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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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2
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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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3
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Xun Q, Song Y, Mei M, Ding Y, Ding C. The SMC5/6 complex subunit MMS21 regulates stem cell proliferation in rice. PLANT CELL REPORTS 2023:10.1007/s00299-023-03030-9. [PMID: 37178216 DOI: 10.1007/s00299-023-03030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE SMC5/6 complex subunit OsMMS21 is involved in cell cycle and hormone signaling and required for stem cell proliferation during shoot and root development in rice. The structural maintenance of chromosome (SMC)5/6 complex is required for nucleolar integrity and DNA metabolism. Moreover, METHYL METHANESULFONATE SENSITIVITY GENE 21 (MMS21), a SUMO E3 ligase that is part of the SMC5/6 complex, is essential for the root stem cell niche and cell cycle transition in Arabidopsis. However, its specific role in rice remains unclear. Here, OsSMC5 and OsSMC6 single heterozygous mutants were generated using CRISPR/Cas9 technology to elucidate the function of SMC5/6 subunits, including OsSMC5, OsSMC6, and OsMMS21, in cell proliferation in rice. ossmc5/ + and ossmc6/ + heterozygous single mutants did not yield homozygous mutants in their progeny, indicating that OsSMC5 and OsSMC6 both play necessary roles during embryo formation. Loss of OsMMS21 caused severe defects in both the shoot and roots in rice. Transcriptome analysis showed a significant decrease in the expression of genes involved in auxin signaling in the roots of osmms21 mutants. Moreover, the expression levels of the cycB2-1 and MCM genes, which are involved the cell cycle, were significantly lower in the shoots of the mutants, indicating that OsMMS21 was involved in both hormone signaling pathways and the cell cycle. Overall, these findings indicate that the SUMO E3 ligase OsMMS21 is required for both shoot and root stem cell niches, improving the understanding of the function of the SMC5/6 complex in rice.
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Affiliation(s)
- Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ye Song
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Min Mei
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China.
- Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China.
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4
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Taschner M, Gruber S. DNA segment capture by Smc5/6 holocomplexes. Nat Struct Mol Biol 2023; 30:619-628. [PMID: 37012407 DOI: 10.1038/s41594-023-00956-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
Three distinct structural maintenance of chromosomes (SMC) complexes facilitate chromosome folding and segregation in eukaryotes, presumably by DNA loop extrusion. How SMCs interact with DNA to extrude loops is not well understood. Among the SMC complexes, Smc5/6 has dedicated roles in DNA repair and preventing a buildup of aberrant DNA junctions. In the present study, we describe the reconstitution of ATP-dependent DNA loading by yeast Smc5/6 rings. Loading strictly requires the Nse5/6 subcomplex which opens the kleisin neck gate. We show that plasmid molecules are topologically entrapped in the kleisin and two SMC subcompartments, but not in the full SMC compartment. This is explained by the SMC compartment holding a looped DNA segment and by kleisin locking it in place when passing between the two flanks of the loop for neck-gate closure. Related segment capture events may provide the power stroke in subsequent DNA extrusion steps, possibly also in other SMC complexes, thus providing a unifying principle for DNA loading and extrusion.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
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5
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Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging. Cell Rep 2022; 41:111778. [PMID: 36476856 PMCID: PMC9756111 DOI: 10.1016/j.celrep.2022.111778] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/15/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
SMC complexes play key roles in genome maintenance, where they ensure efficient genome replication and segregation. The SMC complex Smc5/6 is a crucial player in DNA replication and repair, yet many molecular features that determine its roles are unclear. Here, we use single-molecule microscopy to investigate Smc5/6's interaction with DNA. We find that Smc5/6 forms oligomers that dynamically redistribute on dsDNA by 1D diffusion and statically bind to ssDNA. Using combined force manipulation and single-molecule microscopy, we generate ssDNA-dsDNA junctions that mimic structures present in DNA repair intermediates or replication forks. We show that Smc5/6 accumulates at these junction sites, stabilizes the fork, and promotes the retention of RPA. Our observations provide a model for the complex's enrichment at sites of replication stress and DNA lesions from where it coordinates the recruitment and activation of downstream repair proteins.
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Chang JTH, Li S, Beckwitt EC, Than T, Haluska C, Chandanani J, O’Donnell ME, Zhao X, Liu S. Smc5/6's multifaceted DNA binding capacities stabilize branched DNA structures. Nat Commun 2022; 13:7179. [PMID: 36418314 PMCID: PMC9684126 DOI: 10.1038/s41467-022-34928-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022] Open
Abstract
Smc5/6 is an evolutionarily conserved SMC complex with roles in DNA replication and repair, as well as in viral DNA restriction. Understanding its multiple functions has been hampered by a lack of mechanistic studies on how the Smc5/6 complex associates with different types of DNA. Here we address this question by simultaneously visualizing the behavior of Smc5/6 on three types of DNA, namely double-stranded (ds) DNA, single-stranded (ss) DNA, and junction DNA formed by juxtaposed ss- and dsDNA, using correlative single-molecule fluorescence and force microscopy. We find that Smc5/6 displays distinct behaviors toward different types of DNA, dynamically associating with dsDNA while stably binding to junction DNA. Mechanistically, both the Nse1-3-4 subcomplex and ATP binding enhance the complex's dsDNA association. In contrast, Smc5/6's assembly onto ssDNA emanating from junction DNA, which occurs even in the presence high-affinity ssDNA binders, is aided by Nse1-3-4, but not by ATP. Moreover, we show that Smc5/6 protects junction DNA stability by preventing ssDNA annealing. The multifaceted DNA association behaviors of Smc5/6 provide a framework for understanding its diverse functions in genome maintenance and viral DNA restriction.
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Affiliation(s)
- Jeremy T-H. Chang
- grid.134907.80000 0001 2166 1519Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065 USA ,grid.51462.340000 0001 2171 9952Tri-Institutional MD-PhD Program, The Rockefeller University, Weill Cornell Medical College, and Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Shibai Li
- grid.51462.340000 0001 2171 9952Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Emily C. Beckwitt
- grid.134907.80000 0001 2166 1519Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065 USA
| | - Thane Than
- grid.51462.340000 0001 2171 9952Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Cory Haluska
- grid.51462.340000 0001 2171 9952Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Joshua Chandanani
- grid.134907.80000 0001 2166 1519Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065 USA
| | - Michael E. O’Donnell
- grid.134907.80000 0001 2166 1519Laboratory of DNA Replication, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065 USA
| | - Xiaolan Zhao
- grid.51462.340000 0001 2171 9952Tri-Institutional MD-PhD Program, The Rockefeller University, Weill Cornell Medical College, and Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA ,grid.51462.340000 0001 2171 9952Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Shixin Liu
- grid.134907.80000 0001 2166 1519Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY 10065 USA ,grid.51462.340000 0001 2171 9952Tri-Institutional MD-PhD Program, The Rockefeller University, Weill Cornell Medical College, and Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
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7
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Yang F, Pecinka A. Multiple Roles of SMC5/6 Complex during Plant Sexual Reproduction. Int J Mol Sci 2022; 23:ijms23094503. [PMID: 35562893 PMCID: PMC9099584 DOI: 10.3390/ijms23094503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Chromatin-based processes are essential for cellular functions. Structural maintenance of chromosomes (SMCs) are evolutionarily conserved molecular machines that organize chromosomes throughout the cell cycle, mediate chromosome compaction, promote DNA repair, or control sister chromatid attachment. The SMC5/6 complex is known for its pivotal role during the maintenance of genome stability. However, a dozen recent plant studies expanded the repertoire of SMC5/6 complex functions to the entire plant sexual reproductive phase. The SMC5/6 complex is essential in meiosis, where its activity must be precisely regulated to allow for normal meiocyte development. Initially, it is attenuated by the recombinase RAD51 to allow for efficient strand invasion by the meiosis-specific recombinase DMC1. At later stages, it is essential for the normal ratio of interfering and non-interfering crossovers, detoxifying aberrant joint molecules, preventing chromosome fragmentation, and ensuring normal chromosome/sister chromatid segregation. The latter meiotic defects lead to the production of diploid male gametes in Arabidopsis SMC5/6 complex mutants, increased seed abortion, and production of triploid offspring. The SMC5/6 complex is directly involved in controlling normal embryo and endosperm cell divisions, and pioneer studies show that the SMC5/6 complex is also important for seed development and normal plant growth in cereals.
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Affiliation(s)
- Fen Yang
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Ales Pecinka
- Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Institute of Experimental Botany (IEB), Czech Academy of Sciences, 77900 Olomouc, Czech Republic;
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
- Correspondence:
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8
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Yang F, Fernández-Jiménez N, Tučková M, Vrána J, Cápal P, Díaz M, Pradillo M, Pecinka A. Defects in meiotic chromosome segregation lead to unreduced male gametes in Arabidopsis SMC5/6 complex mutants. THE PLANT CELL 2021; 33:3104-3119. [PMID: 34240187 PMCID: PMC8462810 DOI: 10.1093/plcell/koab178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Structural maintenance of chromosome 5/6 (SMC5/6) complex is a crucial factor for preserving genome stability. Here, we show that mutants for several Arabidopsis (Arabidopsis thaliana) SMC5/6 complex subunits produce triploid offspring. This phenotype is caused by a meiotic defect leading to the production of unreduced male gametes. The SMC5/6 complex mutants show an absence of chromosome segregation during the first and/or the second meiotic division, as well as a partially disorganized microtubule network. Importantly, although the SMC5/6 complex is partly required for the repair of SPO11-induced DNA double-strand breaks, the nonreduction described here is SPO11-independent. The measured high rate of ovule abortion suggests that, if produced, such defects are maternally lethal. Upon fertilization with an unreduced pollen, the unbalanced maternal and paternal genome dosage in the endosperm most likely causes seed abortion observed in several SMC5/6 complex mutants. In conclusion, we describe the function of the SMC5/6 complex in the maintenance of gametophytic ploidy in Arabidopsis.
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Affiliation(s)
- Fen Yang
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nadia Fernández-Jiménez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Martina Tučková
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Mariana Díaz
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Science, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Author for correspondence:
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9
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Alonso-Ramos P, Álvarez-Melo D, Strouhalova K, Pascual-Silva C, Garside GB, Arter M, Bermejo T, Grigaitis R, Wettstein R, Fernández-Díaz M, Matos J, Geymonat M, San-Segundo PA, Carballo JA. The Cdc14 Phosphatase Controls Resolution of Recombination Intermediates and Crossover Formation during Meiosis. Int J Mol Sci 2021; 22:ijms22189811. [PMID: 34575966 PMCID: PMC8470964 DOI: 10.3390/ijms22189811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Meiotic defects derived from incorrect DNA repair during gametogenesis can lead to mutations, aneuploidies and infertility. The coordinated resolution of meiotic recombination intermediates is required for crossover formation, ultimately necessary for the accurate completion of both rounds of chromosome segregation. Numerous master kinases orchestrate the correct assembly and activity of the repair machinery. Although much less is known, the reversal of phosphorylation events in meiosis must also be key to coordinate the timing and functionality of repair enzymes. Cdc14 is a crucial phosphatase required for the dephosphorylation of multiple CDK1 targets in many eukaryotes. Mutations that inactivate this phosphatase lead to meiotic failure, but until now it was unknown if Cdc14 plays a direct role in meiotic recombination. Here, we show that the elimination of Cdc14 leads to severe defects in the processing and resolution of recombination intermediates, causing a drastic depletion in crossovers when other repair pathways are compromised. We also show that Cdc14 is required for the correct activity and localization of the Holliday Junction resolvase Yen1/GEN1. We reveal that Cdc14 regulates Yen1 activity from meiosis I onwards, and this function is essential for crossover resolution in the absence of other repair pathways. We also demonstrate that Cdc14 and Yen1 are required to safeguard sister chromatid segregation during the second meiotic division, a late action that is independent of the earlier role in crossover formation. Thus, this work uncovers previously undescribed functions of the evolutionary conserved Cdc14 phosphatase in the regulation of meiotic recombination.
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Affiliation(s)
- Paula Alonso-Ramos
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - David Álvarez-Melo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Katerina Strouhalova
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
- Department of Cell Biology, Charles University, Viničná 7, 12843 Prague, Czech Republic
| | - Carolina Pascual-Silva
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - George B. Garside
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 4DY, UK;
- Leibniz Institute for Age Research/Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
| | - Meret Arter
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Teresa Bermejo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Rokas Grigaitis
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Rahel Wettstein
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marta Fernández-Díaz
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; (M.A.); (R.G.); (R.W.); (J.M.)
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marco Geymonat
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK;
| | - Pedro A. San-Segundo
- Institute of Functional Biology and Genomics (IBFG), Spanish National Research Council (CSIC) and University of Salamanca, 37007 Salamanca, Spain;
| | - Jesús A. Carballo
- Center for Biological Research Margarita Salas, Department of Cellular and Molecular Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (P.A.-R.); (D.Á.-M.); (K.S.); (C.P.-S.); (T.B.); (M.F.-D.)
- Correspondence:
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10
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Chen H, He C, Wang C, Wang X, Ruan F, Yan J, Yin P, Wang Y, Yan S. RAD51 supports DMC1 by inhibiting the SMC5/6 complex during meiosis. THE PLANT CELL 2021; 33:2869-2882. [PMID: 34009315 PMCID: PMC8408460 DOI: 10.1093/plcell/koab136] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/12/2021] [Indexed: 05/21/2023]
Abstract
Meiosis is a fundamental process for sexual reproduction in most eukaryotes and the evolutionarily conserved recombinases RADiation sensitive51 (RAD51) and Disrupted Meiotic cDNA1 (DMC1) are essential for meiosis and thus fertility. The mitotic function of RAD51 is clear, but the meiotic function of RAD51 remains largely unknown. Here we show that RAD51 functions as an interacting protein to restrain the Structural Maintenance of Chromosomes5/6 (SMC5/6) complex from inhibiting DMC1. We unexpectedly found that loss of the SMC5/6 partially suppresses the rad51 knockout mutant in terms of sterility, pollen inviability, and meiotic chromosome fragmentation in a DMC1-dependent manner in Arabidopsis thaliana. Biochemical and cytological studies revealed that the DMC1 localization in meiotic chromosomes is inhibited by the SMC5/6 complex, which is attenuated by RAD51 through physical interactions. This study not only identified the long-sought-after function of RAD51 in meiosis but also discovered the inhibition of SMC5/6 on DMC1 as a control mechanism during meiotic recombination.
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Affiliation(s)
- Hanchen Chen
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengpeng He
- 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 200438, China
| | - Chongyang Wang
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuanpeng Wang
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengyin Ruan
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Junjie Yan
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, 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 200438, China
- Author for correspondence: (S.Y.), (Y.W.)
| | - Shunping Yan
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan 430070, China
- Author for correspondence: (S.Y.), (Y.W.)
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11
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Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021970118. [PMID: 34385313 PMCID: PMC8379953 DOI: 10.1073/pnas.2021970118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified SNI1 as the causal gene underlying a major modifier locus. To date, SNI1 had no known role in crossover. SNI1 is a component of the SMC5/6 complex that is closely related to cohesin and condensin. Arabidopsis sni1 and other SMC5/6 mutants show similar effects on the interference-independent crossover pathway. Hence, our findings demonstrate that the SMC5/6 complex, which is known for its role in DNA damage repair, is also important for control of meiotic crossover. The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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12
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Smc5/6, an atypical SMC complex with two RING-type subunits. Biochem Soc Trans 2021; 48:2159-2171. [PMID: 32964921 DOI: 10.1042/bst20200389] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023]
Abstract
The Smc5/6 complex plays essential roles in chromosome segregation and repair, by promoting disjunction of sister chromatids. The core of the complex is constituted by an heterodimer of Structural Maintenance of Chromosomes (SMC) proteins that use ATP hydrolysis to dynamically associate with and organize chromosomes. In addition, the Smc5/6 complex contains six non-SMC subunits. Remarkably, and differently to other SMC complexes, the Nse1 and Nse2 subunits contain RING-type domains typically found in E3 ligases, pointing to the capacity to regulate other proteins and complexes through ubiquitin-like modifiers. Nse2 codes for a C-terminal SP-RING domain with SUMO ligase activity, assisting Smc5/6 functions in chromosome segregation through sumoylation of several chromosome-associated proteins. Nse1 codes for a C-terminal NH-RING domain and, although it has been proposed to have ubiquitin ligase activity, no Smc5/6-dependent ubiquitylation target has been described to date. Here, we review the function of the two RING domains of the Smc5/6 complex in the broader context of SMC complexes as global chromosome organizers of the genome.
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13
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Taschner M, Basquin J, Steigenberger B, Schäfer IB, Soh Y, Basquin C, Lorentzen E, Räschle M, Scheltema RA, Gruber S. Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding. EMBO J 2021; 40:e107807. [PMID: 34191293 PMCID: PMC8327961 DOI: 10.15252/embj.2021107807] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cells employ three SMC (structural maintenance of chromosomes) complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo-complex. We found that the Nse5/6 sub-complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross-linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross-linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non-productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.
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Affiliation(s)
- Michael Taschner
- Department of Fundamental Microbiology (DMF)Faculty of Biology and Medicine (FBM)University of Lausanne (UNIL)LausanneSwitzerland
| | | | - Barbara Steigenberger
- Max Planck Institute of BiochemistryMartinsriedGermany
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Netherlands Proteomics CentreUtrechtThe Netherlands
| | | | - Young‐Min Soh
- Department of Fundamental Microbiology (DMF)Faculty of Biology and Medicine (FBM)University of Lausanne (UNIL)LausanneSwitzerland
| | | | - Esben Lorentzen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Markus Räschle
- Molecular GeneticsUniversity of KaiserslauternKaiserslauternGermany
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Netherlands Proteomics CentreUtrechtThe Netherlands
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF)Faculty of Biology and Medicine (FBM)University of Lausanne (UNIL)LausanneSwitzerland
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14
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He W, Verhees GF, Bhagwat N, Yang Y, Kulkarni DS, Lombardo Z, Lahiri S, Roy P, Zhuo J, Dang B, Snyder A, Shastry S, Moezpoor M, Alocozy L, Lee KG, Painter D, Mukerji I, Hunter N. SUMO fosters assembly and functionality of the MutSγ complex to facilitate meiotic crossing over. Dev Cell 2021; 56:2073-2088.e3. [PMID: 34214491 DOI: 10.1016/j.devcel.2021.06.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/31/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Crossing over is essential for chromosome segregation during meiosis. Protein modification by SUMO is implicated in crossover control, but pertinent targets have remained elusive. Here we identify Msh4 as a target of SUMO-mediated crossover regulation. Msh4 and Msh5 constitute the MutSγ complex, which stabilizes joint-molecule (JM) recombination intermediates and facilitates their resolution into crossovers. Msh4 SUMOylation enhances these processes to ensure that each chromosome pair acquires at least one crossover. Msh4 is directly targeted by E2 conjugase Ubc9, initially becoming mono-SUMOylated in response to DNA double-strand breaks, then multi/poly-SUMOylated forms arise as homologs fully engage. Mechanistically, SUMOylation fosters interaction between Msh4 and Msh5. We infer that initial SUMOylation of Msh4 enhances assembly of MutSγ in anticipation of JM formation, while secondary SUMOylation may promote downstream functions. Regulation of Msh4 by SUMO is distinct and independent of its previously described stabilization by phosphorylation, defining MutSγ as a hub for crossover control.
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Affiliation(s)
- Wei He
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Gerrik F Verhees
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Nikhil Bhagwat
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Ye Yang
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Dhananjaya S Kulkarni
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Zane Lombardo
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Pritha Roy
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Jiaming Zhuo
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Brian Dang
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Andriana Snyder
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Shashank Shastry
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Michael Moezpoor
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Lilly Alocozy
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Kathy Gyehyun Lee
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Daniel Painter
- Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, USA; Department of Microbiology & Molecular Genetics, University of California, Davis, Davis, CA, USA.
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15
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Prieler S, Chen D, Huang L, Mayrhofer E, Zsótér S, Vesely M, Mbogning J, Klein F. Spo11 generates gaps through concerted cuts at sites of topological stress. Nature 2021; 594:577-582. [PMID: 34108684 DOI: 10.1038/s41586-021-03632-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/11/2021] [Indexed: 02/08/2023]
Abstract
Meiotic recombination is essential for chromosome segregation at meiosis and fertility. It is initiated by programmed DNA double-strand breaks (DSBs) introduced by Spo11, a eukaryotic homologue of an archaeal topoisomerase (Topo VIA)1. Here we describe previously uncharacterized Spo11-induced lesions, 34 to several hundred base pair-long gaps, which are generated by coordinated pairs of DSBs termed double DSBs. Isolation and genome-wide mapping of the resulting fragments with single base-pair precision revealed enrichment at DSB hotspots but also a widely dispersed distribution across the genome. Spo11 prefers to cut sequences with similarity to a DNA-bending motif2, which indicates that bendability contributes to the choice of cleavage site. Moreover, fragment lengths have a periodicity of approximately (10.4n + 3) base pairs, which indicates that Spo11 favours cleavage on the same face of underwound DNA. Consistently, double DSB signals overlap and correlate with topoisomerase II-binding sites, which points to a role for topological stress and DNA crossings in break formation, and suggests a model for the formation of DSBs and double DSBs in which Spo11 traps two DNA strands. Double DSB gaps, which make up an estimated 20% of all initiation events, can account for full gene conversion events that are independent of both Msh2-dependent heteroduplex repair3,4 and the MutLγ endonuclease4. Because non-homologous gap repair results in deletions, and ectopically re-integrated double DSB fragments result in insertions, the formation of double DSBs is a potential source of evolutionary diversity and pathogenic germline aberrations.
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Affiliation(s)
- Silvia Prieler
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Doris Chen
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Lingzhi Huang
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Elisa Mayrhofer
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.,Austrian Research Institute for Chemistry and Technology, Microbiology and Cell Culture, Vienna, Austria
| | - Soma Zsótér
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.,Humboldt University of Berlin, IRI Life Sciences, Berlin, Germany
| | - Magdalena Vesely
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria
| | - Jean Mbogning
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.,McGill University, Department of Pharmacology and Therapeutics, Montréal, Canada
| | - Franz Klein
- Max Perutz Labs Vienna, University of Vienna, Department of Chromosome Biology, Vienna, Austria.
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16
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Shukla V, Høffding MK, Hoffmann ER. Genome diversity and instability in human germ cells and preimplantation embryos. Semin Cell Dev Biol 2021; 113:132-147. [PMID: 33500205 PMCID: PMC8097364 DOI: 10.1016/j.semcdb.2020.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/18/2020] [Indexed: 12/26/2022]
Abstract
Genome diversity is essential for evolution and is of fundamental importance to human health. Generating genome diversity requires phases of DNA damage and repair that can cause genome instability. Humans have a high incidence of de novo congenital disorders compared to other organisms. Recent access to eggs, sperm and preimplantation embryos is revealing unprecedented rates of genome instability that may result in infertility and de novo mutations that cause genomic imbalance in at least 70% of conceptions. The error type and incidence of de novo mutations differ during developmental stages and are influenced by differences in male and female meiosis. In females, DNA repair is a critical factor that determines fertility and reproductive lifespan. In males, aberrant meiotic recombination causes infertility, embryonic failure and pregnancy loss. Evidence suggest germ cells are remarkably diverse in the type of genome instability that they display and the DNA damage responses they deploy. Additionally, the initial embryonic cell cycles are characterized by a high degree of genome instability that cause congenital disorders and may limit the use of CRISPR-Cas9 for heritable genome editing.
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Affiliation(s)
- Vallari Shukla
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Miya Kudo Høffding
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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17
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Agashe S, Joseph CR, Reyes TAC, Menolfi D, Giannattasio M, Waizenegger A, Szakal B, Branzei D. Smc5/6 functions with Sgs1-Top3-Rmi1 to complete chromosome replication at natural pause sites. Nat Commun 2021; 12:2111. [PMID: 33833229 PMCID: PMC8032827 DOI: 10.1038/s41467-021-22217-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Smc5/6 is essential for genome structural integrity by yet unknown mechanisms. Here we find that Smc5/6 co-localizes with the DNA crossed-strand processing complex Sgs1-Top3-Rmi1 (STR) at genomic regions known as natural pausing sites (NPSs) where it facilitates Top3 retention. Individual depletions of STR subunits and Smc5/6 cause similar accumulation of joint molecules (JMs) composed of reversed forks, double Holliday Junctions and hemicatenanes, indicative of Smc5/6 regulating Sgs1 and Top3 DNA processing activities. We isolate an intra-allelic suppressor of smc6-56 proficient in Top3 retention but affected in pathways that act complementarily with Sgs1 and Top3 to resolve JMs arising at replication termination. Upon replication stress, the smc6-56 suppressor requires STR and Mus81-Mms4 functions for recovery, but not Srs2 and Mph1 helicases that prevent maturation of recombination intermediates. Thus, Smc5/6 functions jointly with Top3 and STR to mediate replication completion and influences the function of other DNA crossed-strand processing enzymes at NPSs.
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Affiliation(s)
- Sumedha Agashe
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Demis Menolfi
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Institute for Cancer Genetics, Department of Pathology and Cell Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Michele Giannattasio
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | | | - Barnabas Szakal
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy. .,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy.
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18
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Bhagwat NR, Owens SN, Ito M, Boinapalli JV, Poa P, Ditzel A, Kopparapu S, Mahalawat M, Davies OR, Collins SR, Johnson JR, Krogan NJ, Hunter N. SUMO is a pervasive regulator of meiosis. eLife 2021; 10:57720. [PMID: 33502312 PMCID: PMC7924959 DOI: 10.7554/elife.57720] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here, we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of meiotic prophase I. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism. Most mammalian, yeast and other eukaryote cells have two sets of chromosomes, one from each parent, which contain all the cell’s DNA. Sex cells – like the sperm and egg – however, have half the number of chromosomes and are formed by a specialized type of cell division known as meiosis. At the start of meiosis, each cell replicates its chromosomes so that it has twice the amount of DNA. The cell then undergoes two rounds of division to form sex cells which each contain only one set of chromosomes. Before the cell divides, the two duplicated sets of chromosomes pair up and swap sections of their DNA. This exchange allows each new sex cell to have a unique combination of DNA, resulting in offspring that are genetically distinct from their parents. This complex series of events is tightly regulated, in part, by a protein called the 'small ubiquitin-like modifier' (or SUMO for short), which attaches itself to other proteins and modifies their behavior. This process, known as SUMOylation, can affect a protein’s stability, where it is located in the cell and how it interacts with other proteins. However, despite SUMO being known as a key regulator of meiosis, only a handful of its protein targets have been identified. To gain a better understanding of what SUMO does during meiosis, Bhagwat et al. set out to find which proteins are targeted by SUMO in budding yeast and to map the specific sites of modification. The experiments identified 2,747 different sites on 775 different proteins, suggesting that SUMO regulates all aspects of meiosis. Consistently, inactivating SUMOylation at different times revealed SUMO plays a role at every stage of meiosis, including the replication of DNA and the exchanges between chromosomes. In depth analysis of the targeted proteins also revealed that SUMOylation targets different groups of proteins at different stages of meiosis and interacts with other protein modifications, including the ubiquitin system which tags proteins for destruction. The data gathered by Bhagwat et al. provide a starting point for future research into precisely how SUMO proteins control meiosis in yeast and other organisms. In humans, errors in meiosis are the leading cause of pregnancy loss and congenital diseases. Most of the proteins identified as SUMO targets in budding yeast are also present in humans. So, this research could provide a platform for medical advances in the future. The next step is to study mammalian models, such as mice, to confirm that the regulation of meiosis by SUMO is the same in mammals as in yeast.
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Affiliation(s)
- Nikhil R Bhagwat
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Shannon N Owens
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Masaru Ito
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jay V Boinapalli
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Philip Poa
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Alexander Ditzel
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Srujan Kopparapu
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Meghan Mahalawat
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Owen Richard Davies
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sean R Collins
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jeffrey R Johnson
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Nevan J Krogan
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States.,Department of Molecular & Cellular Biology, University of California Davis, Davis, United States
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19
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Yang F, Fernández Jiménez N, Majka J, Pradillo M, Pecinka A. Structural Maintenance of Chromosomes 5/6 Complex Is Necessary for Tetraploid Genome Stability in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:748252. [PMID: 34675953 PMCID: PMC8525318 DOI: 10.3389/fpls.2021.748252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/06/2021] [Indexed: 05/04/2023]
Abstract
Polyploidization is a common phenomenon in the evolution of flowering plants. However, only a few genes controlling polyploid genome stability, fitness, and reproductive success are known. Here, we studied the effects of loss-of-function mutations in NSE2 and NSE4A subunits of the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex in autotetraploid Arabidopsis thaliana plants. The diploid nse2 and nse4a plants show partially reduced fertility and produce about 10% triploid offspring with two paternal and one maternal genome copies. In contrast, the autotetraploid nse2 and nse4a plants were almost sterile and produced hexaploid and aneuploid progeny with the extra genome copies or chromosomes coming from both parents. In addition, tetraploid mutants had more severe meiotic defects, possibly due to the presence of four homologous chromosomes instead of two. Overall, our study suggests that the SMC5/6 complex is an important player in the maintenance of tetraploid genome stability and that autotetraploid Arabidopsis plants have a generally higher frequency of but also higher tolerance for aneuploidy compared to diploids.
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Affiliation(s)
- Fen Yang
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Natural Sciences, Palacký University, Olomouc, Czechia
| | - Nadia Fernández Jiménez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Joanna Majka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Mónica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- *Correspondence: Ales Pecinka,
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20
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Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation. Proc Natl Acad Sci U S A 2020; 117:30577-30588. [PMID: 33199619 DOI: 10.1073/pnas.2013012117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Crossovers generated during the repair of programmed meiotic double-strand breaks must be tightly regulated to promote accurate homolog segregation without deleterious outcomes, such as aneuploidy. The Mlh1-Mlh3 (MutLγ) endonuclease complex is critical for crossover resolution, which involves mechanistically unclear interplay between MutLγ and Exo1 and polo kinase Cdc5. Using budding yeast to gain temporal and genetic traction on crossover regulation, we find that MutLγ constitutively interacts with Exo1. Upon commitment to crossover repair, MutLγ-Exo1 associate with recombination intermediates, followed by direct Cdc5 recruitment that triggers MutLγ crossover activity. We propose that Exo1 serves as a central coordinator in this molecular interplay, providing a defined order of interaction that prevents deleterious, premature activation of crossovers. MutLγ associates at a lower frequency near centromeres, indicating that spatial regulation across chromosomal regions reduces risky crossover events. Our data elucidate the temporal and spatial control surrounding a constitutive, potentially harmful, nuclease. We also reveal a critical, noncatalytic role for Exo1, through noncanonical interaction with polo kinase. These mechanisms regulating meiotic crossovers may be conserved across species.
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21
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C-Terminal HA Tags Compromise Function and Exacerbate Phenotypes of Saccharomyces cerevisiae Bloom's Helicase Homolog Sgs1 SUMOylation-Associated Mutants. G3-GENES GENOMES GENETICS 2020; 10:2811-2818. [PMID: 32540865 PMCID: PMC7407464 DOI: 10.1534/g3.120.401324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Sgs1 helicase and Top3-Rmi1 decatenase form a complex that affects homologous recombination outcomes during the mitotic cell cycle and during meiosis. Previous studies have reported that Sgs1-Top3-Rmi1 function is regulated by SUMOylation that is catalyzed by the Smc5-Smc6-Mms21 complex. These studies used strains in which SGS1 was C-terminally tagged with three or six copies of a human influenza hemagglutinin-derived epitope tag (3HA and 6HA). They identified SGS1 mutants that affect its SUMOylation, which we will refer to as SGS1 SUMO-site mutants. In previous work, these mutants showed phenotypes consistent with substantial loss of Sgs1-Top3-Rmi1 function during the mitotic cell cycle. We find that the reported phenotypes are largely due to the presence of the HA epitope tags. Untagged SGS1 SUMO-site mutants show either wild-type or weak hypomorphic phenotypes, depending on the assay. These phenotypes are exacerbated by both 6HA and 3HA epitope tags in two different S. cerevisiae strain backgrounds. Importantly, a C-terminal 6HA tag confers strong hypomorphic or null phenotypes on an otherwise wild-type Sgs1 protein. Taken together, these results suggest that the HA epitope tags used in previous studies seriously compromise Sgs1 function. Furthermore, they raise the possibilities either that sufficient SUMOylation of the Sgs1-Top3-Rmi1 complex might still occur in the SUMO-site mutants isolated, or that Smc5-Smc6-Mms21-mediated SUMOylation plays a minor role in the regulation of Sgs1-Top3-Rmi1 during recombination.
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22
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Resolvases, Dissolvases, and Helicases in Homologous Recombination: Clearing the Road for Chromosome Segregation. Genes (Basel) 2020; 11:genes11010071. [PMID: 31936378 PMCID: PMC7017083 DOI: 10.3390/genes11010071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/29/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The execution of recombinational pathways during the repair of certain DNA lesions or in the meiotic program is associated to the formation of joint molecules that physically hold chromosomes together. These structures must be disengaged prior to the onset of chromosome segregation. Failure in the resolution of these linkages can lead to chromosome breakage and nondisjunction events that can alter the normal distribution of the genomic material to the progeny. To avoid this situation, cells have developed an arsenal of molecular complexes involving helicases, resolvases, and dissolvases that recognize and eliminate chromosome links. The correct orchestration of these enzymes promotes the timely removal of chromosomal connections ensuring the efficient segregation of the genome during cell division. In this review, we focus on the role of different DNA processing enzymes that collaborate in removing the linkages generated during the activation of the homologous recombination machinery as a consequence of the appearance of DNA breaks during the mitotic and meiotic programs. We will also discuss about the temporal regulation of these factors along the cell cycle, the consequences of their loss of function, and their specific role in the removal of chromosomal links to ensure the accurate segregation of the genomic material during cell division.
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23
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Kaur H, Gn K, Lichten M. Unresolved Recombination Intermediates Cause a RAD9-Dependent Cell Cycle Arrest in Saccharomyces cerevisiae. Genetics 2019; 213:805-818. [PMID: 31562181 PMCID: PMC6827386 DOI: 10.1534/genetics.119.302632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023] Open
Abstract
In Saccharomyces cerevisiae, the conserved Sgs1-Top3-Rmi1 helicase-decatenase regulates homologous recombination by limiting accumulation of recombination intermediates that are crossover precursors. In vitro studies have suggested that this may be due to dissolution of double-Holliday junction joint molecules by Sgs1-driven convergent junction migration and Top3-Rmi1 mediated strand decatenation. To ask whether dissolution occurs in vivo, we conditionally depleted Sgs1 and/or Rmi1 during return to growth (RTG), a procedure where recombination intermediates formed during meiosis are resolved when cells resume the mitotic cell cycle. Sgs1 depletion during RTG delayed joint molecule resolution, but, ultimately, most were resolved and cells divided normally. In contrast, Rmi1 depletion resulted in delayed and incomplete joint molecule resolution, and most cells did not divide. rad9 ∆ mutation restored cell division in Rmi1-depleted cells, indicating that the DNA damage checkpoint caused this cell cycle arrest. Restored cell division in Rmi1-depleted rad9 ∆ cells frequently produced anucleate cells, consistent with the suggestion that persistent recombination intermediates prevented chromosome segregation. Our findings indicate that Sgs1-Top3-Rmi1 acts in vivo, as it does in vitro, to promote recombination intermediate resolution by dissolution. They also indicate that, in the absence of Top3-Rmi1 activity, unresolved recombination intermediates persist and activate the DNA damage response, which is usually thought to be activated by much earlier DNA damage-associated lesions.
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Affiliation(s)
- Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Krishnaprasad Gn
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
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24
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Abstract
Smc5 and Smc6, together with the kleisin Nse4, form the heart of the enigmatic and poorly understood Smc5/6 complex, which is frequently viewed as a cousin of cohesin and condensin with functions in DNA repair. As novel functions for cohesin and condensin complexes in the organization of long-range chromatin architecture have recently emerged, new unsuspected roles for Smc5/6 have also surfaced. Here, I aim to provide a comprehensive overview of our current knowledge of the Smc5/6 complex, including its long-established function in genome stability, its multiple roles in DNA repair, and its recently discovered connection to the transcription inhibition of hepatitis B virus genomes. In addition, I summarize new research that is beginning to tease out the molecular details of Smc5/6 structure and function, knowledge that will illuminate the nuclear activities of Smc5/6 in the stability and dynamics of eukaryotic genomes.
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Affiliation(s)
- Luis Aragón
- Cell Cycle Group, MRC London Institute of Medical Sciences, Hammersmith Hospital Campus, London W12 0NN, United Kingdom;
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25
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Zelkowski M, Zelkowska K, Conrad U, Hesse S, Lermontova I, Marzec M, Meister A, Houben A, Schubert V. Arabidopsis NSE4 Proteins Act in Somatic Nuclei and Meiosis to Ensure Plant Viability and Fertility. FRONTIERS IN PLANT SCIENCE 2019; 10:774. [PMID: 31281325 PMCID: PMC6596448 DOI: 10.3389/fpls.2019.00774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/28/2019] [Indexed: 05/02/2023]
Abstract
The SMC 5/6 complex together with cohesin and condensin is a member of the structural maintenance of chromosome (SMC) protein family. In non-plant organisms SMC5/6 is engaged in DNA repair, meiotic synapsis, genome organization and stability. In plants, the function of SMC5/6 is still enigmatic. Therefore, we analyzed the crucial δ-kleisin component NSE4 of the SMC5/6 complex in the model plant Arabidopsis thaliana. Two functional conserved Nse4 paralogs (Nse4A and Nse4B) are present in A. thaliana, which may have evolved via gene subfunctionalization. Due to its high expression level, Nse4A seems to be the more essential gene, whereas Nse4B appears to be involved mainly in seed development. The morphological characterization of A. thaliana T-DNA mutants suggests that the NSE4 proteins are essential for plant growth and fertility. Detailed investigations in wild-type and the mutants based on live cell imaging of transgenic GFP lines, fluorescence in situ hybridization (FISH), immunolabeling and super-resolution microscopy suggest that NSE4A acts in several processes during plant development, such as mitosis, meiosis and chromatin organization of differentiated nuclei, and that NSE4A operates in a cell cycle-dependent manner. Differential response of NSE4A and NSE4B mutants after induced DNA double strand breaks (DSBs) suggests their involvement in DNA repair processes.
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Affiliation(s)
- Mateusz Zelkowski
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Katarzyna Zelkowska
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Susann Hesse
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Plant Cytogenomics Research Group, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Marek Marzec
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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26
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Hesse S, Zelkowski M, Mikhailova EI, Keijzer CJ, Houben A, Schubert V. Ultrastructure and Dynamics of Synaptonemal Complex Components During Meiotic Pairing and Synapsis of Standard (A) and Accessory (B) Rye Chromosomes. FRONTIERS IN PLANT SCIENCE 2019; 10:773. [PMID: 31281324 PMCID: PMC6596450 DOI: 10.3389/fpls.2019.00773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 05/03/2023]
Abstract
During prophase I a meiosis-specific proteinaceous tripartite structure, the synaptonemal complex (SC), forms a scaffold to connect homologous chromosomes along their lengths. This process, called synapsis, is required in most organisms to promote recombination between homologs facilitating genetic variability and correct chromosome segregations during anaphase I. Recent studies in various organisms ranging from yeast to mammals identified several proteins involved in SC formation. However, the process of SC disassembly remains largely enigmatic. In this study we determined the structural changes during SC formation and disassembly in rye meiocytes containing accessory (B) chromosomes. The use of electron and super-resolution microscopy (3D-SIM) combined with immunohistochemistry and FISH allowed us to monitor the structural changes during prophase I. Visualization of the proteins ASY1, ZYP1, NSE4A, and HEI10 revealed an extensive SC remodeling during prophase I. The ultrastructural investigations of the dynamics of these four proteins showed that the SC disassembly is accompanied by the retraction of the lateral and axial elements from the central region of the SC. In addition, SC fragmentation and the formation of ball-like SC structures occur at late diakinesis. Moreover, we show that the SC composition of rye B chromosomes does not differ from that of the standard (A) chromosome complement. Our ultrastructural investigations indicate that the dynamic behavior of the studied proteins is involved in SC formation and synapsis. In addition, they fulfill also functions during desynapsis and chromosome condensation to realize proper recombination and homolog separation. We propose a model for the homologous chromosome behavior during prophase I based on the observed dynamics of ASY1, ZYP1, NSE4A, and HEI10.
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Affiliation(s)
- Susann Hesse
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Mateusz Zelkowski
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Elena I. Mikhailova
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint-Petersburg State University, Saint-Petersburg, Russia
| | | | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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27
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Brc1 Promotes the Focal Accumulation and SUMO Ligase Activity of Smc5-Smc6 during Replication Stress. Mol Cell Biol 2019; 39:MCB.00271-18. [PMID: 30348841 DOI: 10.1128/mcb.00271-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022] Open
Abstract
As genetic instability drives disease or loss of cell fitness, cellular safeguards have evolved to protect the genome, especially during sensitive cell cycle phases, such as DNA replication. Fission yeast Brc1 has emerged as a key factor in promoting cell survival when replication forks are stalled or collapsed. Brc1 is a multi-BRCT protein that is structurally related to the budding yeast Rtt107 and human PTIP DNA damage response factors, but functional similarities appear limited. Brc1 is a dosage suppressor of a mutation in the essential Smc5-Smc6 genome stability complex and is thought to act in a bypass pathway. In this study, we reveal an unexpectedly intimate connection between Brc1 and Smc5-Smc6 function. Brc1 is required for the accumulation of the Smc5-Smc6 genome stability complex in foci during replication stress and for activation of the intrinsic SUMO ligase activity of the complex by collapsed replication forks. Moreover, we show that the chromatin association and SUMO ligase activity of Smc5-Smc6 require the Nse5-Nse6 heterodimer, explaining how this nonessential cofactor critically supports the DNA repair roles of Smc5-Smc6. We also found that Brc1 interacts with Nse5-Nse6, as well as gamma-H2A, so it can tether Smc5-Smc6 at replicative DNA lesions to promote survival.
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28
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Dikicioglu D, Dereli Eke E, Eraslan S, Oliver SG, Kirdar B. Saccharomyces cerevisiae adapted to grow in the presence of low-dose rapamycin exhibit altered amino acid metabolism. Cell Commun Signal 2018; 16:85. [PMID: 30458881 PMCID: PMC6245637 DOI: 10.1186/s12964-018-0298-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/08/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Rapamycin is a potent inhibitor of the highly conserved TOR kinase, the nutrient-sensitive controller of growth and aging. It has been utilised as a chemotherapeutic agent due to its anti-proliferative properties and as an immunosuppressive drug, and is also known to extend lifespan in a range of eukaryotes from yeast to mammals. However, the mechanisms through which eukaryotic cells adapt to sustained exposure to rapamycin have not yet been thoroughly investigated. METHODS Here, S. cerevisiae response to long-term rapamycin exposure was investigated by identifying the physiological, transcriptomic and metabolic differences observed for yeast populations inoculated into low-dose rapamycin-containing environment. The effect of oxygen availability and acidity of extracellular environment on this response was further deliberated by controlling or monitoring the dissolved oxygen level and pH of the culture. RESULTS Yeast populations grown in the presence of rapamycin reached higher cell densities complemented by an increase in their chronological lifespan, and these physiological adaptations were associated with a rewiring of the amino acid metabolism, particularly that of arginine. The ability to synthesise amino acids emerges as the key factor leading to the major mechanistic differences between mammalian and microbial TOR signalling pathways in relation to nutrient recognition. CONCLUSION Oxygen levels and extracellular acidity of the culture were observed to conjointly affect yeast populations, virtually acting as coupled physiological effectors; cells were best adapted when maximal oxygenation of the culture was maintained in slightly acidic pH, any deviation necessitated more extensive readjustment to additional stress factors.
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Affiliation(s)
- Duygu Dikicioglu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK. .,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK. .,Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.
| | - Elif Dereli Eke
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.,Present address: Unit of Blood Diseases and Stem Cells Transplantation, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Serpil Eraslan
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.,Present address: Diagnostic Centre for Genetic Diseases, Koc University Hospital, Istanbul, Turkey
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Betul Kirdar
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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29
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Hwang G, Verver DE, Handel MA, Hamer G, Jordan PW. Depletion of SMC5/6 sensitizes male germ cells to DNA damage. Mol Biol Cell 2018; 29:3003-3016. [PMID: 30281394 PMCID: PMC6333175 DOI: 10.1091/mbc.e18-07-0459] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The structural maintenance of chromosomes complex SMC5/6 is thought to be essential for DNA repair and chromosome segregation during mitosis and meiosis. To determine the requirements of the SMC5/6 complex during mouse spermatogenesis we combined a conditional knockout allele for Smc5, with four germ cell–specific Cre-recombinase transgenes, Ddx4-Cre, Stra8-Cre, Spo11-Cre, and Hspa2-Cre, to mutate Smc5 in spermatogonia, in spermatocytes before meiotic entry, during early meiotic stages, and during midmeiotic stages, respectively. Conditional mutation of Smc5 resulted in destabilization of the SMC5/6 complex. Despite this, we observed only mild defects in spermatogenesis. Mutation of Smc5 mediated by Ddx4-Cre and Stra8-Cre resulted in partial loss of preleptotene spermatocytes; however, spermatogenesis progresses and mice are fertile. Mutation of Smc5 via Spo11-Cre or Hspa2-Cre did not result in detectable defects of spermatogenesis. Upon exposure to gamma irradiation or etoposide treatment, each conditional Smc5 mutant demonstrated an increase in the number of enlarged round spermatids with multiple acrosomes and supernumerary chromosome content. We propose that the SMC5/6 complex is not acutely required for premeiotic DNA replication and meiotic progression during mouse spermatogenesis; however, when germ cells are challenged by exogenous DNA damage, the SMC5/6 complex ensures genome integrity, and thus, fertility.
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Affiliation(s)
- G Hwang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - D E Verver
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - M A Handel
- The Jackson Laboratory, Bar Harbor, ME 04609
| | - G Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - P W Jordan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
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30
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Karányi Z, Halász L, Acquaviva L, Jónás D, Hetey S, Boros-Oláh B, Peng F, Chen D, Klein F, Géli V, Székvölgyi L. Nuclear dynamics of the Set1C subunit Spp1 prepares meiotic recombination sites for break formation. J Cell Biol 2018; 217:3398-3415. [PMID: 30037925 PMCID: PMC6168271 DOI: 10.1083/jcb.201712122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/18/2018] [Accepted: 07/09/2018] [Indexed: 01/22/2023] Open
Abstract
Spp1 is the H3K4me3 reader subunit of the Set1 complex (COMPASS/Set1C) that contributes to the mechanism by which meiotic DNA break sites are mechanistically selected. We previously proposed a model in which Spp1 interacts with H3K4me3 and the chromosome axis protein Mer2 that leads to DSB formation. Here we show that spatial interactions of Spp1 and Mer2 occur independently of Set1C. Spp1 exhibits dynamic chromatin binding features during meiosis, with many de novo appearing and disappearing binding sites. Spp1 chromatin binding dynamics depends on its PHD finger and Mer2-interacting domain and on modifiable histone residues (H3R2/K4). Remarkably, association of Spp1 with Mer2 axial sites reduces the effective turnover rate and diffusion coefficient of Spp1 upon chromatin binding, compared with other Set1C subunits. Our results indicate that "chromosomal turnover rate" is a major molecular determinant of Spp1 function in the framework of meiotic chromatin structure that prepares recombination initiation sites for break formation.
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Affiliation(s)
- Zsolt Karányi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Department of Internal Medicine, University of Debrecen, Debrecen, Hungary
| | - László Halász
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laurent Acquaviva
- Marseille Cancer Research Center (CRCM), U1068 Institut National de la Santé et de la Recherche Médicale, UMR7258 Centre National de la Recherche Scientifique, Aix Marseille University, Institut Paoli-Calmettes, Marseille, France. Equipe labellisée Ligue
| | - Dávid Jónás
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szabolcs Hetey
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Beáta Boros-Oláh
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Feng Peng
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Doris Chen
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Franz Klein
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 Institut National de la Santé et de la Recherche Médicale, UMR7258 Centre National de la Recherche Scientifique, Aix Marseille University, Institut Paoli-Calmettes, Marseille, France. Equipe labellisée Ligue
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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31
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Zilio N, Eifler-Olivi K, Ulrich HD. Functions of SUMO in the Maintenance of Genome Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:51-87. [PMID: 28197906 DOI: 10.1007/978-3-319-50044-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates. However, establishing a functional connection between a given SUMO target, the cognate SUMO ligase and a relevant phenotype has remained a challenge, mainly because of the difficulties involved in identifying important modification sites and downstream effectors that specifically recognize the target in its sumoylated state. This review will give an overview over the major pathways of DNA repair and genome maintenance influenced by the SUMO system and discuss selected examples of SUMO's actions in these pathways where the biological consequences of the modification have been elucidated.
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Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | | | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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32
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Zheng Y, Jongejan A, Mulder CL, Mastenbroek S, Repping S, Wang Y, Li J, Hamer G. Trivial role for NSMCE2 during in vitro proliferation and differentiation of male germline stem cells. Reproduction 2017; 154:181-195. [DOI: 10.1530/rep-17-0173] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022]
Abstract
Spermatogenesis, starting with spermatogonial differentiation, is characterized by ongoing and dramatic alterations in composition and function of chromatin. Failure to maintain proper chromatin dynamics during spermatogenesis may lead to mutations, chromosomal aberrations or aneuploidies. When transmitted to the offspring, these can cause infertility or congenital malformations. The structural maintenance of chromosomes (SMC) 5/6 protein complex has recently been described to function in chromatin modeling and genomic integrity maintenance during spermatogonial differentiation and meiosis. Among the subunits of the SMC5/6 complex, non-SMC element 2 (NSMCE2) is an important small ubiquitin-related modifier (SUMO) ligase. NSMCE2 has been reported to be essential for mouse development, prevention of cancer and aging in adult mice and topological stress relief in human somatic cells. By using in vitro cultured primary mouse spermatogonial stem cells (SSCs), referred to as male germline stem (GS) cells, we investigated the function of NSMCE2 during spermatogonial proliferation and differentiation. We first optimized a protocol to generate genetically modified GS cell lines using CRISPR-Cas9 and generated an Nsmce2−/− GS cell line. Using this Nsmce2−/− GS cell line, we found that NSMCE2 was dispensable for proliferation, differentiation and topological stress relief in mouse GS cells. Moreover, RNA sequencing analysis demonstrated that the transcriptome was only minimally affected by the absence of NSMCE2. Only differential expression of Sgsm1 appeared highly significant, but with SGSM1 protein levels being unaffected without NSMCE2. Hence, despite the essential roles of NSMCE2 in somatic cells, chromatin integrity maintenance seems differentially regulated in the germline.
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33
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Hwang G, Sun F, O'Brien M, Eppig JJ, Handel MA, Jordan PW. SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes. Development 2017; 144:1648-1660. [PMID: 28302748 PMCID: PMC5450844 DOI: 10.1242/dev.145607] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 03/07/2017] [Indexed: 01/11/2023]
Abstract
SMC complexes include three major classes: cohesin, condensin and SMC5/6. However, the localization pattern and genetic requirements for the SMC5/6 complex during mammalian oogenesis have not previously been examined. In mouse oocytes, the SMC5/6 complex is enriched at the pericentromeric heterochromatin, and also localizes along chromosome arms during meiosis. The infertility phenotypes of females with a Zp3-Cre-driven conditional knockout (cKO) of Smc5 demonstrated that maternally expressed SMC5 protein is essential for early embryogenesis. Interestingly, protein levels of SMC5/6 complex components in oocytes decline as wild-type females age. When SMC5/6 complexes were completely absent in oocytes during meiotic resumption, homologous chromosomes failed to segregate accurately during meiosis I. Despite what appears to be an inability to resolve concatenation between chromosomes during meiosis, localization of topoisomerase IIα to bivalents was not affected; however, localization of condensin along the chromosome axes was perturbed. Taken together, these data demonstrate that the SMC5/6 complex is essential for the formation of segregation-competent bivalents during meiosis I, and findings suggest that age-dependent depletion of the SMC5/6 complex in oocytes could contribute to increased incidence of oocyte aneuploidy and spontaneous abortion in aging females.
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Affiliation(s)
- Grace Hwang
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Fengyun Sun
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - John J Eppig
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Philip W Jordan
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
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Li G, Zou W, Jian L, Qian J, Deng Y, Zhao J. Non-SMC elements 1 and 3 are required for early embryo and seedling development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1039-1054. [PMID: 28207059 PMCID: PMC5441860 DOI: 10.1093/jxb/erx016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Early embryo development from the zygote is an essential stage in the formation of the seed, while seedling development is the beginning of the formation of an individual plant. AtNSE1 and AtNSE3 are subunits of the structural maintenance of chromosomes (SMC) 5/6 complex and have been identified as non-SMC elements, but their functions in Arabidopsis growth and development remain as yet unknown. In this study, we found that loss of function of AtNSE1 and AtNSE3 led to severe defects in early embryo development. Partially complemented mutants showed that the development of mutant seedlings was inhibited, that chromosome fragments occurred during anaphase, and that the cell cycle was delayed at G2/M, which led to the occurrence of endoreduplication. Further, a large number of DNA double-strand breaks (DSBs) occurred in the nse1 and nse3 mutants, and the expression of AtNSE1 and AtNSE3 was up-regulated following treatment of the plants with DSB inducer compounds, suggesting that AtNSE1 and AtNSE3 have a role in DNA damage repair. Therefore, we conclude that AtNSE1 and AtNSE3 facilitate DSB repair and contribute to maintaining genome stability and cell division in mitotic cells. Thus, we think that AtNSE1 and AtNSE3 may be crucial factors for maintaining proper early embryonic and post-embryonic development.
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Affiliation(s)
- Gang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenxuan Zou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Liufang Jian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Qian
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingtian Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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35
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Alt A, Dang HQ, Wells OS, Polo LM, Smith MA, McGregor GA, Welte T, Lehmann AR, Pearl LH, Murray JM, Oliver AW. Specialized interfaces of Smc5/6 control hinge stability and DNA association. Nat Commun 2017; 8:14011. [PMID: 28134253 PMCID: PMC5290277 DOI: 10.1038/ncomms14011] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023] Open
Abstract
The Structural Maintenance of Chromosomes (SMC) complexes: cohesin, condensin and Smc5/6 are involved in the organization of higher-order chromosome structure-which is essential for accurate chromosome duplication and segregation. Each complex is scaffolded by a specific SMC protein dimer (heterodimer in eukaryotes) held together via their hinge domains. Here we show that the Smc5/6-hinge, like those of cohesin and condensin, also forms a toroidal structure but with distinctive subunit interfaces absent from the other SMC complexes; an unusual 'molecular latch' and a functional 'hub'. Defined mutations in these interfaces cause severe phenotypic effects with sensitivity to DNA-damaging agents in fission yeast and reduced viability in human cells. We show that the Smc5/6-hinge complex binds preferentially to ssDNA and that this interaction is affected by both 'latch' and 'hub' mutations, suggesting a key role for these unique features in controlling DNA association by the Smc5/6 complex.
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Affiliation(s)
- Aaron Alt
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Hung Q. Dang
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Owen S. Wells
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Luis M. Polo
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Matt A. Smith
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Grant A. McGregor
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Thomas Welte
- Dynamic Biosensors GmbH, Lochhamer Strasse, D-81252 Martinsreid/Planegg, Germany
| | - Alan R. Lehmann
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Laurence H. Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
| | - Johanne M. Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W. Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, BN1 9RQ, UK
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Verver DE, Zheng Y, Speijer D, Hoebe R, Dekker HL, Repping S, Stap J, Hamer G. Non-SMC Element 2 (NSMCE2) of the SMC5/6 Complex Helps to Resolve Topological Stress. Int J Mol Sci 2016; 17:ijms17111782. [PMID: 27792189 PMCID: PMC5133783 DOI: 10.3390/ijms17111782] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/14/2016] [Accepted: 10/20/2016] [Indexed: 01/05/2023] Open
Abstract
The structural maintenance of chromosomes (SMC) protein complexes shape and regulate the structure and dynamics of chromatin, thereby controlling many chromosome-based processes such as cell cycle progression, differentiation, gene transcription and DNA repair. The SMC5/6 complex is previously described to promote DNA double-strand breaks (DSBs) repair by sister chromatid recombination, and found to be essential for resolving recombination intermediates during meiotic recombination. Moreover, in budding yeast, SMC5/6 provides structural organization and topological stress relief during replication in mitotically dividing cells. Despite the essential nature of the SMC5/6 complex, the versatile mechanisms by which SMC5/6 functions and its molecular regulation in mammalian cells remain poorly understood. By using a human osteosarcoma cell line (U2OS), we show that after the CRISPR-Cas9-mediated removal of the SMC5/6 subunit NSMCE2, treatment with the topoisomerase II inhibitor etoposide triggered an increased sensitivity in cells lacking NSMCE2. In contrast, NSMCE2 appeared not essential for a proper DNA damage response or cell survival after DSB induction by ionizing irradiation (IR). Interestingly, by way of immunoprecipitations (IPs) and mass spectrometry, we found that the SMC5/6 complex physically interacts with the DNA topoisomerase II α (TOP2A). We therefore propose that the SMC5/6 complex functions in resolving TOP2A-mediated DSB-repair intermediates generated during replication.
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Affiliation(s)
- Dideke E Verver
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Yi Zheng
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ron Hoebe
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Henk L Dekker
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands.
| | - Sjoerd Repping
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Jan Stap
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Geert Hamer
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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37
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Peng J, Feng W. Incision of damaged DNA in the presence of an impaired Smc5/6 complex imperils genome stability. Nucleic Acids Res 2016; 44:10216-10229. [PMID: 27536003 PMCID: PMC5137426 DOI: 10.1093/nar/gkw720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 11/14/2022] Open
Abstract
The Smc5/6 complex is implicated in homologous recombination-mediated DNA repair during DNA damage or replication stress. Here, we analysed genome-wide replication dynamics in a hypomorphic budding yeast mutant, smc6-P4. The overall replication dynamics in the smc6 mutant is similar to that in the wild-type cells. However, we captured a difference in the replication profile of an early S phase sample in the mutant, prompting the hypothesis that the mutant incorporates ribonucleotides and/or accumulates single-stranded DNA gaps during replication. We tested if inhibiting the ribonucleotide excision repair pathway would exacerbate the smc6 mutant in response to DNA replication stress. Contrary to our expectation, impairment of ribonucleotide excision repair, as well as virtually all other DNA repair pathways, alleviated smc6 mutant's hypersensitivity to induced replication stress. We propose that nucleotide incision in the absence of a functional Smc5/6 complex has more disastrous outcomes than the damage per se. Our study provides novel perspectives for the role of the Smc5/6 complex during DNA replication.
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Affiliation(s)
- Jie Peng
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Wenyi Feng
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
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Ohta S, Montaño-Gutierrez LF, de Lima Alves F, Ogawa H, Toramoto I, Sato N, Morrison CG, Takeda S, Hudson DF, Rappsilber J, Earnshaw WC. Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes. Mol Cell Proteomics 2016; 15:2802-18. [PMID: 27231315 PMCID: PMC4974353 DOI: 10.1074/mcp.m116.057885] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
Packaging of DNA into condensed chromosomes during mitosis is essential for the faithful segregation of the genome into daughter nuclei. Although the structure and composition of mitotic chromosomes have been studied for over 30 years, these aspects are yet to be fully elucidated. Here, we used stable isotope labeling with amino acids in cell culture to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes. Our analysis revealed that these complexes associate with chromosomes independently of each other, with the SMC5/6 complex showing no significant dependence on any other chromosomal proteins during mitosis. To identify subtle relationships between chromosomal proteins, we employed a nano Random Forest (nanoRF) approach to detect protein complexes and the relationships between them. Our nanoRF results suggested that as few as 113 of 5058 detected chromosomal proteins are functionally linked to chromosome structure and segregation. Furthermore, nanoRF data revealed 23 proteins that were not previously suspected to have functional interactions with complexes playing important roles in mitosis. Subsequent small-interfering-RNA-based validation and localization tracking by green fluorescent protein-tagging highlighted novel candidates that might play significant roles in mitotic progression.
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Affiliation(s)
- Shinya Ohta
- From the ‡Center for Innovative and Translational Medicine, Medical School, Kochi University Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan; §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, UK;
| | - Luis F Montaño-Gutierrez
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Flavia de Lima Alves
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Hiromi Ogawa
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, UK
| | - Iyo Toramoto
- From the ‡Center for Innovative and Translational Medicine, Medical School, Kochi University Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Nobuko Sato
- From the ‡Center for Innovative and Translational Medicine, Medical School, Kochi University Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Ciaran G Morrison
- ¶Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Shunichi Takeda
- ‖Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Damien F Hudson
- **Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Juri Rappsilber
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, UK; ‡‡Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - William C Earnshaw
- §Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3BF, UK
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Tran M, Tsarouhas V, Kegel A. Early development of Drosophila embryos requires Smc5/6 function during oogenesis. Biol Open 2016; 5:928-41. [PMID: 27288507 PMCID: PMC4958276 DOI: 10.1242/bio.019000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mutations in structural maintenance of chromosomes (Smc) proteins are frequently associated with chromosomal abnormalities commonly observed in developmental disorders. However, the role of Smc proteins in development still remains elusive. To investigate Smc5/6 function during early embryogenesis we examined smc5 and smc6 mutants of the fruit fly Drosophila melanogaster using a combination of reverse genetics and microscopy approaches. Smc5/6 exhibited a maternally contributed function in maintaining chromosome stability during early embryo development, which manifested as female subfertility in its absence. Loss of Smc5/6 caused an arrest and a considerable delay in embryo development accompanied by fragmented nuclei and increased anaphase-bridge formation, respectively. Surprisingly, early embryonic arrest was attributable to the absence of Smc5/6 during oogenesis, which resulted in insufficient repair of pre-meiotic and meiotic DNA double-strand breaks. Thus, our findings contribute to the understanding of Smc proteins in higher eukaryotic development by highlighting a maternal function in chromosome maintenance and a link between oogenesis and early embryogenesis. Summary: Early emerging problems during oogenesis, such as DNA double-strand breaks, can affect chromosome duplication and segregation in embryogenesis in Drosophila. Moreover, environmental cues including temperature are important for proper oogenesis.
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Affiliation(s)
- Martin Tran
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
| | - Vasilios Tsarouhas
- Department of Molecular Bioscience, The Wenner-Gren Institute, Stockholm University, Stockholm S-10691, Sweden
| | - Andreas Kegel
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
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40
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Jagut M, Hamminger P, Woglar A, Millonigg S, Paulin L, Mikl M, Dello Stritto MR, Tang L, Habacher C, Tam A, Gallach M, von Haeseler A, Villeneuve AM, Jantsch V. Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance. PLoS Biol 2016; 14:e1002412. [PMID: 27011106 PMCID: PMC4807110 DOI: 10.1371/journal.pbio.1002412] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/19/2016] [Indexed: 11/30/2022] Open
Abstract
During the first meiotic division, crossovers (COs) between homologous chromosomes ensure their correct segregation. COs are produced by homologous recombination (HR)-mediated repair of programmed DNA double strand breaks (DSBs). As more DSBs are induced than COs, mechanisms are required to establish a regulated number of COs and to repair remaining intermediates as non-crossovers (NCOs). We show that the Caenorhabditis elegans RMI1 homolog-1 (RMH-1) functions during meiosis to promote both CO and NCO HR at appropriate chromosomal sites. RMH-1 accumulates at CO sites, dependent on known pro-CO factors, and acts to promote CO designation and enforce the CO outcome of HR-intermediate resolution. RMH-1 also localizes at NCO sites and functions in parallel with SMC-5 to antagonize excess HR-based connections between chromosomes. Moreover, RMH-1 also has a major role in channeling DSBs into an NCO HR outcome near the centers of chromosomes, thereby ensuring that COs form predominantly at off-center positions. A nematode homolog of the conserved DNA repair factor RMI1 plays multiple genetically separable roles that together ensure the faithful inheritance of intact genomes during sexual reproduction. During meiosis, faithful separation of chromosomes into gametes is essential for fertility and healthy progeny. During the first meiotic division, crossovers (CO) between parental homologs ensure their correct segregation. Programmed DNA double strand breaks (DSBs) and resection steps generate single-stranded overhangs that invade a sister chromatid of the homolog to initiate homologous recombination. This culminates in the generation of a DNA double Holliday junction (dHJ). This can be acted upon by resolvases to produce CO and non-crossover (NCO) products, depending on where the resolvases cut the DNA. Alternatively, NCOs can also be produced by decatenation via the RecQ helicase–topoisomeraseIII–Rmi1 (RTR) complex. The mammalian RTR contains a topoisomerase, Bloom’s helicase, and RMI1/2 scaffolding components. It disassembles dHJs in vitro and contributes the major NCO activity in mitosis. Here, we provide evidence that the Caenorhabditis elegans RMH-1 functions in distinct complexes during meiosis to produce both COs and NCOs in an in vivo animal model system. Strikingly, RMH-1 spatially regulates the distribution of COs on chromosomes, demonstrating that the RTR complex can act locally within specific chromosome domains.
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Affiliation(s)
- Marlène Jagut
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Patricia Hamminger
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Alexander Woglar
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sophia Millonigg
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Luis Paulin
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Martin Mikl
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Maria Rosaria Dello Stritto
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Lois Tang
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Cornelia Habacher
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Angela Tam
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Miguel Gallach
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna and Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Austria
| | - Anne M. Villeneuve
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
- * E-mail:
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Hong Y, Sonneville R, Agostinho A, Meier B, Wang B, Blow JJ, Gartner A. The SMC-5/6 Complex and the HIM-6 (BLM) Helicase Synergistically Promote Meiotic Recombination Intermediate Processing and Chromosome Maturation during Caenorhabditis elegans Meiosis. PLoS Genet 2016; 12:e1005872. [PMID: 27010650 PMCID: PMC4807058 DOI: 10.1371/journal.pgen.1005872] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/25/2016] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is essential for the repair of programmed double strand breaks (DSBs) to generate crossovers (COs) during meiosis. The efficient processing of meiotic recombination intermediates not only needs various resolvases but also requires proper meiotic chromosome structure. The Smc5/6 complex belongs to the structural maintenance of chromosome (SMC) family and is closely related to cohesin and condensin. Although the Smc5/6 complex has been implicated in the processing of recombination intermediates during meiosis, it is not known how Smc5/6 controls meiotic DSB repair. Here, using Caenorhabditis elegans we show that the SMC-5/6 complex acts synergistically with HIM-6, an ortholog of the human Bloom syndrome helicase (BLM) during meiotic recombination. The concerted action of the SMC-5/6 complex and HIM-6 is important for processing recombination intermediates, CO regulation and bivalent maturation. Careful examination of meiotic chromosomal morphology reveals an accumulation of inter-chromosomal bridges in smc-5; him-6 double mutants, leading to compromised chromosome segregation during meiotic cell divisions. Interestingly, we found that the lethality of smc-5; him-6 can be rescued by loss of the conserved BRCA1 ortholog BRC-1. Furthermore, the combined deletion of smc-5 and him-6 leads to an irregular distribution of condensin and to chromosome decondensation defects reminiscent of condensin depletion. Lethality conferred by condensin depletion can also be rescued by BRC-1 depletion. Our results suggest that SMC-5/6 and HIM-6 can synergistically regulate recombination intermediate metabolism and suppress ectopic recombination by controlling chromosome architecture during meiosis.
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Affiliation(s)
- Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Remi Sonneville
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Ana Agostinho
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Bin Wang
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
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Zabrady K, Adamus M, Vondrova L, Liao C, Skoupilova H, Novakova M, Jurcisinova L, Alt A, Oliver AW, Lehmann AR, Palecek JJ. Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA. Nucleic Acids Res 2016; 44:1064-79. [PMID: 26446992 PMCID: PMC4756808 DOI: 10.1093/nar/gkv1021] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 11/13/2022] Open
Abstract
SMC5/6 is a highly conserved protein complex related to cohesin and condensin, which are the key components of higher-order chromatin structures. The SMC5/6 complex is essential for proliferation in yeast and is involved in replication fork stability and processing. However, the precise mechanism of action of SMC5/6 is not known. Here we present evidence that the NSE1/NSE3/NSE4 sub-complex of SMC5/6 binds to double-stranded DNA without any preference for DNA-replication/recombination intermediates. Mutations of key basic residues within the NSE1/NSE3/NSE4 DNA-binding surface reduce binding to DNA in vitro. Their introduction into the Schizosaccharomyces pombe genome results in cell death or hypersensitivity to DNA damaging agents. Chromatin immunoprecipitation analysis of the hypomorphic nse3 DNA-binding mutant shows a reduced association of fission yeast SMC5/6 with chromatin. Based on our results, we propose a model for loading of the SMC5/6 complex onto the chromatin.
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Affiliation(s)
- Katerina Zabrady
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marek Adamus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Lucie Vondrova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Chunyan Liao
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Hana Skoupilova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Marketa Novakova
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Lenka Jurcisinova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
| | - Aaron Alt
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Antony W Oliver
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, United Kingdom
| | - Jan J Palecek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 61137, Czech Republic
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43
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Palecek JJ, Gruber S. Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes. Structure 2015; 23:2183-2190. [DOI: 10.1016/j.str.2015.10.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/23/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
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44
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Abstract
The study of homologous recombination has its historical roots in meiosis. In this context, recombination occurs as a programmed event that culminates in the formation of crossovers, which are essential for accurate chromosome segregation and create new combinations of parental alleles. Thus, meiotic recombination underlies both the independent assortment of parental chromosomes and genetic linkage. This review highlights the features of meiotic recombination that distinguish it from recombinational repair in somatic cells, and how the molecular processes of meiotic recombination are embedded and interdependent with the chromosome structures that characterize meiotic prophase. A more in-depth review presents our understanding of how crossover and noncrossover pathways of meiotic recombination are differentiated and regulated. The final section of this review summarizes the studies that have defined defective recombination as a leading cause of pregnancy loss and congenital disease in humans.
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Affiliation(s)
- Neil Hunter
- Howard Hughes Medical Institute, Department of Microbiology & Molecular Genetics, Department of Molecular & Cellular Biology, Department of Cell Biology & Human Anatomy, University of California Davis, Davis, California 95616
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45
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Jacome A, Gutierrez-Martinez P, Schiavoni F, Tenaglia E, Martinez P, Rodríguez-Acebes S, Lecona E, Murga M, Méndez J, Blasco MA, Fernandez-Capetillo O. NSMCE2 suppresses cancer and aging in mice independently of its SUMO ligase activity. EMBO J 2015; 34:2604-19. [PMID: 26443207 DOI: 10.15252/embj.201591829] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/01/2015] [Indexed: 01/16/2023] Open
Abstract
The SMC5/6 complex is the least understood of SMC complexes. In yeast, smc5/6 mutants phenocopy mutations in sgs1, the BLM ortholog that is deficient in Bloom's syndrome (BS). We here show that NSMCE2 (Mms21, in Saccharomyces cerevisiae), an essential SUMO ligase of the SMC5/6 complex, suppresses cancer and aging in mice. Surprisingly, a mutation that compromises NSMCE2-dependent SUMOylation does not have a detectable impact on murine lifespan. In contrast, NSMCE2 deletion in adult mice leads to pathologies resembling those found in patients of BS. Moreover, and whereas NSMCE2 deletion does not have a detectable impact on DNA replication, NSMCE2-deficient cells also present the cellular hallmarks of BS such as increased recombination rates and an accumulation of micronuclei. Despite the similarities, NSMCE2 and BLM foci do not colocalize and concomitant deletion of Blm and Nsmce2 in B lymphocytes further increases recombination rates and is synthetic lethal due to severe chromosome mis-segregation. Our work reveals that SUMO- and BLM-independent activities of NSMCE2 limit recombination and facilitate segregation; functions of the SMC5/6 complex that are necessary to prevent cancer and aging in mice.
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Affiliation(s)
- Ariana Jacome
- Genomic Instability Group, Spanish National Cancer Research Centre, Madrid, Spain
| | | | - Federica Schiavoni
- Genomic Instability Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Enrico Tenaglia
- Genomic Instability Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Paula Martinez
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre, Madrid, Spain
| | | | - Emilio Lecona
- Genomic Instability Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Matilde Murga
- Genomic Instability Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Juan Méndez
- DNA Replication Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre, Madrid, Spain Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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46
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Abstract
Recombination is a central process to stably maintain and transmit a genome through somatic cell divisions and to new generations. Hence, recombination needs to be coordinated with other events occurring on the DNA template, such as DNA replication, transcription, and the specialized chromosomal functions at centromeres and telomeres. Moreover, regulation with respect to the cell-cycle stage is required as much as spatiotemporal coordination within the nuclear volume. These regulatory mechanisms impinge on the DNA substrate through modifications of the chromatin and directly on recombination proteins through a myriad of posttranslational modifications (PTMs) and additional mechanisms. Although recombination is primarily appreciated to maintain genomic stability, the process also contributes to gross chromosomal arrangements and copy-number changes. Hence, the recombination process itself requires quality control to ensure high fidelity and avoid genomic instability. Evidently, recombination and its regulatory processes have significant impact on human disease, specifically cancer and, possibly, neurodegenerative diseases.
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Affiliation(s)
- Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616-8665 Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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47
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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48
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Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6. Chromosoma 2015; 125:15-27. [PMID: 25947290 PMCID: PMC4761004 DOI: 10.1007/s00412-015-0518-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/02/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
Abstract
The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to have roles in homologous recombination, restart of stalled replication forks, maintenance of ribosomal DNA (rDNA) and heterochromatin, telomerase-independent telomere elongation, and regulation of chromosome topology. The nature of these functions implies that the Smc5/6 complex also contributes to the profound chromatin changes, including meiotic recombination, that characterize meiosis. Only recently, studies in diverse model organisms have focused on the potential meiotic roles of the Smc5/6 complex. Indeed, Smc5/6 appears to be essential for meiotic recombination. However, due to both the complexity of the process of meiosis and the versatility of the Smc5/6 complex, many additional meiotic functions have been described. In this review, we provide a clear overview of the multiple functions found so far for the Smc5/6 complex in meiosis. Additionally, we compare these meiotic functions with the known mitotic functions in an attempt to find a common denominator and thereby create clarity in the field of Smc5/6 research.
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49
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Bermúdez-López M, Pociño-Merino I, Sánchez H, Bueno A, Guasch C, Almedawar S, Bru-Virgili S, Garí E, Wyman C, Reverter D, Colomina N, Torres-Rosell J. ATPase-dependent control of the Mms21 SUMO ligase during DNA repair. PLoS Biol 2015; 13:e1002089. [PMID: 25764370 PMCID: PMC4357442 DOI: 10.1371/journal.pbio.1002089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/26/2015] [Indexed: 11/18/2022] Open
Abstract
Modification of proteins by SUMO is essential for the maintenance of genome integrity. During DNA replication, the Mms21-branch of the SUMO pathway counteracts recombination intermediates at damaged replication forks, thus facilitating sister chromatid disjunction. The Mms21 SUMO ligase docks to the arm region of the Smc5 protein in the Smc5/6 complex; together, they cooperate during recombinational DNA repair. Yet how the activity of the SUMO ligase is controlled remains unknown. Here we show that the SUMO ligase and the chromosome disjunction functions of Mms21 depend on its docking to an intact and active Smc5/6 complex, indicating that the Smc5/6-Mms21 complex operates as a large SUMO ligase in vivo. In spite of the physical distance separating the E3 and the nucleotide-binding domains in Smc5/6, Mms21-dependent sumoylation requires binding of ATP to Smc5, a step that is part of the ligase mechanism that assists Ubc9 function. The communication is enabled by the presence of a conserved disruption in the coiled coil domain of Smc5, pointing to potential conformational changes for SUMO ligase activation. In accordance, scanning force microscopy of the Smc5-Mms21 heterodimer shows that the molecule is physically remodeled in an ATP-dependent manner. Our results demonstrate that the ATP-binding activity of the Smc5/6 complex is coordinated with its SUMO ligase, through the coiled coil domain of Smc5 and the physical remodeling of the molecule, to promote sumoylation and chromosome disjunction during DNA repair. Conserved conformational joints in the Mms21-Smc5/6 complex allow coordination between its ATPase and E3 SUMO ligase activities, integrating its structural and signaling roles during DNA repair to allow correct chromosome separation. The modification of target proteins by conjugation to SUMO—a small protein that acts as a regulatory tag—is essential for maintaining the integrity of genomes in most eukaryotic organisms. One critical step during the attachment of SUMO is the activation of the enzymes that catalyze this reaction—E1, E2, and the SUMO ligases. However, we currently do not fully understand how the different enzymes in the SUMO pathway are regulated. The SUMO ligase Mms21 is known to bind to Smc5/6, a large protein complex involved in the structural maintenance of chromosomes. Both Mms21 and Smc5/6 counteract the accumulation of recombination intermediates, which otherwise join replicated chromosomes, preventing their separation. Not surprisingly, the few known targets of the Mms21 ligase are mostly related to the repair of sister chromatids by recombination. Here, we show that the Mms21 SUMO ligase needs to bind to the Smc5/6 complex to promote chromosome separation. We used two Mms21-dependent SUMO conjugation targets—Smc5 and cohesin—to study the connection between the Mms21’s SUMO ligase activity and its binding partner, Smc5/6. Our results indicated that Mms21 activation is tightly coordinated with the intrinsic ATPase function of the Smc5/6 complex. However, the SUMO ligase and the ATPase lie in different domains of the Smc5/6-Mms21 complex that are normally distant from each other; we show that communication between these enzyme sites is enabled by the presence of conserved joints, which we suggest allow the necessary conformational changes required for SUMO ligase activation. This coordination of activities is extremely helpful for the cell, enabling it to integrate a structural role on chromatin during DNA repair with a signaling function, thereby promoting correct separation of the chromosomes.
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Affiliation(s)
| | - Irene Pociño-Merino
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Humberto Sánchez
- Department of Genetics and Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andrés Bueno
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Clàudia Guasch
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Seba Almedawar
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Sergi Bru-Virgili
- Institut de Biotecnologia i Biomedicina, Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Eloi Garí
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Claire Wyman
- Department of Genetics and Radiation Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David Reverter
- Institut de Biotecnologia i Biomedicina, Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Neus Colomina
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Jordi Torres-Rosell
- IRBLLEIDA, Dept. Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
- * E-mail:
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50
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Jeppsson K, Carlborg KK, Nakato R, Berta DG, Lilienthal I, Kanno T, Lindqvist A, Brink MC, Dantuma NP, Katou Y, Shirahige K, Sjögren C. The chromosomal association of the Smc5/6 complex depends on cohesion and predicts the level of sister chromatid entanglement. PLoS Genet 2014; 10:e1004680. [PMID: 25329383 PMCID: PMC4199498 DOI: 10.1371/journal.pgen.1004680] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/18/2014] [Indexed: 11/24/2022] Open
Abstract
The cohesin complex, which is essential for sister chromatid cohesion and chromosome segregation, also inhibits resolution of sister chromatid intertwinings (SCIs) by the topoisomerase Top2. The cohesin-related Smc5/6 complex (Smc5/6) instead accumulates on chromosomes after Top2 inactivation, known to lead to a buildup of unresolved SCIs. This suggests that cohesin can influence the chromosomal association of Smc5/6 via its role in SCI protection. Using high-resolution ChIP-sequencing, we show that the localization of budding yeast Smc5/6 to duplicated chromosomes indeed depends on sister chromatid cohesion in wild-type and top2-4 cells. Smc5/6 is found to be enriched at cohesin binding sites in the centromere-proximal regions in both cell types, but also along chromosome arms when replication has occurred under Top2-inhibiting conditions. Reactivation of Top2 after replication causes Smc5/6 to dissociate from chromosome arms, supporting the assumption that Smc5/6 associates with a Top2 substrate. It is also demonstrated that the amount of Smc5/6 on chromosomes positively correlates with the level of missegregation in top2-4, and that Smc5/6 promotes segregation of short chromosomes in the mutant. Altogether, this shows that the chromosomal localization of Smc5/6 predicts the presence of the chromatid segregation-inhibiting entities which accumulate in top2-4 mutated cells. These are most likely SCIs, and our results thus indicate that, at least when Top2 is inhibited, Smc5/6 facilitates their resolution.
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Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Kristian K. Carlborg
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Ryuichiro Nakato
- University of Tokyo, Institute of Molecular and Cellular Biosciences, Laboratory of Genome Structure and Function Center for Epigenetic Disease, Bunkyo-ku, Tokyo, Japan
| | - Davide G. Berta
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Ingrid Lilienthal
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Takaharu Kanno
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Arne Lindqvist
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Maartje C. Brink
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Nico P. Dantuma
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Yuki Katou
- University of Tokyo, Institute of Molecular and Cellular Biosciences, Laboratory of Genome Structure and Function Center for Epigenetic Disease, Bunkyo-ku, Tokyo, Japan
| | - Katsuhiko Shirahige
- University of Tokyo, Institute of Molecular and Cellular Biosciences, Laboratory of Genome Structure and Function Center for Epigenetic Disease, Bunkyo-ku, Tokyo, Japan
| | - Camilla Sjögren
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
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