant) at the early stages of meiosis. But efficient binding to DSB hotspots and chromosome axes requires DSB formation and resection and is enhanced by double Holliday junction structures. Msh5 binding is also correlated to DSB frequency and enhanced on small chromosomes with higher DSB and crossover density. The axis protein Red1 is required for Msh5 association with the chromosome axes and DSB hotspots but not centromeres. Although binding sites of Msh5 and other pro-crossover factors like Zip3 show extensive overlap, Msh5 associates with centromeres independent of Zip3. These results on Msh5 localization in wild type and meiotic mutants have implications for how Msh4-Msh5 works with other pro-crossover factors to ensure crossover formation.
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Affiliation(s)
- Krishnaprasad G Nandanan
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India
| | - Sagar Salim
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India
| | - Ajith V Pankajam
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India
| | - Miki Shinohara
- Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Gen Lin
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Parijat Chakraborty
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India
| | - Amamah Farnaz
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany.,Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India.,Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
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Alonso-Ramos P, Álvarez-Melo D, Strouhalova K, Pascual-Silva C, Garside GB, Arter M, Bermejo T, Grigaitis R, Wettstein R, Fernández-Díaz M, Matos J, Geymonat M, San-Segundo PA, Carballo JA. The Cdc14 Phosphatase Controls Resolution of Recombination Intermediates and Crossover Formation during Meiosis. Int J Mol Sci 2021; 22:ijms22189811. [PMID: 34575966 PMCID: PMC8470964 DOI: 10.3390/ijms22189811] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Meiotic defects derived from incorrect DNA repair during gametogenesis can lead to mutations, aneuploidies and infertility. The coordinated resolution of meiotic recombination intermediates is required for crossover formation, ultimately necessary for the accurate completion of both rounds of chromosome segregation. Numerous master kinases orchestrate the correct assembly and activity of the repair machinery. Although much less is known, the reversal of phosphorylation events in meiosis must also be key to coordinate the timing and functionality of repair enzymes. Cdc14 is a crucial phosphatase required for the dephosphorylation of multiple CDK1 targets in many eukaryotes. Mutations that inactivate this phosphatase lead to meiotic failure, but until now it was unknown if Cdc14 plays a direct role in meiotic recombination. Here, we show that the elimination of Cdc14 leads to severe defects in the processing and resolution of recombination intermediates, causing a drastic depletion in crossovers when other repair pathways are compromised. We also show that Cdc14 is required for the correct activity and localization of the Holliday Junction resolvase Yen1/GEN1. We reveal that Cdc14 regulates Yen1 activity from meiosis I onwards, and this function is essential for crossover resolution in the absence of other repair pathways. We also demonstrate that Cdc14 and Yen1 are required to safeguard sister chromatid segregation during the second meiotic division, a late action that is independent of the earlier role in crossover formation. Thus, this work uncovers previously undescribed functions of the evolutionary conserved Cdc14 phosphatase in the regulation of meiotic recombination.
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Affiliation(s)
- Paula Alonso-Ramos
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - David Álvarez-Melo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Katerina Strouhalova
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic
| | - Carolina Pascual-Silva
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - George B. Garside
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 4DY, UK;
- Leibniz Institute for Age Research/Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Meret Arter
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Teresa Bermejo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Rokas Grigaitis
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Rahel Wettstein
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marta Fernández-Díaz
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marco Geymonat
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK;
| | - Pedro A. San-Segundo
- Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC) and University of Salamanca, 37007 Salamanca, Spain;
| | - Jesús A. Carballo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
- Correspondence:
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Pazhayam NM, Turcotte CA, Sekelsky J. Meiotic Crossover Patterning. Front Cell Dev Biol 2021; 9:681123. [PMID: 34368131 PMCID: PMC8344875 DOI: 10.3389/fcell.2021.681123] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
Proper number and placement of meiotic crossovers is vital to chromosome segregation, with failures in normal crossover distribution often resulting in aneuploidy and infertility. Meiotic crossovers are formed via homologous repair of programmed double-strand breaks (DSBs). Although DSBs occur throughout the genome, crossover placement is intricately patterned, as observed first in early genetic studies by Muller and Sturtevant. Three types of patterning events have been identified. Interference, first described by Sturtevant in 1915, is a phenomenon in which crossovers on the same chromosome do not occur near one another. Assurance, initially identified by Owen in 1949, describes the phenomenon in which a minimum of one crossover is formed per chromosome pair. Suppression, first observed by Beadle in 1932, dictates that crossovers do not occur in regions surrounding the centromere and telomeres. The mechanisms behind crossover patterning remain largely unknown, and key players appear to act at all scales, from the DNA level to inter-chromosome interactions. There is also considerable overlap between the known players that drive each patterning phenomenon. In this review we discuss the history of studies of crossover patterning, developments in methods used in the field, and our current understanding of the interplay between patterning phenomena.
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Affiliation(s)
- Nila M. Pazhayam
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carolyn A. Turcotte
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Sanchez A, Reginato G, Cejka P. Crossover or non-crossover outcomes: tailored processing of homologous recombination intermediates. Curr Opin Genet Dev 2021; 71:39-47. [PMID: 34293660 DOI: 10.1016/j.gde.2021.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
DNA breaks may arise accidentally in vegetative cells or in a programmed manner in meiosis. The usage of a DNA template makes homologous recombination potentially error-free, however, recombination is not always accurate. Cells possess a remarkable capacity to tailor processing of recombination intermediates to fulfill a particular need. Vegetatively growing cells aim to maintain genome stability and therefore repair accidental breaks largely accurately, using sister chromatids as templates, into mostly non-crossovers products. Recombination in meiotic cells is instead more likely to employ homologous chromosomes as templates and result in crossovers to allow proper chromosome segregation and promote genetic diversity. Here we review models explaining the processing of recombination intermediates in vegetative and meiotic cells and its regulation, with a focus on MLH1-MLH3-dependent crossing-over during meiotic recombination.
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Affiliation(s)
- Aurore Sanchez
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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He W, Verhees GF, Bhagwat N, Yang Y, Kulkarni DS, Lombardo Z, Lahiri S, Roy P, Zhuo J, Dang B, Snyder A, Shastry S, Moezpoor M, Alocozy L, Lee KG, Painter D, Mukerji I, Hunter N. SUMO fosters assembly and functionality of the MutSγ complex to facilitate meiotic crossing over. Dev Cell 2021; 56:2073-2088.e3. [PMID: 34214491 DOI: 10.1016/j.devcel.2021.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/31/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Crossing over is essential for chromosome segregation during meiosis. Protein modification by SUMO is implicated in crossover control, but pertinent targets have remained elusive. Here we identify Msh4 as a target of SUMO-mediated crossover regulation. Msh4 and Msh5 constitute the MutSγ complex, which stabilizes joint-molecule (JM) recombination intermediates and facilitates their resolution into crossovers. Msh4 SUMOylation enhances these processes to ensure that each chromosome pair acquires at least one crossover. Msh4 is directly targeted by E2 conjugase Ubc9, initially becoming mono-SUMOylated in response to DNA double-strand breaks, then multi/poly-SUMOylated forms arise as homologs fully engage. Mechanistically, SUMOylation fosters interaction between Msh4 and Msh5. We infer that initial SUMOylation of Msh4 enhances assembly of MutSγ in anticipation of JM formation, while secondary SUMOylation may promote downstream functions. Regulation of Msh4 by SUMO is distinct and independent of its previously described stabilization by phosphorylation, defining MutSγ as a hub for crossover control.
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Affiliation(s)
- Wei He
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Gerrik F Verhees
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Nikhil Bhagwat
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Ye Yang
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Dhananjaya S Kulkarni
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Zane Lombardo
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Pritha Roy
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Jiaming Zhuo
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Brian Dang
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Andriana Snyder
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Shashank Shastry
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Michael Moezpoor
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Lilly Alocozy
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Kathy Gyehyun Lee
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Daniel Painter
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA.
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46
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Strand discrimination in DNA mismatch repair. DNA Repair (Amst) 2021; 105:103161. [PMID: 34171627 DOI: 10.1016/j.dnarep.2021.103161] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
DNA mismatch repair (MMR) corrects non-Watson-Crick basepairs generated by replication errors, recombination intermediates, and some forms of chemical damage to DNA. In MutS and MutL homolog-dependent MMR, damaged bases do not identify the error-containing daughter strand that must be excised and resynthesized. In organisms like Escherichia coli that use methyl-directed MMR, transient undermethylation identifies the daughter strand. For other organisms, growing in vitro and in vivo evidence suggest that strand discrimination is mediated by DNA replication-associated daughter strand nicks that direct asymmetric loading of the replicative clamp (the β-clamp in bacteria and the proliferating cell nuclear antigen, PCNA, in eukaryotes). Structural modeling suggests that replicative clamps mediate strand specificity either through the ability of MutL homologs to recognize the fixed orientation of the daughter strand relative to one face of the replicative clamps or through parental strand-specific diffusion of replicative clamps on DNA, which places the daughter strand in the MutL homolog endonuclease active site. Finally, identification of bacteria that appear to lack strand discrimination mediated by a replicative clamp and a pre-existing nick suggest that other strand discrimination mechanisms exist or that these organisms perform MMR by generating a double-stranded DNA break intermediate, which may be analogous to NucS-mediated MMR.
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Furman CM, Elbashir R, Pannafino G, Clark NL, Alani E. Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication. G3 (BETHESDA, MD.) 2021; 11:jkab111. [PMID: 33871573 PMCID: PMC8495741 DOI: 10.1093/g3journal/jkab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/31/2021] [Indexed: 01/24/2023]
Abstract
Baker's yeast contains a large number of duplicated genes; some function redundantly, whereas others have more specialized roles. We used the MLH family of DNA mismatch repair (MMR) proteins as a model to better understand the steps that lead to gene specialization following a gene duplication event. We focused on two highly conserved yeast MLH proteins, Pms1 and Mlh3, with Pms1 having a major role in the repair of misincorporation events during DNA replication and Mlh3 acting to resolve recombination intermediates in meiosis to form crossovers. The baker's yeast Mlh3 and Pms1 proteins are significantly diverged (19% overall identity), suggesting that an extensive number of evolutionary steps, some major, others involving subtle refinements, took place to diversify the MLH proteins. Using phylogenetic and molecular approaches, we provide evidence that all three domains (N-terminal ATP binding, linker, C-terminal endonuclease/MLH interaction) in the MLH protein family are critical for conferring pathway specificity. Importantly, mlh3 alleles in the ATP binding and endonuclease domains improved MMR functions in strains lacking the Pms1 protein and did not disrupt Mlh3 meiotic functions. This ability for mlh3 alleles to complement the loss of Pms1 suggests that an ancestral Pms1/Mlh3 protein was capable of performing both MMR and crossover functions. Our strategy for analyzing MLH pathway specificity provides an approach to understand how paralogs have evolved to support distinct cellular processes.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84132, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation. Proc Natl Acad Sci U S A 2021; 118:2022704118. [PMID: 34088835 DOI: 10.1073/pnas.2022704118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In budding yeast, the MutL homolog heterodimer Mlh1-Mlh3 (MutLγ) plays a central role in the formation of meiotic crossovers. It is also involved in the repair of a subset of mismatches besides the main mismatch repair (MMR) endonuclease Mlh1-Pms1 (MutLα). The heterodimer interface and endonuclease sites of MutLγ and MutLα are located in their C-terminal domain (CTD). The molecular basis of MutLγ's dual roles in MMR and meiosis is not known. To better understand the specificity of MutLγ, we characterized the crystal structure of Saccharomyces cerevisiae MutLγ(CTD). Although MutLγ(CTD) presents overall similarities with MutLα(CTD), it harbors some rearrangement of the surface surrounding the active site, which indicates altered substrate preference. The last amino acids of Mlh1 participate in the Mlh3 endonuclease site as previously reported for Pms1. We characterized mlh1 alleles and showed a critical role of this Mlh1 extreme C terminus both in MMR and in meiotic recombination. We showed that the MutLγ(CTD) preferentially binds Holliday junctions, contrary to MutLα(CTD). We characterized Mlh3 positions on the N-terminal domain (NTD) and CTD that could contribute to the positioning of the NTD close to the CTD in the context of the full-length MutLγ. Finally, crystal packing revealed an assembly of MutLγ(CTD) molecules in filament structures. Mutation at the corresponding interfaces reduced crossover formation, suggesting that these superstructures may contribute to the oligomer formation proposed for MutLγ. This study defines clear divergent features between the MutL homologs and identifies, at the molecular level, their specialization toward MMR or meiotic recombination functions.
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Johnson D, Crawford M, Cooper T, Claeys Bouuaert C, Keeney S, Llorente B, Garcia V, Neale MJ. Concerted cutting by Spo11 illuminates meiotic DNA break mechanics. Nature 2021; 594:572-576. [PMID: 34108687 PMCID: PMC7611867 DOI: 10.1038/s41586-021-03389-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Genetic recombination arises during meiosis through the repair of DNA double-strand breaks (DSBs) that are created by Spo11, a topoisomerase-like protein1,2. Spo11 DSBs form preferentially in nucleosome-depleted regions termed hotspots3,4, yet how Spo11 engages with its DNA substrate to catalyse DNA cleavage is poorly understood. Although most recombination events are initiated by a single Spo11 cut, here we show in Saccharomyces cerevisiae that hyperlocalized, concerted Spo11 DSBs separated by 33 to more than 100 base pairs also form, which we term 'double cuts'. Notably, the lengths of double cuts vary with a periodicity of 10.5 base pairs, which is conserved in yeast and mice. This finding suggests a model in which the orientation of adjacent Spo11 molecules is fixed relative to the DNA helix-a proposal supported by the in vitro DNA-binding properties of the Spo11 core complex. Deep sequencing of meiotic progeny identifies recombination scars that are consistent with repair initiated from gaps generated by adjacent Spo11 DSBs. Collectively, these results revise our present understanding of the mechanics of Spo11-DSB formation and expand on the original concepts of gap repair during meiosis to include DNA gaps that are generated by Spo11 itself.
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Affiliation(s)
- Dominic Johnson
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Margaret Crawford
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Tim Cooper
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Corentin Claeys Bouuaert
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, Belgium
| | - Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bertrand Llorente
- Cancer Research Centre of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Valerie Garcia
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
- Cancer Research Centre of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
| | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
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50
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Abstract
The formation of crossovers between homologous chromosomes is key to sexual reproduction. In most species, crossovers are spaced further apart than would be expected if they formed independently, a phenomenon termed crossover interference. Despite more than a century of study, the molecular mechanisms implementing crossover interference remain a subject of active debate. Recent findings of how signaling proteins control the formation of crossovers and about the interchromosomal interface in which crossovers form offer new insights into this process. In this Review, we present a cell biological and biophysical perspective on crossover interference, summarizing the evidence that links interference to the spatial, dynamic, mechanical and molecular properties of meiotic chromosomes. We synthesize this physical understanding in the context of prevailing mechanistic models that aim to explain how crossover interference is implemented.
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Affiliation(s)
- Lexy von Diezmann
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA.,School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA.,School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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