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Kutashev K, Meschichi A, Reeck S, Fonseca A, Sartori K, White CI, Sicard A, Rosa S. Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types. THE NEW PHYTOLOGIST 2024; 243:966-980. [PMID: 38840557 DOI: 10.1111/nph.19875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024]
Abstract
Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adapt to the changing environment, which can induce varying amounts of DNA damage. Using a combination of whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH) and plant cell cycle reporter lines, we investigated the transcriptional activation of a key homologous recombination (HR) gene, RAD51, in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. The results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. This work advances the current comprehension of DNA damage response in plants by demonstrating quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants.
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Affiliation(s)
- Konstantin Kutashev
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Anis Meschichi
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zürich, Zürich, 8092, Switzerland
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Research Park, Norwich, NR4 7UH, UK
| | - Alejandro Fonseca
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Kevin Sartori
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Charles I White
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERM, Clermont-Ferrand, 63001, France
| | - Adrien Sicard
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
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2
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Mwaniki S, Sawant P, Osemwenkhae OP, Fujita Y, Ito M, Furukohri A, Shinohara A. Mutational analysis of Mei5, a subunit of Mei5-Sae3 complex, in Dmc1-mediated recombination during yeast meiosis. Genes Cells 2024. [PMID: 38924305 DOI: 10.1111/gtc.13138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/21/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Interhomolog recombination in meiosis is mediated by the Dmc1 recombinase. The Mei5-Sae3 complex of Saccharomyces cerevisiae promotes Dmc1 assembly and functions with Dmc1 for homology-mediated repair of meiotic DNA double-strand breaks. How Mei5-Sae3 facilitates Dmc1 assembly remains poorly understood. In this study, we created and characterized several mei5 mutants featuring the amino acid substitutions of basic residues. We found that Arg97 of Mei5, conserved in its ortholog, SFR1 (complex with SWI5), RAD51 mediator, in humans and other organisms, is critical for complex formation with Sae3 for Dmc1 assembly. Moreover, the substitution of either Arg117 or Lys133 with Ala in Mei5 resulted in the production of a C-terminal truncated Mei5 protein during yeast meiosis. Notably, the shorter Mei5-R117A protein was observed in meiotic cells but not in mitotic cells when expressed, suggesting a unique regulation of Dmc1-mediated recombination by posttranslational processing of Mei5-Sae3.
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Affiliation(s)
- Stephen Mwaniki
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | | | - Osaretin P Osemwenkhae
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yurika Fujita
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masaru Ito
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Asako Furukohri
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Akira Shinohara
- Division of Integrated Protein Functions, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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3
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Meyer D, Ceballos SJ, Gore S, Liu J, Reginato G, Cano-Linares MI, Maslowska KH, Villafañez F, Ede C, Pagès V, Prado F, Cejka P, Heyer WD. Rad51 determines pathway usage in post-replication repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599120. [PMID: 38915629 PMCID: PMC11195247 DOI: 10.1101/2024.06.14.599120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Stalled replication forks can be processed by several distinct mechanisms collectively called post-replication repair which includes homologous recombination, fork regression, and translesion DNA synthesis. However, the regulation of the usage between these pathways is not fully understood. The Rad51 protein plays a pivotal role in maintaining genomic stability through its roles in HR and in protecting stalled replication forks from degradation. We report the isolation of separation-of-function mutations in Saccharomyces cerevisiae Rad51 that retain their recombination function but display a defect in fork protection leading to a shift in post-replication repair pathway usage from HR to alternate pathways including mutagenic translesion synthesis. Rad51-E135D and Rad51-K305N show normal in vivo and in vitro recombination despite changes in their DNA binding profiles, in particular to dsDNA, with a resulting effect on their ATPase activities. The mutants lead to a defect in Rad51 recruitment to stalled forks in vivo as well as a defect in the protection of dsDNA from degradation by Dna2-Sgs1 and Exo1 in vitro . A high-resolution cryo-electron microscopy structure of the Rad51-ssDNA filament at 2.4 Å resolution provides a structural basis for a mechanistic understanding of the mutant phenotypes. Together, the evidence suggests a model in which Rad51 binding to duplex DNA is critical to control pathway usage at stalled replication forks.
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4
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Morozumi R, Shimizu N, Tamura K, Nakamura M, Suzuki A, Ishiniwa H, Ide H, Tsuda M. Changes in repair pathways of radiation-induced DNA double-strand breaks at the midblastula transition in Xenopus embryo. JOURNAL OF RADIATION RESEARCH 2024; 65:315-322. [PMID: 38648785 PMCID: PMC11115444 DOI: 10.1093/jrr/rrae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/25/2024] [Indexed: 04/25/2024]
Abstract
Ionizing radiation (IR) causes DNA damage, particularly DNA double-strand breaks (DSBs), which have significant implications for genome stability. The major pathways of repairing DSBs are homologous recombination (HR) and nonhomologous end joining (NHEJ). However, the repair mechanism of IR-induced DSBs in embryos is not well understood, despite extensive research in somatic cells. The externally developing aquatic organism, Xenopus tropicalis, serves as a valuable model for studying embryo development. A significant increase in zygotic transcription occurs at the midblastula transition (MBT), resulting in a longer cell cycle and asynchronous cell divisions. This study examines the impact of X-ray irradiation on Xenopus embryos before and after the MBT. The findings reveal a heightened X-ray sensitivity in embryos prior to the MBT, indicating a distinct shift in the DNA repair pathway during embryo development. Importantly, we show a transition in the dominant DSB repair pathway from NHEJ to HR before and after the MBT. These results suggest that the MBT plays a crucial role in altering DSB repair mechanisms, thereby influencing the IR sensitivity of developing embryos.
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Affiliation(s)
- Ryosuke Morozumi
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Naoto Shimizu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kouhei Tamura
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Makoto Nakamura
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Department of Physiology, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atsushi Suzuki
- Amphibian Research Center, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Hiroko Ishiniwa
- Institute of Environmental Radioactivity, Fukushima University, Fukushima, 960-1296, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Masataka Tsuda
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
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5
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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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6
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Sampathkumar A, Zhong C, Tang Y, Fujita Y, Ito M, Shinohara A. Replication protein-A, RPA, plays a pivotal role in the maintenance of recombination checkpoint in yeast meiosis. Sci Rep 2024; 14:9550. [PMID: 38664461 PMCID: PMC11045724 DOI: 10.1038/s41598-024-60082-x] [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: 09/27/2023] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
DNA double-strand breaks (DSBs) activate DNA damage responses (DDRs) in both mitotic and meiotic cells. A single-stranded DNA (ssDNA) binding protein, Replication protein-A (RPA) binds to the ssDNA formed at DSBs to activate ATR/Mec1 kinase for the response. Meiotic DSBs induce homologous recombination monitored by a meiotic DDR called the recombination checkpoint that blocks the pachytene exit in meiotic prophase I. In this study, we further characterized the essential role of RPA in the maintenance of the recombination checkpoint during Saccharomyces cerevisiae meiosis. The depletion of an RPA subunit, Rfa1, in a recombination-defective dmc1 mutant, fully alleviates the pachytene arrest with the persistent unrepaired DSBs. RPA depletion decreases the activity of a meiosis-specific CHK2 homolog, Mek1 kinase, which in turn activates the Ndt80 transcriptional regulator for pachytene exit. These support the idea that RPA is a sensor of ssDNAs for the activation of meiotic DDR. Rfa1 depletion also accelerates the prophase I delay in the zip1 mutant defective in both chromosome synapsis and the recombination, consistent with the notion that the accumulation of ssDNAs rather than defective synapsis triggers prophase I delay in the zip1 mutant.
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Affiliation(s)
- Arivarasan Sampathkumar
- Institute for Protein Research, University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Chen Zhong
- Institute for Protein Research, University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuting Tang
- Institute for Protein Research, University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yurika Fujita
- Institute for Protein Research, University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masaru Ito
- Institute for Protein Research, University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akira Shinohara
- Institute for Protein Research, University of Osaka, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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7
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Grubb J, Bishop DK. Chk2 homologue Mek1 limits Exo1-dependent DNA end resection during meiotic recombination in S. cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589255. [PMID: 38645032 PMCID: PMC11030327 DOI: 10.1101/2024.04.12.589255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The conserved Rad2/XPG family 5'-3' exonuclease, Exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double strand breaks (DSBs) via homologous recombination. Prior studies provided evidence that the end-resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here we provide evidence that the master meiotic kinase Mek1, a paralogue of Rad53, limits 5'-3' single strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53. Article Summary Meiotic recombination involves formation of programmed DNA double strand breaks followed by 5' to 3' single strand specific resection by nucleases including Exo1. We find that the activity of budding yeast Exo1 is downregulated during meiotic recombination by the master meiotic kinase Mek1. The mechanism of downregulation of Exo1 by Mek1 in meiosis does not depend on the same phospho-sites as those used by the mitotic kinase Rad53, a relative of Mek1 that downregulates Exo1 in mitosis.
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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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Shioi T, Hatazawa S, Oya E, Hosoya N, Kobayashi W, Ogasawara M, Kobayashi T, Takizawa Y, Kurumizaka H. Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Nature 2024; 628:212-220. [PMID: 38509361 PMCID: PMC10990931 DOI: 10.1038/s41586-024-07196-4] [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: 06/17/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
RAD51 is the central eukaryotic recombinase required for meiotic recombination and mitotic repair of double-strand DNA breaks (DSBs)1,2. However, the mechanism by which RAD51 functions at DSB sites in chromatin has remained elusive. Here we report the cryo-electron microscopy structures of human RAD51-nucleosome complexes, in which RAD51 forms ring and filament conformations. In the ring forms, the N-terminal lobe domains (NLDs) of RAD51 protomers are aligned on the outside of the RAD51 ring, and directly bind to the nucleosomal DNA. The nucleosomal linker DNA that contains the DSB site is recognized by the L1 and L2 loops-active centres that face the central hole of the RAD51 ring. In the filament form, the nucleosomal DNA is peeled by the RAD51 filament extension, and the NLDs of RAD51 protomers proximal to the nucleosome bind to the remaining nucleosomal DNA and histones. Mutations that affect nucleosome-binding residues of the RAD51 NLD decrease nucleosome binding, but barely affect DNA binding in vitro. Consistently, yeast Rad51 mutants with the corresponding mutations are substantially defective in DNA repair in vivo. These results reveal an unexpected function of the RAD51 NLD, and explain the mechanism by which RAD51 associates with nucleosomes, recognizes DSBs and forms the active filament in chromatin.
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Affiliation(s)
- Takuro Shioi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Eriko Oya
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Hosoya
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wataru Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mitsuo Ogasawara
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Takehiko Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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10
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Zou M, Shabala S, Zhao C, Zhou M. Molecular mechanisms and regulation of recombination frequency and distribution in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:86. [PMID: 38512498 PMCID: PMC10957645 DOI: 10.1007/s00122-024-04590-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
KEY MESSAGE Recent developments in understanding the distribution and distinctive features of recombination hotspots are reviewed and approaches are proposed to increase recombination frequency in coldspot regions. Recombination events during meiosis provide the foundation and premise for creating new varieties of crops. The frequency of recombination in different genomic regions differs across eukaryote species, with recombination generally occurring more frequently at the ends of chromosomes. In most crop species, recombination is rare in centromeric regions. If a desired gene variant is linked in repulsion with an undesired variant of a second gene in a region with a low recombination rate, obtaining a recombinant plant combining two favorable alleles will be challenging. Traditional crop breeding involves combining desirable genes from parental plants into offspring. Therefore, understanding the mechanisms of recombination and factors affecting the occurrence of meiotic recombination is important for crop breeding. Here, we review chromosome recombination types, recombination mechanisms, genes and proteins involved in the meiotic recombination process, recombination hotspots and their regulation systems and discuss how to increase recombination frequency in recombination coldspot regions.
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Affiliation(s)
- Meilin Zou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, 6009, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, Prospect, TAS, 7250, Australia.
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11
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Shibata T, Ikawa S, Iwasaki W, Sasanuma H, Masai H, Hirota K. Homology recognition without double-stranded DNA-strand separation in D-loop formation by RecA. Nucleic Acids Res 2024; 52:2565-2577. [PMID: 38214227 PMCID: PMC10954442 DOI: 10.1093/nar/gkad1260] [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: 09/05/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024] Open
Abstract
RecA protein and RecA/Rad51 orthologues are required for homologous recombination and DNA repair in all living creatures. RecA/Rad51 catalyzes formation of the D-loop, an obligatory recombination intermediate, through an ATP-dependent reaction consisting of two phases: homology recognition between double-stranded (ds)DNA and single-stranded (ss)DNA to form a hybrid-duplex core of 6-8 base pairs and subsequent hybrid-duplex/D-loop processing. How dsDNA recognizes homologous ssDNA is controversial. The aromatic residue at the tip of the β-hairpin loop (L2) was shown to stabilize dsDNA-strand separation. We tested a model in which dsDNA strands were separated by the aromatic residue before homology recognition and found that the aromatic residue was not essential to homology recognition, but was required for D-loop processing. Contrary to the model, we found that the double helix was not unwound even a single turn during search for sequence homology, but rather was unwound only after the homologous sequence was recognized. These results suggest that dsDNA recognizes its homologous ssDNA before strand separation. The search for homologous sequence with homologous ssDNA without dsDNA-strand separation does not generate stress within the dsDNA; this would be an advantage for dsDNA to express homology-dependent functions in vivo and also in vitro.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Ohsawa, Hachioji, Tokyo 192-0397, Japan
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Shukuko Ikawa
- Cellular & Molecular Biology Laboratory, RIKEN, Wako-shi, Saitama 351-0198, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Sasanuma
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Ohsawa, Hachioji, Tokyo 192-0397, Japan
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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: 0] [Impact Index Per Article: 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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Fajish G, Challa K, Salim S, Vp A, Mwaniki S, Zhang R, Fujita Y, Ito M, Nishant KT, Shinohara A. DNA double-strand breaks regulate the cleavage-independent release of Rec8-cohesin during yeast meiosis. Genes Cells 2024; 29:86-98. [PMID: 37968127 DOI: 10.1111/gtc.13081] [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: 01/23/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
The mitotic cohesin complex necessary for sister chromatid cohesion and chromatin loop formation shows local and global association to chromosomes in response to DNA double-strand breaks (DSBs). Here, by genome-wide binding analysis of the meiotic cohesin with Rec8, we found that the Rec8-localization profile along chromosomes is altered from middle to late meiotic prophase I with cleavage-independent dissociation. Each Rec8-binding site on the chromosome axis follows a unique alternation pattern with dissociation and probably association. Centromeres showed altered Rec8 binding in late prophase I relative to mid-prophase I, implying chromosome remodeling of the regions. Rec8 dissociation ratio per chromosome is correlated well with meiotic DSB density. Indeed, the spo11 mutant deficient in meiotic DSB formation did not change the distribution of Rec8 along chromosomes in late meiotic prophase I. These suggest the presence of a meiosis-specific regulatory pathway for the global binding of Rec8-cohesin in response to DSBs.
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Affiliation(s)
- Ghanim Fajish
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kiran Challa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Sagar Salim
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Ajith Vp
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Stephen Mwaniki
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Ruihao Zhang
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masaru Ito
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Koodali T Nishant
- School of Biology, Indian Institute of Science, Education and Research, Thiruvananthapuram, India
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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14
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Mu Y, Han J, Wu M, Li Z, DU K, Wei Y, Wu M, Huang J. Fibrillarin promotes homologous recombination repair by facilitating the recruitment of recombinase RAD51 to DNA damage sites. J Zhejiang Univ Sci B 2023; 24:1165-1173. [PMID: 38057273 PMCID: PMC10710916 DOI: 10.1631/jzus.b2300518] [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: 07/19/2023] [Accepted: 10/10/2023] [Indexed: 12/08/2023]
Abstract
Eukaryotic organisms constantly face a wide range of internal and external factors that cause damage to their DNA. Failure to accurately and efficiently repair these DNA lesions can result in genomic instability and the development of tumors (Canela et al., 2017). Among the various forms of DNA damage, DNA double-strand breaks (DSBs) are particularly harmful. Two major pathways, non-homologous end joining (NHEJ) and homologous recombination (HR), are primarily responsible for repairing DSBs (Katsuki et al., 2020; Li and Yuan, 2021; Zhang and Gong, 2021; Xiang et al., 2023). NHEJ is an error-prone repair mechanism that simply joins the broken ends together (Blunt et al., 1995; Hartley et al., 1995). In contrast, HR is a precise repair process. It involves multiple proteins in eukaryotic cells, with the RAD51 recombinase being the key player, which is analogous to bacterial recombinase A (RecA) (Shinohara et al., 1992). The central event in HR is the formation of RAD51-single-stranded DNA (ssDNA) nucleoprotein filaments that facilitate homology search and DNA strand invasion, ultimately leading to the initiation of repair synthesis (Miné et al., 2007; Hilario et al., 2009; Ma et al., 2017).
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Affiliation(s)
- Yanhua Mu
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jinhua Han
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310030, China
| | - Mingjie Wu
- Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Zongfang Li
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Ke DU
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Yameng Wei
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Mengjie Wu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China. ,
| | - Jun Huang
- Zhejiang Provincial Key Lab of Geriatrics and Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou 310030, China.
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
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15
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Liu S, Shinohara A, Furukohri A. Fanconi anemia-associated mutation in RAD51 compromises the coordinated action of DNA-binding and ATPase activities. J Biol Chem 2023; 299:105424. [PMID: 37924868 PMCID: PMC10716581 DOI: 10.1016/j.jbc.2023.105424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease caused by a defect in DNA repair pathway for DNA interstrand crosslinks. These crosslinks can potentially impede the progression of the DNA replication fork, consequently leading to DNA double-strand breaks. Heterozygous RAD51-Q242R mutation has been reported to cause FA-like symptoms. However, the molecular defect of RAD51 underlying the disease is largely unknown. In this study, we conducted a biochemical analysis of RAD51-Q242R protein, revealing notable deficiencies in its DNA-dependent ATPase activity and its ATP-dependent regulation of DNA-binding activity. Interestingly, although RAD51-Q242R exhibited the filament instability and lacked the ability to form displacement loop, it efficiently stimulated the formation of displacement loops mediated by wild-type RAD51. These findings facilitate understanding of the biochemical properties of the mutant protein and how RAD51 works in the FA patient cells.
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Affiliation(s)
- Sijia Liu
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Asako Furukohri
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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16
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Štambuk N, Konjevoda P, Brčić-Kostić K, Baković J, Štambuk A. New algorithm for the analysis of nucleotide and amino acid evolutionary relationships based on Klein four-group. Biosystems 2023; 233:105030. [PMID: 37717902 DOI: 10.1016/j.biosystems.2023.105030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Phylogenetics is the study of ancestral relationships among biological species. Such sequence analyses are often represented as phylogenetic trees. The branching pattern of each tree and its topology reflect the evolutionary relatedness between analyzed sequences. We present a Klein four-group algorithm (K4A) for the evolutionary analysis of nucleotide and amino acid sequences. Klein four-group set of operators consists of: identity e (U), and three elements-a = transition (C), b = transversion (G) and c = transition-transversion or complementarity (A). We generated Klein four-group based distance matrices of: 1. Cayley table (CK4), 2. Table rows (K4R), 3. Table columns (K4C), and 4. Euclidean 2D distance (K4E). The performance of the matrices was tested on a dataset of RecA proteins in bacteria, eukaryotes (Rad51 homolog) and archaea (RadA homolog). RecA and its functional homologs are found in all species, and are essential for the repair and maintenance of DNA. Consequently, they represent a good model for the study of evolutionary relationship of protein and nucleotide sequences. The ancestral relationship between the sequences was correctly classified by all K4A matrices concerning general topology. All distance matrices exhibited small variations among species, and overall results of tree classification were in agreement with the general patterns obtained by standard BLOSUM and PAM substitution matrices. During the evolution of a code there is a phase of optimization of system rules, the ambiguity of a code is eliminated, and the system starts producing specific components. Klein four-group algorithm is consistent with the concept of ambiguity reduction. It also enables the use of different genetic code table variants optimized for particular transitions in evolution based on biological specificity.
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Affiliation(s)
- Nikola Štambuk
- Centre for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Krunoslav Brčić-Kostić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Josip Baković
- University Hospital Dubrava, Department of Surgery, Avenija Gojka Šuška 6, HR-10000, Zagreb, Croatia
| | - Albert Štambuk
- Faculty of Kinesiology, University of Zagreb, Horvaćanski zavoj 15, HR-10000 Zagreb, Croatia
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17
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Morciano L, Elgrabli RM, Zenvirth D, Arbel-Eden A. Homologous Recombination and Repair Functions Required for Mutagenicity during Yeast Meiosis. Genes (Basel) 2023; 14:2017. [PMID: 38002960 PMCID: PMC10671739 DOI: 10.3390/genes14112017] [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: 09/29/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Several meiotic events reshape the genome prior to its transfer (via gametes) to the next generation. The occurrence of new meiotic mutations is tightly linked to homologous recombination (HR) and firmly depends on Spo11-induced DNA breaks. To gain insight into the molecular mechanisms governing mutagenicity during meiosis, we examined the timing of mutation and recombination events in cells deficient in various DNA HR-repair genes, which represent distinct functions along the meiotic recombination process. Despite sequence similarities and overlapping activities of the two DNA translocases, Rad54 and Tid1, we observed essential differences in their roles in meiotic mutation occurrence: in the absence of Rad54, meiotic mutagenicity was elevated 8-fold compared to the wild type (WT), while in the tid1Δ mutant, there were few meiotic mutations, nine percent compared to the WT. We propose that the presence of Rad54 channels recombinational repair to a less mutagenic pathway, whereas repair assisted by Tid1 is more mutagenic. A 3.5-fold increase in mutation level was observed in dmc1∆ cells, suggesting that single-stranded DNA (ssDNA) may be a potential source for mutagenicity during meiosis. Taken together, we suggest that the introduction of de novo mutations also contributes to the diversification role of meiotic recombination. These rare meiotic mutations revise genomic sequences and may contribute to long-term evolutionary changes.
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Affiliation(s)
- Liat Morciano
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel; (L.M.); (R.M.E.)
| | - Renana M. Elgrabli
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel; (L.M.); (R.M.E.)
| | - Drora Zenvirth
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel; (L.M.); (R.M.E.)
| | - Ayelet Arbel-Eden
- Department of Genetics, Hebrew University of Jerusalem, Jerusalem 91904, Israel; (L.M.); (R.M.E.)
- The Medical Laboratory Sciences Department, Hadassah Academic College, Jerusalem 91010, Israel
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18
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Ito M, Furukohri A, Matsuzaki K, Fujita Y, Toyoda A, Shinohara A. FIGNL1 AAA+ ATPase remodels RAD51 and DMC1 filaments in pre-meiotic DNA replication and meiotic recombination. Nat Commun 2023; 14:6857. [PMID: 37891173 PMCID: PMC10611733 DOI: 10.1038/s41467-023-42576-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The formation of RAD51/DMC1 filaments on single-stranded (ss)DNAs essential for homology search and strand exchange in DNA double-strand break (DSB) repair is tightly regulated. FIGNL1 AAA+++ ATPase controls RAD51-mediated recombination in human cells. However, its role in gametogenesis remains unsolved. Here, we characterized a germ line-specific conditional knockout (cKO) mouse of FIGNL1. Fignl1 cKO male mice showed defective chromosome synapsis and impaired meiotic DSB repair with the accumulation of RAD51/DMC1 on meiotic chromosomes, supporting a positive role of FIGNL1 in homologous recombination at a post-assembly stage of RAD51/DMC1 filaments. Fignl1 cKO spermatocytes also accumulate RAD51/DMC1 on chromosomes in pre-meiotic S-phase. These RAD51/DMC1 assemblies are independent of meiotic DSB formation. We also showed that purified FIGNL1 dismantles RAD51 filament on double-stranded (ds)DNA as well as ssDNA. These results suggest an additional role of FIGNL1 in limiting the non-productive assembly of RAD51/DMC1 on native dsDNAs during pre-meiotic S-phase and meiotic prophase I.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Asako Furukohri
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kenichiro Matsuzaki
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
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19
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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: 2] [Impact Index Per Article: 2.0] [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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20
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Antoniuk-Majchrzak J, Enkhbaatar T, Długajczyk A, Kaminska J, Skoneczny M, Klionsky DJ, Skoneczna A. Stability of Rad51 recombinase and persistence of Rad51 DNA repair foci depends on post-translational modifiers, ubiquitin and SUMO. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119526. [PMID: 37364618 DOI: 10.1016/j.bbamcr.2023.119526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023]
Abstract
The DNA double-strand breaks are particularly deleterious, especially when an error-free repair pathway is unavailable, enforcing the error-prone recombination pathways to repair the lesion. Cells can resume the cell cycle but at the expense of decreased viability due to genome rearrangements. One of the major players involved in recombinational repair of DNA damage is Rad51 recombinase, a protein responsible for presynaptic complex formation. We previously showed that an increased level of this protein promotes the usage of illegitimate recombination. Here we show that the level of Rad51 is regulated via the ubiquitin-dependent proteolytic pathway. The ubiquitination of Rad51 depends on multiple E3 enzymes, including SUMO-targeted ubiquitin ligases. We also demonstrate that Rad51 can be modified by both ubiquitin and SUMO. Moreover, its modification with ubiquitin may lead to opposite effects: degradation dependent on Rad6, Rad18, Slx8, Dia2, and the anaphase-promoting complex, or stabilization dependent on Rsp5. We also show that post-translational modifications with SUMO and ubiquitin affect Rad51's ability to form and disassemble DNA repair foci, respectively, influencing cell cycle progression and cell viability in genotoxic stress conditions. Our data suggest the existence of a complex E3 ligases network that regulates Rad51 recombinase's turnover, its molecular activity, and access to DNA, limiting it to the proportions optimal for the actual cell cycle stage and growth conditions, e.g., stress. Dysregulation of this network would result in a drop in cell viability due to uncontrolled genome rearrangement in the yeast cells. In mammals would promote the development of genetic diseases and cancer.
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Affiliation(s)
| | - Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Anna Długajczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
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21
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Yamaya K, Wang B, Memar N, Odiba A, Woglar A, Gartner A, Villeneuve A. Disparate roles for C. elegans DNA translocase paralogs RAD-54.L and RAD-54.B in meiotic prophase germ cells. Nucleic Acids Res 2023; 51:9183-9202. [PMID: 37548405 PMCID: PMC10516670 DOI: 10.1093/nar/gkad638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/06/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023] Open
Abstract
RAD54 family DNA translocases partner with RAD51 recombinases to ensure stable genome inheritance, exhibiting biochemical activities both in promoting recombinase removal and in stabilizing recombinase association with DNA. Understanding how such disparate activities of RAD54 paralogs align with their biological roles is an ongoing challenge. Here we investigate the in vivo functions of Caenorhabditis elegans RAD54 paralogs RAD-54.L and RAD-54.B during meiotic prophase, revealing distinct contributions to the dynamics of RAD-51 association with DNA and to the progression of meiotic double-strand break repair (DSBR). While RAD-54.L is essential for RAD-51 removal from meiotic DSBR sites to enable recombination progression, RAD-54.B is largely dispensable for meiotic DSBR. However, RAD-54.B is required to prevent hyperaccumulation of RAD-51 on unbroken DNA during the meiotic sub-stage when DSBs and early recombination intermediates form. Moreover, DSB-independent hyperaccumulation of RAD-51 foci in the absence of RAD-54.B is RAD-54.L-dependent, revealing a hidden activity of RAD-54.L in promoting promiscuous RAD-51 association that is antagonized by RAD-54.B. We propose a model wherein a division of labor among RAD-54 paralogs allows germ cells to ramp up their capacity for efficient homologous recombination that is crucial to successful meiosis while counteracting potentially deleterious effects of unproductive RAD-51 association with unbroken DNA.
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Affiliation(s)
- Kei Yamaya
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bin Wang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 530007 Nanning, China
| | - Nadin Memar
- IBS Center for Genomic Integrity and Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Arome Solomon Odiba
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, 530007 Nanning, China
| | - Alexander Woglar
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Swiss Institute for Experimental Cancer Research (ISREC) and School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Anton Gartner
- IBS Center for Genomic Integrity and Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Anne M Villeneuve
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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22
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Hou B, Yang H, Li E, Jiang X. The disulphide cleavage derivative (C42-4) of 11'-deoxyverticillin A (C42) fails to induce apoptosis and genomic instability in HeLa cells. Mycology 2023; 14:358-370. [PMID: 38187884 PMCID: PMC10769127 DOI: 10.1080/21501203.2023.2248168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/09/2023] [Indexed: 01/09/2024] Open
Abstract
Our previous study revealed 11'-deoxyverticillin A (C42), a natural product isolated from the Ophiocordyceps-associated fungus Clonostachys rogersoniana and a member of the epipolythiodioxopiperazines (ETPs), induced both apoptosis and autophagy in HCT116 cells; however, the role of disulphide/polysulphide bridges of C42 in the regulation of autophagy remains unexplored. Here, we revealed that C42 activated both caspase-dependent apoptosis and autophagy in HeLa cells, whereas its disulphide cleavage derivative C42-4 failed to induce the cleavage of both caspase-3 and PARP-1. In contrast, both C42 and C42-4 increased the formation of autophagosomes, punctate staining of LC3, and the ratio of LC3-II to actin, suggesting that disulphide/polysulphide bridges are dispensable for the induction of the autophagic process. Moreover, we found that C42 but not C42-4 led to nuclear instability by increasing the formation of micronuclei and expression of phosphorylated histone H2AX (γ-H2AX), a widely used marker for DNA double strand breaks (DSBs), while Rad51, a protein pivotal for DNA repair, was decreased upon challenge with C42. These results demonstrate that the disulphide bonds in ETPs play an essential role in the induction of caspase-dependent apoptosis and nuclear stability.
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Affiliation(s)
- Bolin Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaiyi Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Erwei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xuejun Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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23
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Sugaya N, Tanaka S, Keyamura K, Noda S, Akanuma G, Hishida T. N-terminal acetyltransferase NatB regulates Rad51-dependent repair of double-strand breaks in Saccharomyces cerevisiae. Genes Genet Syst 2023; 98:61-72. [PMID: 37331807 DOI: 10.1266/ggs.23-00013] [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: 06/20/2023] Open
Abstract
Homologous recombination (HR) is a highly accurate mechanism for repairing DNA double-strand breaks (DSBs) that arise from various genotoxic insults and blocked replication forks. Defects in HR and unscheduled HR can interfere with other cellular processes such as DNA replication and chromosome segregation, leading to genome instability and cell death. Therefore, the HR process has to be tightly controlled. Protein N-terminal acetylation is one of the most common modifications in eukaryotic organisms. Studies in budding yeast implicate a role for NatB acetyltransferase in HR repair, but precisely how this modification regulates HR repair and genome integrity is unknown. In this study, we show that cells lacking NatB, a dimeric complex composed of Nat3 and Mdm2, are sensitive to the DNA alkylating agent methyl methanesulfonate (MMS), and that overexpression of Rad51 suppresses the MMS sensitivity of nat3Δ cells. Nat3-deficient cells have increased levels of Rad52-yellow fluorescent protein foci and fail to repair DSBs after release from MMS exposure. We also found that Nat3 is required for HR-dependent gene conversion and gene targeting. Importantly, we observed that nat3Δ mutation partially suppressed MMS sensitivity in srs2Δ cells and the synthetic sickness of srs2Δ sgs1Δ cells. Altogether, our results indicate that NatB functions upstream of Srs2 to activate the Rad51-dependent HR pathway for DSB repair.
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Affiliation(s)
- Natsuki Sugaya
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Shion Tanaka
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Shunsuke Noda
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Genki Akanuma
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
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24
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.553855. [PMID: 37693500 PMCID: PMC10491117 DOI: 10.1101/2023.08.28.553855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a g enome engineering c atalyst (GATALYST) for efficient and safe targeted gene knock-in. However, the engineering efficiency is bottlenecked by the nucleoplasm trafficking and genomic tethering of cssDNA donor, especially for extra-large transgene integration. Here we developed enGager, en hanced G ATALYST a ssociated g enome e ditor system by fusion of nucleus localization signal (NLS) peptide tagged Cas9 with various single stranded DNA binding protein modules through a GFP reporter Knock-in screening. The enGager system assembles an integrative genome integration machinery by forming tripartite complex for engineered nuclease editors, sgRNA and ssDNA donors, thereby facilitate the nucleus trafficking of DNA donors and increase their active local concentration at the targeted genomic site. When applied for genome integration with cssDNA donor templates to diverse genomic loci in various cell types, these enGagers outperform unfused editors. The enhancement of integration efficiency ranges from 1.5- to more than 6-fold, with the effect being more prominent for > 4Kb transgene knock-in in primary cells. We further demonstrated that enGager mediated enhancement for genome integration is ssDNA, but less dsDNA dependent. Using one of the mini-enGagers, we demonstrated large chimeric antigen receptor (CAR) transgene integration in primary T cells with exceptional efficiency and anti-tumor function. These tripartite e ditors with s sDNA o ptimized g enome en gineering system (TESOGENASE TM ) add a set of novel endonuclease editors into the gene-editing toolbox for potential cell and gene therapeutic development based on ssDNA mediated non-viral genome engineering. Highlight A reporter Knock-in screening establishes enGager system to identify TESOGENASE editor to improving ssDNA mediated genome integrationMini-TESOGENASEs developed by fusing Cas9 nuclease with novel ssDNA binding motifsmRNA mini-TESOGENASEs enhance targeted genome integration via various non-viral delivery approachesEfficient functional CAR-T cell engineering by mini-TESOGENASE.
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Xu W, Yu Y, Jing J, Wu Z, Zhang X, You C, Ma H, Copenhaver GP, He Y, Wang Y. SCF RMF mediates degradation of the meiosis-specific recombinase DMC1. Nat Commun 2023; 14:5044. [PMID: 37598222 PMCID: PMC10439943 DOI: 10.1038/s41467-023-40799-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/10/2023] [Indexed: 08/21/2023] Open
Abstract
Meiotic recombination requires the specific RecA homolog DMC1 recombinase to stabilize strand exchange intermediates in most eukaryotes. Normal DMC1 levels are crucial for its function, yet the regulatory mechanisms of DMC1 stability are unknown in any organism. Here, we show that the degradation of Arabidopsis DMC1 by the 26S proteasome depends on F-box proteins RMF1/2-mediated ubiquitination. Furthermore, RMF1/2 interact with the Skp1 ortholog ASK1 to form the ubiquitin ligase complex SCFRMF1/2. Genetic analyses demonstrate that RMF1/2, ASK1 and DMC1 act in the same pathway downstream of SPO11-1 dependent meiotic DNA double strand break formation and that the proper removal of DMC1 is crucial for meiotic crossover formation. Moreover, six DMC1 lysine residues were identified as important for its ubiquitination but not its interaction with RMF1/2. Our results reveal mechanistic insights into how the stability of a key meiotic recombinase that is broadly conserved in eukaryotes is regulated.
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Affiliation(s)
- Wanyue Xu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Yu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Juli Jing
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhen Wu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Chenjiang You
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Gregory P Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China.
- College of Life Sciences, Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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26
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Hu R, Li X, Hu Y, Zhang R, Lv Q, Zhang M, Sheng X, Zhao F, Chen Z, Ding Y, Yuan H, Wu X, Xing S, Yan X, Bao F, Wan P, Xiao L, Wang X, Xiao W, Decker EL, van Gessel N, Renault H, Wiedemann G, Horst NA, Haas FB, Wilhelmsson PKI, Ullrich KK, Neumann E, Lv B, Liang C, Du H, Lu H, Gao Q, Cheng Z, You H, Xin P, Chu J, Huang CH, Liu Y, Dong S, Zhang L, Chen F, Deng L, Duan F, Zhao W, Li K, Li Z, Li X, Cui H, Zhang YE, Ma C, Zhu R, Jia Y, Wang M, Hasebe M, Fu J, Goffinet B, Ma H, Rensing SA, Reski R, He Y. Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet. Cell 2023; 186:3558-3576.e17. [PMID: 37562403 DOI: 10.1016/j.cell.2023.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/23/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
The most extreme environments are the most vulnerable to transformation under a rapidly changing climate. These ecosystems harbor some of the most specialized species, which will likely suffer the highest extinction rates. We document the steepest temperature increase (2010-2021) on record at altitudes of above 4,000 m, triggering a decline of the relictual and highly adapted moss Takakia lepidozioides. Its de-novo-sequenced genome with 27,467 protein-coding genes includes distinct adaptations to abiotic stresses and comprises the largest number of fast-evolving genes under positive selection. The uplift of the study site in the last 65 million years has resulted in life-threatening UV-B radiation and drastically reduced temperatures, and we detected several of the molecular adaptations of Takakia to these environmental changes. Surprisingly, specific morphological features likely occurred earlier than 165 mya in much warmer environments. Following nearly 400 million years of evolution and resilience, this species is now facing extinction.
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Affiliation(s)
- Ruoyang Hu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China; State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xuedong Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Yong Hu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Runjie Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Qiang Lv
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Min Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xianyong Sheng
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Feng Zhao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Zhijia Chen
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Yuhan Ding
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Huan Yuan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xiaofeng Wu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Shuang Xing
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Xiaoyu Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Fang Bao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Ping Wan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Lihong Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Xiaoqin Wang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Wei Xiao
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Nico van Gessel
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Hugues Renault
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, University of Strasbourg, 67084 Strasbourg, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Inselspital, University of Bern, 3010 Bern, Switzerland
| | - Nelly A Horst
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; MetaSystems Hard & Software GmbH, 68804 Altlussheim, Germany
| | - Fabian B Haas
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | | | - Kristian K Ullrich
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Eva Neumann
- Department of Biology, University of Marburg, 35043 Marburg, Germany
| | - Bin Lv
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China
| | - Chengzhi Liang
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Hongwei Lu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Qiang Gao
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhukuan Cheng
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hanli You
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Peiyong Xin
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010031, China
| | - Yang Liu
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, Storrs, CT 06269, USA; Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518085, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fei Chen
- Sanya Nanfan Research Institute from Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Lei Deng
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Fuzhou Duan
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Wenji Zhao
- College of Resource Environment and Tourism, CNU, Beijing 100048, China
| | - Kai Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Zhongfeng Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Xingru Li
- Department of Chemistry, CNU, Beijing 100048, China
| | - Hengjian Cui
- School of Mathematical Sciences, CNU, Beijing 100048, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan Ma
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruiliang Zhu
- Department of Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meizhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mitsuyasu Hasebe
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, The Graduate School for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Unit 3043, Storrs, CT 06269, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Stefan A Rensing
- Department of Biology, University of Marburg, 35043 Marburg, Germany; Faculty of Chemistry and Pharmacy, University of Freiburg, 79104 Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.
| | - Yikun He
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University (CNU), Beijing 100048, China.
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27
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Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O’Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals. CELL GENOMICS 2023; 3:100349. [PMID: 37601968 PMCID: PMC10435384 DOI: 10.1016/j.xgen.2023.100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 08/22/2023]
Abstract
Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we reveal the tumor suppressor FANCM as a meiotic anti-crossover factor in mammals. We use unique large-scale crossover analyses with both single-gamete sequencing and pedigree-based bulk-sequencing datasets to identify a genome-wide increase in crossover frequencies in Fancm-deficient mice. Gametogenesis is heavily perturbed in Fancm loss-of-function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway after birth. Despite the gametogenesis phenotypes in Fancm mutants, both sexes are capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
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Affiliation(s)
- Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jessica M. Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jessica E.M. Dunleavy
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Elissah Granger
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Anna Leichter
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Lucy McNeill
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Nadeen Zerafa
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Eva R. Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moira K. O’Bryan
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Deans
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Genome Stability Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jörg Heierhorst
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Molecular Genetics Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
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28
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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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29
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Emmenecker C, Mézard C, Kumar R. Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators. PLANT REPRODUCTION 2023; 36:17-41. [PMID: 35641832 DOI: 10.1007/s00497-022-00443-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Homologous recombination during meiosis is crucial for the DNA double-strand breaks (DSBs) repair that promotes the balanced segregation of homologous chromosomes and enhances genetic variation. In most eukaryotes, two recombinases RAD51 and DMC1 form nucleoprotein filaments on single-stranded DNA generated at DSB sites and play a central role in the meiotic DSB repair and genome stability. These nucleoprotein filaments perform homology search and DNA strand exchange to initiate repair using homologous template-directed sequences located elsewhere in the genome. Multiple factors can regulate the assembly, stability, and disassembly of RAD51 and DMC1 nucleoprotein filaments. In this review, we summarize the current understanding of the meiotic functions of RAD51 and DMC1 and the role of their positive and negative modulators. We discuss the current models and regulators of homology searches and strand exchange conserved during plant meiosis. Manipulation of these repair factors during plant meiosis also holds a great potential to accelerate plant breeding for crop improvements and productivity.
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Affiliation(s)
- Côme Emmenecker
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France
- University of Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin (IJPB), CNRS, Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
| | - Rajeev Kumar
- Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, AgroParisTech, 78000, Versailles, France.
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30
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Abstract
KEY MESSAGE Chromatin state, and dynamic loading of pro-crossover protein HEI10 at recombination intermediates shape meiotic chromosome patterning in plants. Meiosis is the basis of sexual reproduction, and its basic progression is conserved across eukaryote kingdoms. A key feature of meiosis is the formation of crossovers which result in the reciprocal exchange of segments of maternal and paternal chromosomes. This exchange generates chromosomes with new combinations of alleles, increasing the efficiency of both natural and artificial selection. Crossovers also form a physical link between homologous chromosomes at metaphase I which is critical for accurate chromosome segregation and fertility. The patterning of crossovers along the length of chromosomes is a highly regulated process, and our current understanding of its regulation forms the focus of this review. At the global scale, crossover patterning in plants is largely governed by the classically observed phenomena of crossover interference, crossover homeostasis and the obligatory crossover which regulate the total number of crossovers and their relative spacing. The molecular actors behind these phenomena have long remained obscure, but recent studies in plants implicate HEI10 and ZYP1 as key players in their coordination. In addition to these broad forces, a wealth of recent studies has highlighted how genomic and epigenomic features shape crossover formation at both chromosomal and local scales, revealing that crossovers are primarily located in open chromatin associated with gene promoters and terminators with low nucleosome occupancy.
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Affiliation(s)
- Andrew Lloyd
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3DA, Ceredigion, UK.
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A Natural Fungal Gene Drive Enacts Killing via DNA Disruption. mBio 2023; 14:e0317322. [PMID: 36537809 PMCID: PMC9972908 DOI: 10.1128/mbio.03173-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Fungal spore killers are a class of selfish genetic elements that positively bias their own inheritance by killing non-inheriting gametes following meiosis. As killing takes place specifically within the developing fungal ascus, a tissue which is experimentally difficult to isolate, our understanding of the mechanisms underlying spore killers are limited. In particular, how these loci kill other spores within the fungal ascus is largely unknown. Here, we overcome these experimental barriers by developing model systems in 2 evolutionary distant organisms, Escherichia coli (bacterium) and Saccharomyces cerevisiae (yeast), similar to previous approaches taken to examine the wtf spore killers. Using these systems, we show that the Podospora anserina spore killer protein SPOK1 enacts killing through targeting DNA. IMPORTANCE Natural gene drives have shaped the genomes of many eukaryotes and recently have been considered for applications to control undesirable species. In fungi, these loci are called spore killers. Despite their importance in evolutionary processes and possible applications, our understanding of how they enact killing is limited. We show that the spore killer protein Spok1, which has homologues throughout the fungal tree of life, acts via DNA disruption. Spok1 is only the second spore killer locus in which the cellular target of killing has been identified and is the first known to target DNA. We also show that the DNA disrupting activity of Spok1 is functional in both bacteria and yeast suggesting a highly conserved mode of action.
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RAD51 and RAD51B Play Diverse Roles in the Repair of DNA Double Strand Breaks in Physcomitrium patens. Genes (Basel) 2023; 14:genes14020305. [PMID: 36833232 PMCID: PMC9956106 DOI: 10.3390/genes14020305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
RAD51 is involved in finding and invading homologous DNA sequences for accurate homologous recombination (HR). Its paralogs have evolved to regulate and promote RAD51 functions. The efficient gene targeting and high HR rates are unique in plants only in the moss Physcomitrium patens (P. patens). In addition to two functionally equivalent RAD51 genes (RAD1-1 and RAD51-2), other RAD51 paralogues were also identified in P. patens. For elucidation of RAD51's involvement during DSB repair, two knockout lines were constructed, one mutated in both RAD51 genes (Pprad51-1-2) and the second with mutated RAD51B gene (Pprad51B). Both lines are equally hypersensitive to bleomycin, in contrast to their very different DSB repair efficiency. Whereas DSB repair in Pprad51-1-2 is even faster than in WT, in Pprad51B, it is slow, particularly during the second phase of repair kinetic. We interpret these results as PpRAD51-1 and -2 being true functional homologs of ancestral RAD51 involved in the homology search during HR. Absence of RAD51 redirects DSB repair to the fast NHEJ pathway and leads to a reduced 5S and 18S rDNA copy number. The exact role of the RAD51B paralog remains unclear, though it is important in damage recognition and orchestrating HR response.
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Ziesel A, Weng Q, Ahuja JS, Bhattacharya A, Dutta R, Cheng E, Börner GV, Lichten M, Hollingsworth NM. Rad51-mediated interhomolog recombination during budding yeast meiosis is promoted by the meiotic recombination checkpoint and the conserved Pif1 helicase. PLoS Genet 2022; 18:e1010407. [PMID: 36508468 PMCID: PMC9779700 DOI: 10.1371/journal.pgen.1010407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/22/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
During meiosis, recombination between homologous chromosomes (homologs) generates crossovers that promote proper segregation at the first meiotic division. Recombination is initiated by Spo11-catalyzed DNA double strand breaks (DSBs). 5' end resection of the DSBs creates 3' single strand tails that two recombinases, Rad51 and Dmc1, bind to form presynaptic filaments that search for homology, mediate strand invasion and generate displacement loops (D-loops). D-loop processing then forms crossover and non-crossover recombinants. Meiotic recombination occurs in two temporally distinct phases. During Phase 1, Rad51 is inhibited and Dmc1 mediates the interhomolog recombination that promotes homolog synapsis. In Phase 2, Rad51 becomes active and functions with Rad54 to repair residual DSBs, making increasing use of sister chromatids. The transition from Phase 1 to Phase 2 is controlled by the meiotic recombination checkpoint through the meiosis-specific effector kinase Mek1. This work shows that constitutive activation of Rad51 in Phase 1 results in a subset of DSBs being repaired by a Rad51-mediated interhomolog recombination pathway that is distinct from that of Dmc1. Strand invasion intermediates generated by Rad51 require more time to be processed into recombinants, resulting in a meiotic recombination checkpoint delay in prophase I. Without the checkpoint, Rad51-generated intermediates are more likely to involve a sister chromatid, thereby increasing Meiosis I chromosome nondisjunction. This Rad51 interhomolog recombination pathway is specifically promoted by the conserved 5'-3' helicase PIF1 and its paralog, RRM3 and requires Pif1 helicase activity and its interaction with PCNA. This work demonstrates that (1) inhibition of Rad51 during Phase 1 is important to prevent competition with Dmc1 for DSB repair, (2) Rad51-mediated meiotic recombination intermediates are initially processed differently than those made by Dmc1, and (3) the meiotic recombination checkpoint provides time during prophase 1 for processing of Rad51-generated recombination intermediates.
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Affiliation(s)
- Andrew Ziesel
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Qixuan Weng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Jasvinder S. Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Abhishek Bhattacharya
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Raunak Dutta
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Evan Cheng
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - G. Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nancy M. Hollingsworth
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
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Li Y, Meng R, Li S, Gu B, Xu X, Zhang H, Tan X, Shao T, Wang J, Xu D, Wang F. The ZFP541-KCTD19 complex is essential for pachytene progression by activating meiotic genes during mouse spermatogenesis. J Genet Genomics 2022; 49:1029-1041. [PMID: 35341968 DOI: 10.1016/j.jgg.2022.03.005] [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: 12/13/2021] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 12/29/2022]
Abstract
Meiosis is essential for fertility in sexually reproducing species and this sophisticated process has been extensively studied. Notwithstanding these efforts, key factors involved in meiosis have not been fully characterized. In this study, we investigate the regulatory roles of zinc finger protein 541 (ZFP541) and its interacting protein potassium channel tetramerization domain containing 19 (KCTD19) in spermatogenesis. ZFP541 is expressed from leptotene to the round spermatid stage, while the expression of KCTD19 is initiated in pachytene. Depletion of Zfp541 or Kctd19 leads to infertility in male mice and delays progression from early to mid/late pachynema. In addition, Zfp541-/- spermatocytes show abnormal programmed DNA double-strand break repair, impaired crossover formation and resolution, and asynapsis of the XY chromosomes. ZFP541 interacts with KCTD19, histone deacetylase 1/2 (HDAC1/2), and deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1). Moreover, ZFP541 binds to and activates the expression of genes involved in meiosis and post-meiosis including Kctd19; in turn, KCTD19 promotes the transcriptional activation activity of ZFP541. Taken together, our studies reveal that the ZFP541/KCTD19 signaling complex, acting as a key transcription regulator, plays an indispensable role in male fertility by regulating pachytene progression.
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Affiliation(s)
- Yushan Li
- The School of Public Health, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Ranran Meng
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Shanze Li
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Bowen Gu
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Xiaotong Xu
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Haihang Zhang
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Xinshui Tan
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Tianyu Shao
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Jiawen Wang
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Dan Xu
- National Institute of Biological Sciences Beijing, Beijing 102206, China
| | - Fengchao Wang
- National Institute of Biological Sciences Beijing, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China.
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35
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Skoko JJ, Cao J, Gaboriau D, Attar M, Asan A, Hong L, Paulsen CE, Ma H, Liu Y, Wu H, Harkness T, Furdui CM, Manevich Y, Morrison CG, Brown ET, Normolle D, Spies M, Spies MA, Carroll K, Neumann CA. Redox regulation of RAD51 Cys319 and homologous recombination by peroxiredoxin 1. Redox Biol 2022; 56:102443. [PMID: 36058112 PMCID: PMC9450138 DOI: 10.1016/j.redox.2022.102443] [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: 05/05/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022] Open
Abstract
RAD51 is a critical recombinase that functions in concert with auxiliary mediator proteins to direct the homologous recombination (HR) DNA repair pathway. We show that Cys319 RAD51 possesses nucleophilic characteristics and is important for irradiation-induced RAD51 foci formation and resistance to inhibitors of poly (ADP-ribose) polymerase (PARP). We have previously identified that cysteine (Cys) oxidation of proteins can be important for activity and modulated via binding to peroxiredoxin 1 (PRDX1). PRDX1 reduces peroxides and coordinates the signaling actions of protein binding partners. Loss of PRDX1 inhibits irradiation-induced RAD51 foci formation and represses HR DNA repair. PRDX1-deficient human breast cancer cells and mouse embryonic fibroblasts display disrupted RAD51 foci formation and decreased HR, resulting in increased DNA damage and sensitization of cells to irradiation. Following irradiation cells deficient in PRDX1 had increased incorporation of the sulfenylation probe DAz-2 in RAD51 Cys319, a functionally-significant, thiol that PRDX1 is critical for maintaining in a reduced state. Molecular dynamics (MD) simulations of dT-DNA bound to a non-oxidized RAD51 protein showed tight binding throughout the simulation, while dT-DNA dissociated from an oxidized Cys319 RAD51 filament. These novel data establish RAD51 Cys319 as a functionally-significant site for the redox regulation of HR and cellular responses to IR. A functionally-significant Cys319 was identified in RAD51 that possesses nucleophilic characteristics. RAD51 Cys319 plays a central role in RAD51-mediated repair of DNA double strand breaks (DSB). Loss of peroxiredoxin 1 (PRDX1) impairs DNA DSB repair by homologous recombination and results in DNA damage. PRDX1 is critical for maintaining RAD51 Cys319 in a reduced state. Molecular dynamic (MD) simulations suggest ssDNA to dissociate from sulfenylated and not reduced RAD51 Cys319.
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Affiliation(s)
- John J Skoko
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Juxiang Cao
- Department of Cell and Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29425, USA
| | - David Gaboriau
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland; Facility for Imaging By Light Microscopy, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Myriam Attar
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Alparslan Asan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Lisa Hong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Candice E Paulsen
- Department of Chemistry, Scripps Research Institute Florida, Jupiter, FL, 33458, USA
| | - Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Trey Harkness
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yefim Manevich
- Department of Cell and Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ciaran G Morrison
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Erika T Brown
- Dartmouth Geisel School of Medicine, Hanover, NH, 03755, USA
| | - Daniel Normolle
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa, IA, 52242, USA
| | - Michael Ashley Spies
- Department of Biochemistry and Molecular Biology, Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, IA, 52242, USA
| | - Kate Carroll
- Department of Chemistry, Scripps Research Institute Florida, Jupiter, FL, 33458, USA
| | - Carola A Neumann
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA.
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Choi J, Kong M, Gallagher DN, Li K, Bronk G, Cao Y, Greene EC, Haber JE. Repair of mismatched templates during Rad51-dependent Break-Induced Replication. PLoS Genet 2022; 18:e1010056. [PMID: 36054210 PMCID: PMC9477423 DOI: 10.1371/journal.pgen.1010056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 09/15/2022] [Accepted: 08/10/2022] [Indexed: 12/02/2022] Open
Abstract
Using budding yeast, we have studied Rad51-dependent break-induced replication (BIR), where the invading 3’ end of a site-specific double-strand break (DSB) and a donor template share 108 bp of homology that can be easily altered. BIR still occurs about 10% as often when every 6th base is mismatched as with a perfectly matched donor. Here we explore the tolerance of mismatches in more detail, by examining donor templates that each carry 10 mismatches, each with different spatial arrangements. Although 2 of the 6 arrangements we tested were nearly as efficient as the evenly-spaced reference, 4 were significantly less efficient. A donor with all 10 mismatches clustered at the 3’ invading end of the DSB was not impaired compared to arrangements where mismatches were clustered at the 5’ end. Our data suggest that the efficiency of strand invasion is principally dictated by thermodynamic considerations, i.e., by the total number of base pairs that can be formed; but mismatch position-specific effects are also important. We also addressed an apparent difference between in vitro and in vivo strand exchange assays, where in vitro studies had suggested that at a single contiguous stretch of 8 consecutive bases was needed to be paired for stable strand pairing, while in vivo assays using 108-bp substrates found significant recombination even when every 6th base was mismatched. Now, using substrates of either 90 or 108 nt–the latter being the size of the in vivo templates–we find that in vitro D-loop results are very similar to the in vivo results. However, there are still notable differences between in vivo and in vitro assays that are especially evident with unevenly-distributed mismatches. Mismatches in the donor template are incorporated into the BIR product in a strongly polar fashion up to ~40 nucleotides from the 3’ end. Mismatch incorporation depends on the 3’→ 5’ proofreading exonuclease activity of DNA polymerase δ, with little contribution from Msh2/Mlh1 mismatch repair proteins, or from Rad1-Rad10 flap nuclease or the Mph1 helicase. Surprisingly, the probability of a mismatch 27 nt from the 3’ end being replaced by donor sequence was the same whether the preceding 26 nucleotides were mismatched every 6th base or fully homologous. These data suggest that DNA polymerase δ “chews back” the 3’ end of the invading strand without any mismatch-dependent cues from the strand invasion structure. However, there appears to be an alternative way to incorporate a mismatch at the first base at the 3’ end of the donor. DNA double-strand breaks (DSBs) are the most lethal forms of DNA damage and inaccurate repair of these breaks presents a serious threat to genomic integrity and cell viability. Break-induced replication (BIR) is a homologous recombination pathway that results in a nonreciprocal translocation of chromosome ends. We used budding yeast Saccharomyces cerevisiae to investigate Rad51-mediated BIR, where the invading 3’ end of the DSB and a donor template share 108 bp of homology. We examined the tolerance of differently distributed mismatches on a homologous donor template. A donor with all 10 mismatches clustered every 6th base at the 3’ invading end of the DSB was not impaired compared to arrangements where mismatches were clustered at the 5’ end. We also compared the efficiency of in vivo BIR with in vitro D-loop formation and find that for substrates of the same length, the tolerance for mismatches is comparable. However, there are still notable differences between in vivo and in vitro assays that are especially evident in substrates with unevenly-distributed mismatches. Mismatches are incorporated into the BIR product in a strongly polar fashion as far as about 40 nucleotides from the 3’ end, dependent on the 5’ to 3’ proofreading activity of DNA polymerase δ. Pol δ can “chew back” the 3’ end of the invading strand even when the sequences removed have no mismatches for the first 26 nucleotides. However, a mismatch at the first base can be removed from the 3’ end by another, unidentified mechanism.
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Affiliation(s)
- Jihyun Choi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Muwen Kong
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Danielle N. Gallagher
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Kevin Li
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Gabriel Bronk
- Department of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yiting Cao
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Eric C. Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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OsRAD51 Plays a Vital Role in Promoting Homologous Recombination in Rice Meiosis. Int J Mol Sci 2022; 23:ijms23179906. [PMID: 36077304 PMCID: PMC9456343 DOI: 10.3390/ijms23179906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Meiotic recombination plays a pivotal role in achieving accurate chromosomal segregation and increasing genetic diversity. In the homologous recombination pathway, the detailed mechanisms of how OsRAD51 and OsDMC1 work in rice meiosis remain to be explored. Here, we obtained different types of mutants for Osrad51a1, Osrad51a2, Osdmc1a, and Osdmc1b through CRISPR/Cas9. Both Osrad51a1 and Osrad51a2 exhibited normal vegetative growth and fertility. Osrad51 (Osrad51a1 Osrad51a2) mutant plants show normal vegetative growth but exhibit complete sterility, indicating that OsRAD51A1 and OsRAD51A2 are functionally redundant in rice fertility. In contrast to the wild type, Osrad51 chromosomes are not paired perfectly at pachytene and synaptonemal complex (SC) formation is deficient. Moreover, univalents and multivalent associations were observed at metaphase I, chromosome fragments presented at anaphase I, and crossover formation is basically suppressed in Osrad51 pollen mother cells (PMCs). OsRAD51 foci emerge at leptotene and disappear from late pachytene and chromosome localization of OsRAD51 depends on the formation of double-strand breaks (DSBs). Most OsRAD51 foci can co-localize with OsDMC1 signals. OsRAD51 is essential for the loading of OsDMC1 onto chromosomes, and vice versa. In addition, both OsRAD51 and OsDMC1 can interact with OsFIGL1 and OsBRCA2, two important components in rice meiosis. Moreover, the Osrad51 Osdmc1 (Osrad51a1 Osrad51a2 Osdmc1a Osdmc1b) quadruple mutant PMCs exhibited similar defective phenotypes as Osrad51 in homologous pairing, synapsis, and DSB repair. Taken together, our results suggest that the recombinases DMC1 and RAD51 may functionally depend on each other and play important roles in meiotic recombination during meiosis in rice.
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Xie H, Wang X, Jin M, Li L, Zhu J, Kang Y, Chen Z, Sun Y, Zhao C. Cilia regulate meiotic recombination in zebrafish. J Mol Cell Biol 2022; 14:6671532. [PMID: 35981808 PMCID: PMC9764210 DOI: 10.1093/jmcb/mjac049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/16/2022] [Accepted: 08/15/2022] [Indexed: 01/14/2023] Open
Abstract
Meiosis is essential for evolution and genetic diversity in almost all sexual eukaryotic organisms. The mechanisms of meiotic recombination, such as synapsis, have been extensively investigated. However, it is still unclear whether signals from the cytoplasm or even from outside of the cell can regulate the meiosis process. Cilia are microtubule-based structures that protrude from the cell surface and function as signaling hubs to sense extracellular signals. Here, we reported an unexpected and critical role of cilia during meiotic recombination. During gametogenesis of zebrafish, cilia were specifically present in the prophase stages of both primary spermatocytes and primary oocytes. By developing a germ cell-specific CRISPR/Cas9 system, we demonstrated that germ cell-specific depletion of ciliary genes resulted in compromised double-strand break repair, reduced crossover formation, and increased germ cell apoptosis. Our study reveals a previously undiscovered role for cilia during meiosis and suggests that extracellular signals may regulate meiotic recombination via this particular organelle.
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Affiliation(s)
| | | | - Minjun Jin
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Sars-Fang Centre, Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lanqin Li
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Sars-Fang Centre, Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Junwen Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy for Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan 430072, China,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunsi Kang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China,Sars-Fang Centre, Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Zhe Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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Multi-color dSTORM microscopy in Hormad1-/- spermatocytes reveals alterations in meiotic recombination intermediates and synaptonemal complex structure. PLoS Genet 2022; 18:e1010046. [PMID: 35857787 PMCID: PMC9342782 DOI: 10.1371/journal.pgen.1010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 08/01/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022] Open
Abstract
Recombinases RAD51 and its meiosis-specific paralog DMC1 accumulate on single-stranded DNA (ssDNA) of programmed DNA double strand breaks (DSBs) in meiosis. Here we used three-color dSTORM microscopy, and a mouse model with severe defects in meiotic DSB formation and synapsis (Hormad1-/-) to obtain more insight in the recombinase accumulation patterns in relation to repair progression. First, we used the known reduction in meiotic DSB frequency in Hormad1-/- spermatocytes to be able to conclude that the RAD51/DMC1 nanofoci that preferentially localize at distances of ~300 nm form within a single DSB site, whereas a second preferred distance of ~900 nm, observed only in wild type, represents inter-DSB distance. Next, we asked whether the proposed role of HORMAD1 in repair inhibition affects the RAD51/DMC1 accumulation patterns. We observed that the two most frequent recombinase configurations (1 DMC1 and 1 RAD51 nanofocus (D1R1), and D2R1) display coupled frequency dynamics over time in wild type, but were constant in the Hormad1-/- model, indicating that the lifetime of these intermediates was altered. Recombinase nanofoci were also smaller in Hormad1-/- spermatocytes, consistent with changes in ssDNA length or protein accumulation. Furthermore, we established that upon synapsis, recombinase nanofoci localized closer to the synaptonemal complex (SYCP3), in both wild type and Hormad1-/- spermatocytes. Finally, the data also revealed a hitherto unknown function of HORMAD1 in inhibiting coil formation in the synaptonemal complex. SPO11 plays a similar but weaker role in coiling and SYCP1 had the opposite effect. Using this large super-resolution dataset, we propose models with the D1R1 configuration representing one DSB end containing recombinases, and the other end bound by other ssDNA binding proteins, or both ends loaded by the two recombinases, but in below-resolution proximity. This may then often evolve into D2R1, then D1R2, and finally back to D1R1, when DNA synthesis has commenced. In order to correctly pair homologous chromosomes in the first meiotic prophase, repair of programmed double strand breaks (DSBs) is essential. By unravelling molecular details of the protein assemblies at single DSBs, using super-resolution microscopy, we aim to understand the dynamics of repair intermediates and their functions. We investigated the localization of the two recombinases RAD51 and DMC1 in wild type and HORMAD1-deficient cells. HORMAD1 is involved in multiple aspects of homologous chromosome association: it regulates formation and repair of DSBs, and it stimulates formation of the synaptonemal complex (SC), the macromolecular protein assembly that connects paired chromosomes. RAD51 and DMC1 enable chromosome pairing by promoting the invasions of the intact chromatids by single-stranded DNA ends that result from DSBs. We found that in absence of HORMAD1, RAD51 and DMC1 showed small but significant morphological and positional changes, combined with altered kinetics of specific RAD51/DMC1 configurations. We also determined that there is a generally preferred distance of ~900 nm between meiotic DSBs along the SC. Finally, we observed changes in the structure of the SC in Hormad1-/- spermatocytes. This study contributes to a better understanding of the molecular details of meiotic homologous recombination and the role of HORMAD1 in meiotic prophase.
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A Homozygous Loss-of-Function Mutation in MSH5 Abolishes MutSγ Axial Loading and Causes Meiotic Arrest in NOA-Affected Individuals. Int J Mol Sci 2022; 23:ijms23126522. [PMID: 35742973 PMCID: PMC9224491 DOI: 10.3390/ijms23126522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Non-obstructive azoospermia (NOA), characterized by spermatogenesis failure and the absence of sperm in ejaculation, is the most severe form of male infertility. However, the etiology and pathology between meiosis-associated monogenic alterations and human NOA remain largely unknown. A homozygous MSH5 mutation (c.1126del) was identified from two idiopathic NOA patients in the consanguineous family. This mutation led to the degradation of MSH5 mRNA and abolished chromosome axial localization of MutSγ in spermatocytes from the affected males. Chromosomal spreading analysis of the patient's meiotic prophase I revealed that the meiosis progression was arrested at a zygotene-like stage with extensive failure of homologous synapsis and DSB repair. Therefore, our study demonstrates that the MSH5 c.1126del could cause meiotic recombination failure and lead to human infertility, improving the genetic diagnosis of NOA clinically. Furthermore, the study of human spermatocytes elucidates the meiosis defects caused by MSH5 variant, and reveals a conserved and indispensable role of MutSγ in human synapsis and meiotic recombination, which have not previously been well-described.
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Divergent binding mode for a protozoan BRC repeat to RAD51. Biochem J 2022; 479:1031-1043. [PMID: 35502837 PMCID: PMC9162458 DOI: 10.1042/bcj20220141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/20/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022]
Abstract
Interaction of BRCA2 through ca. 30 amino acid residue motifs, BRC repeats, with RAD51 is a conserved feature of the double-strand DNA break repair by homologous recombination in eukaryotes. In humans the binding of the eight BRC repeats is defined by two sequence motifs, FxxA and LFDE, interacting with distinct sites on RAD51. Little is known of the interaction of BRC repeats in other species, especially in protozoans, where variable number of BRC repeats are found in BRCA2 proteins. Here, we have studied in detail the interactions of the two BRC repeats in Leishmania infantum BRCA2 with RAD51. We show LiBRC1 is a high-affinity repeat and determine the crystal structure of its complex with LiRAD51. Using truncation mutagenesis of the LiBRC1 repeat, we demonstrate that high affinity binding is maintained in the absence of an LFDE-like motif and suggest compensatory structural features. These observations point towards a divergent evolution of BRC repeats, where a common FxxA-binding ancestor evolved additional contacts for affinity maturation and fine-tuning.
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Modulating DNA Repair Pathways to Diversify Genomic Alterations in Saccharomyces cerevisiae. Microbiol Spectr 2022; 10:e0232621. [PMID: 35352941 PMCID: PMC9045378 DOI: 10.1128/spectrum.02326-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Nuclease based genome editing systems have emerged as powerful tools to drive genomic alterations and enhance genome evolution via precise engineering in the various human and microbial cells. However, error-prone DNA repair has not been well studied previously to generate diverse genomic alterations and novel phenotypes. Here, we systematically investigated the potential interplay between DNA double strand break (DSB) repair and genome editing tools, and found that modulating the DSB end resection proteins could significantly improve mutational efficiency and diversity without exogenous DNA template in yeast. Deleting SAE2, EXO1, or FUN30, or overexpressing MRE11-H125N (nuclease-dead allele of MRE11), for DSB end resection markedly increased the efficiency of CRISPR/SpCas9 (more than 22-fold) and CRISPR/AsCpf1 (more than 30-fold)-induced mutagenesis. Deleting SAE2 or overexpressing MRE11-H125N substantially diversified CRISPR/SpCas9 or AsCpf1-induced mutation 2–3-fold at URA3 locus, and 3–5-fold at ADE2 locus. Thus, the error-prone DNA repair protein was employed to develop a novel mutagenic genome editing (mGE) strategy, which can increase the mutation numbers and effectively improve the ethanol/glycerol ratio of Saccharomyces cerevisiae through modulating the expression of FPS1 and GPD1. This study highlighted the feasibility of potentially reshaping the capability of genome editing by regulating the different DSB repair proteins and can thus expand the application of genome editing in diversifying gene expression and enhancing genome evolution. IMPORTANCE Most of the published papers about nuclease-assisted genome editing focused on precision engineering in human cells. However, the topic of inducing mutagenesis via error-prone repair has often been ignored in yeast. In this study, we reported that perturbing DNA repair, especially modifications of the various DSB end resection-related proteins, could greatly improve the mutational efficiency and diversity, and thus functionally reshape the capability of the different genome editing tools without requiring an exogenous DNA template in yeast. Specifically, mutagenic genome editing (mGE) was developed based on CRISPR/AsCpf1 and MRE11-H125N overexpression, and used to generate promoters of different strengths more efficiently. Thus, this work provides a novel method to diversify gene expression and enhance genome evolution.
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Milsted C, Dai B, Garcia N, Yin L, He Y, Kianian S, Pawlowski W, Chen C. Genome-wide investigation of maize RAD51 binding affinity through phage display. BMC Genomics 2022; 23:199. [PMID: 35279087 PMCID: PMC8917730 DOI: 10.1186/s12864-022-08419-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
RAD51 proteins, which are conserved in all eukaryotes, repair DNA double-strand breaks. This is critical to homologous chromosome pairing and recombination enabling successful reproduction. Work in Arabidopsis suggests that RAD51 also plays a role in plant defense; the Arabidopsis rad51 mutant is more susceptible to Pseudomonas syringae. However, the defense functions of RAD51 and the proteins interacting with RAD51 have not been thoroughly investigated in maize. Uncovering ligands of RAD51 would help to understand meiotic recombination and possibly the role of RAD51 in defense. This study used phage display, a tool for discovery of protein-protein interactions, to search for proteins interacting with maize RAD51A1.
Results
Maize RAD51A1 was screened against a random phage library. Eleven short peptide sequences were recovered from 15 phages which bound ZmRAD51A1 in vitro; three sequences were found in multiple successfully binding phages. Nine of these phage interactions were verified in vitro through ELISA and/or dot blotting.
BLAST searches did not reveal any maize proteins which contained the exact sequence of any of the selected phage peptides, although one of the selected phages had a strong alignment (E-value = 0.079) to a binding domain of maize BRCA2. Therefore, we designed 32 additional short peptides using amino acid sequences found in the predicted maize proteome. These peptides were not contained within phages. Of these synthesized peptides, 14 bound to ZmRAD51A1 in a dot blot experiment. These 14 sequences are found in known maize proteins including transcription factors putatively involved in defense.
Conclusions
These results reveal several peptides which bind ZmRAD51A1 and support a potential role for ZmRAD51A1 in transcriptional regulation and plant defense. This study also demonstrates the applicability of phage display to basic science questions, such as the search for binding partners of a known protein, and raises the possibility of an iterated approach to test peptide sequences that closely but imperfectly align with the selected phages.
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Somatic PMK-1/p38 signaling links environmental stress to germ cell apoptosis and heritable euploidy. Nat Commun 2022; 13:701. [PMID: 35121747 PMCID: PMC8816960 DOI: 10.1038/s41467-022-28225-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/08/2022] [Indexed: 01/20/2023] Open
Abstract
Inheritance of stable and euploid genomes is a prerequisite for species maintenance. The DNA damage response in germ cells controls the integrity of heritable genomes. Whether and how somatic stress responses impact the quality control of germline genomes has remained unclear. Here, we show that PMK-1/p38-mediated stress signaling in intestinal cells is required for germ cell apoptosis amid ionizing radiation (IR)-induced or meiotic DNA double strand breaks (DSBs) in C. elegans. We demonstrate that intestinal PMK-1/p38 signaling regulates the germ cell death in response to environmental stress. The PMK-1/p38 target SYSM-1 is secreted from the intestine into the germline to trigger apoptosis of meiotic pachytene cells. Compromised PMK-1/p38 signaling in intestinal cells leads to stress-induced aneuploidy in the consequent generation. Our data suggest that somatic stress surveillance controls heritable genome integrity and euploidy.
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X Chromosome Inactivation during Grasshopper Spermatogenesis. Genes (Basel) 2021; 12:genes12121844. [PMID: 34946793 PMCID: PMC8700825 DOI: 10.3390/genes12121844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Regulation of transcriptional activity during meiosis depends on the interrelated processes of recombination and synapsis. In eutherian mammal spermatocytes, transcription levels change during prophase-I, being low at the onset of meiosis but highly increased from pachytene up to the end of diplotene. However, X and Y chromosomes, which usually present unsynapsed regions throughout prophase-I in male meiosis, undergo a specific pattern of transcriptional inactivation. The interdependence of synapsis and transcription has mainly been studied in mammals, basically in mouse, but our knowledge in other unrelated phylogenetically species is more limited. To gain new insights on this issue, here we analyzed the relationship between synapsis and transcription in spermatocytes of the grasshopper Eyprepocnemis plorans. Autosomal chromosomes of this species achieve complete synapsis; however, the single X sex chromosome remains always unsynapsed and behaves as a univalent. We studied transcription in meiosis by immunolabeling with RNA polymerase II phosphorylated at serine 2 and found that whereas autosomes are active from leptotene up to diakinesis, the X chromosome is inactive throughout meiosis. This inactivation is accompanied by the accumulation of, at least, two repressive epigenetic modifications: H3 methylated at lysine 9 and H2AX phosphorylated at serine 139. Furthermore, we identified that X chromosome inactivation occurs in premeiotic spermatogonia. Overall, our results indicate: (i) transcription regulation in E. plorans spermatogenesis differs from the canonical pattern found in mammals and (ii) X chromosome inactivation is likely preceded by a process of heterochromatinization before the initiation of meiosis.
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PCNA Loaders and Unloaders-One Ring That Rules Them All. Genes (Basel) 2021; 12:genes12111812. [PMID: 34828416 PMCID: PMC8618651 DOI: 10.3390/genes12111812] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
During each cell duplication, the entirety of the genomic DNA in every cell must be accurately and quickly copied. Given the short time available for the chore, the requirement of many proteins, and the daunting amount of DNA present, DNA replication poses a serious challenge to the cell. A high level of coordination between polymerases and other DNA and chromatin-interacting proteins is vital to complete this task. One of the most important proteins for maintaining such coordination is PCNA. PCNA is a multitasking protein that forms a homotrimeric ring that encircles the DNA. It serves as a processivity factor for DNA polymerases and acts as a landing platform for different proteins interacting with DNA and chromatin. Therefore, PCNA is a signaling hub that influences the rate and accuracy of DNA replication, regulates DNA damage repair, controls chromatin formation during the replication, and the proper segregation of the sister chromatids. With so many essential roles, PCNA recruitment and turnover on the chromatin is of utmost importance. Three different, conserved protein complexes are in charge of loading/unloading PCNA onto DNA. Replication factor C (RFC) is the canonical complex in charge of loading PCNA during the S-phase. The Ctf18 and Elg1 (ATAD5 in mammalian) proteins form complexes similar to RFC, with particular functions in the cell’s nucleus. Here we summarize our current knowledge about the roles of these important factors in yeast and mammals.
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Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Sex without crossing over in the yeast Saccharomycodes ludwigii. Genome Biol 2021; 22:303. [PMID: 34732243 PMCID: PMC8567612 DOI: 10.1186/s13059-021-02521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad. RESULTS We demonstrate that recombination is extremely suppressed during meiosis in Sd. ludwigii. DNA double-strand break formation by the conserved transesterase Spo11, processing and repair involving interhomolog interactions are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers in its genome. A strong AT bias of spontaneous mutations and the absence of recombination are likely responsible for its unusually low genomic GC level. CONCLUSIONS Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent mating between products of the same meiotic event with the extreme suppression of meiotic recombination. This life style ensures preservation of heterozygosity throughout its genome and may enable the species to adapt to its environment and survive with only minimal levels of rare meiotic recombination. We propose Sd. ludwigii as an excellent natural forum for the study of genome evolution and recombination rates.
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Affiliation(s)
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - France A. Peltier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Hiromi Maekawa
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Current affiliation: Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Amit Bardhan
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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Miao Y, Shi W, Wang H, Xue Z, You H, Zhang F, Du G, Tang D, Li Y, Shen Y, Cheng Z. Replication protein A large subunit (RPA1a) limits chiasma formation during rice meiosis. PLANT PHYSIOLOGY 2021; 187:1605-1618. [PMID: 34618076 PMCID: PMC8566244 DOI: 10.1093/plphys/kiab365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2021] [Indexed: 05/06/2023]
Abstract
Replication protein A (RPA), a single-stranded DNA-binding protein, plays essential role in homologous recombination. However, because deletion of RPA causes embryonic lethality in mammals, the exact function of RPA in meiosis remains unclear. In this study, we generated an rpa1a mutant using CRISPR/Cas9 technology and explored its function in rice (Oryza sativa) meiosis. In rpa1a, 12 bivalents were formed at metaphase I, just like in wild-type, but chromosome fragmentations were consistently observed at anaphase I. Fluorescence in situ hybridization assays indicated that these fragmentations were due to the failure of the recombination intermediates to resolve. Importantly, the mutant had a highly elevated chiasma number, and loss of RPA1a could completely restore the 12 bivalent formations in the zmm (for ZIP1-4, MSH4/5, and MER3) mutant background. Protein-protein interaction assays showed that RPA1a formed a complex with the methyl methansulfonate and UV sensitive 81 (and the Fanconi anemia complementation group M-Bloom syndrome protein homologs (RECQ4A)-Topoisomerase3α-RecQ-mediated genome instability 1 complex to regulate chiasma formation and processing of the recombination intermediates. Thus, our data establish a pivotal role for RPA1a in promoting the accurate resolution of recombination intermediates and in limiting redundant chiasma formation during rice meiosis.
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Affiliation(s)
- Yongjie Miao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Shi
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongjun Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihui Xue
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hanli You
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanfan Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guijie Du
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
- Author for Communication:
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Epigenetic Dysregulation of Mammalian Male Meiosis Caused by Interference of Recombination and Synapsis. Cells 2021; 10:cells10092311. [PMID: 34571960 PMCID: PMC8467405 DOI: 10.3390/cells10092311] [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] [Received: 07/04/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023] Open
Abstract
Meiosis involves a series of specific chromosome events, namely homologous synapsis, recombination, and segregation. Disruption of either recombination or synapsis in mammals results in the interruption of meiosis progression during the first meiotic prophase. This is usually accompanied by a defective transcriptional inactivation of the X and Y chromosomes, which triggers a meiosis breakdown in many mutant models. However, epigenetic changes and transcriptional regulation are also expected to affect autosomes. In this work, we studied the dynamics of epigenetic markers related to chromatin silencing, transcriptional regulation, and meiotic sex chromosome inactivation throughout meiosis in knockout mice for genes encoding for recombination proteins SPO11, DMC1, HOP2 and MLH1, and the synaptonemal complex proteins SYCP1 and SYCP3. These models are defective in recombination and/or synapsis and promote apoptosis at different stages of progression. Our results indicate that impairment of recombination and synapsis alter the dynamics and localization pattern of epigenetic marks, as well as the transcriptional regulation of both autosomes and sex chromosomes throughout prophase-I progression. We also observed that the morphological progression of spermatocytes throughout meiosis and the dynamics of epigenetic marks are processes that can be desynchronized upon synapsis or recombination alteration. Moreover, we detected an overlap of early and late epigenetic signatures in most mutants, indicating that the normal epigenetic transitions are disrupted. This can alter the transcriptional shift that occurs in spermatocytes in mid prophase-I and suggest that the epigenetic regulation of sex chromosomes, but also of autosomes, is an important factor in the impairment of meiosis progression in mammals.
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Raices M, Bowman R, Smolikove S, Yanowitz JL. Aging Negatively Impacts DNA Repair and Bivalent Formation in the C. elegans Germ Line. Front Cell Dev Biol 2021; 9:695333. [PMID: 34422819 PMCID: PMC8371636 DOI: 10.3389/fcell.2021.695333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/12/2021] [Indexed: 12/18/2022] Open
Abstract
Defects in crossover (CO) formation during meiosis are a leading cause of birth defects, embryonic lethality, and infertility. In a wide range of species, maternal aging increases aneuploidy and decreases oocyte quality. In C. elegans which produce oocytes throughout the first half of adulthood, aging both decreases oocytes quality and increases meiotic errors. Phenotypes of mutations in genes encoding double-strand break (DSB)-associated proteins get more severe with maternal age suggesting that early meiosis reflects a particularly sensitive node during reproductive aging in the worm. We observed that aging has a direct effect on the integrity of C. elegans meiotic CO formation, as observed by an increase of univalent chromosomes and fusions at diakinesis, with a considerable increase starting at 4 days. We also characterize the possible causes for the age-related changes in CO formation by analyzing both steady-state levels and kinetics of the ssDNA binding proteins RPA-1 and RAD-51. Profound reductions in numbers of both RPA-1 and RAD-51 foci suggests that both DSB formation and early meiotic repair are compromised in aging worms. Using laser microirradiation and γ-irradiation to induce exogenous damage, we show specifically that recruitment of these homologous recombination proteins is altered. Repair defects can be seen in two-and-one-half day-old adults making the loss of germline repair capacity among the earliest aging phenotypes in the worm.
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Affiliation(s)
- Marilina Raices
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Richard Bowman
- Department of Biology, The University of Iowa, Iowa City, IA, United States
| | - Sarit Smolikove
- Department of Biology, The University of Iowa, Iowa City, IA, United States
| | - Judith L Yanowitz
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Developmental Biology, Microbiology and Molecular Genetics, Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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