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Ruszkiewicz J, Endig L, Güver E, Bürkle A, Mangerich A. Life-Cycle-Dependent Toxicities of Mono- and Bifunctional Alkylating Agents in the 3R-Compliant Model Organism C. elegans. Cells 2023; 12:2728. [PMID: 38067156 PMCID: PMC10705807 DOI: 10.3390/cells12232728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Caenorhabditis elegans (C. elegans) is gaining recognition and importance as an organismic model for toxicity testing in line with the 3Rs principle (replace, reduce, refine). In this study, we explored the use of C. elegans to examine the toxicities of alkylating sulphur mustard analogues, specifically the monofunctional agent 2-chloroethyl-ethyl sulphide (CEES) and the bifunctional, crosslinking agent mechlorethamine (HN2). We exposed wild-type worms at different life cycle stages (from larvae L1 to adulthood day 10) to CEES or HN2 and scored their viability 24 h later. The susceptibility of C. elegans to CEES and HN2 paralleled that of human cells, with HN2 exhibiting higher toxicity than CEES, reflected in LC50 values in the high µM to low mM range. Importantly, the effects were dependent on the worms' developmental stage as well as organismic age: the highest susceptibility was observed in L1, whereas the lowest was observed in L4 worms. In adult worms, susceptibility to alkylating agents increased with advanced age, especially to HN2. To examine reproductive effects, L4 worms were exposed to CEES and HN2, and both the offspring and the percentage of unhatched eggs were assessed. Moreover, germline apoptosis was assessed by using ced-1p::GFP (MD701) worms. In contrast to concentrations that elicited low toxicities to L4 worms, CEES and HN2 were highly toxic to germline cells, manifesting as increased germline apoptosis as well as reduced offspring number and percentage of eggs hatched. Again, HN2 exhibited stronger effects than CEES. Compound specificity was also evident in toxicities to dopaminergic neurons-HN2 exposure affected expression of dopamine transporter DAT-1 (strain BY200) at lower concentrations than CEES, suggesting a higher neurotoxic effect. Mechanistically, nicotinamide adenine dinucleotide (NAD+) has been linked to mustard agent toxicities. Therefore, the NAD+-dependent system was investigated in the response to CEES and HN2 treatment. Overall NAD+ levels in worm extracts were revealed to be largely resistant to mustard exposure except for high concentrations, which lowered the NAD+ levels in L4 worms 24 h post-treatment. Interestingly, however, mutant worms lacking components of NAD+-dependent pathways involved in genome maintenance, namely pme-2, parg-2, and sirt-2.1 showed a higher and compound-specific susceptibility, indicating an active role of NAD+ in genotoxic stress response. In conclusion, the present results demonstrate that C. elegans represents an attractive model to study the toxicology of alkylating agents, which supports its use in mechanistic as well as intervention studies with major strength in the possibility to analyze toxicities at different life cycle stages.
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Affiliation(s)
- Joanna Ruszkiewicz
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany (A.B.)
| | - Lisa Endig
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany (A.B.)
| | - Ebru Güver
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany (A.B.)
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany (A.B.)
| | - Aswin Mangerich
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany (A.B.)
- Nutritional Toxicology, Institute Nutritional Science, University of Potsdam, 14469 Potsdam, Germany
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2
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Odiba AS, Liao G, Ezechukwu CS, Zhang L, Hong Y, Fang W, Jin C, Gartner A, Wang B. Caenorhabditis elegans NSE3 homolog (MAGE-1) is involved in genome stability and acts in inter-sister recombination during meiosis. Genetics 2023; 225:iyad149. [PMID: 37579186 PMCID: PMC10691751 DOI: 10.1093/genetics/iyad149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/16/2023] Open
Abstract
Melanoma antigen (MAGE) genes encode for a family of proteins that share a common MAGE homology domain. These genes are conserved in eukaryotes and have been linked to a variety of cellular and developmental processes including ubiquitination and oncogenesis in cancer. Current knowledge on the MAGE family of proteins mainly comes from the analysis of yeast and human cell lines, and their functions have not been reported at an organismal level in animals. Caenorhabditis elegans only encodes 1 known MAGE gene member, mage-1 (NSE3 in yeast), forming part of the SMC-5/6 complex. Here, we characterize the role of mage-1/nse-3 in mitosis and meiosis in C. elegans. mage-1/nse-3 has a role in inter-sister recombination repair during meiotic recombination and for preserving chromosomal integrity upon treatment with a variety of DNA-damaging agents. MAGE-1 directly interacts with NSE-1 and NSE-4. In contrast to smc-5, smc-6, and nse-4 mutants which cause the loss of NSE-1 nuclear localization and strong cytoplasmic accumulation, mage-1/nse-3 mutants have a reduced level of NSE-1::GFP, remnant NSE-1::GFP being partially nuclear but largely cytoplasmic. Our data suggest that MAGE-1 is essential for NSE-1 stability and the proper functioning of the SMC-5/6 complex.
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Affiliation(s)
- Arome Solomon Odiba
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guiyan Liao
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Chiemekam Samuel Ezechukwu
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Lanlan Zhang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ye Hong
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Wenxia Fang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
| | - Cheng Jin
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Anton Gartner
- IBS Center for Genomic Integrity, Department for Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Bin Wang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
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Kaczmarczyk AP, Déclais AC, Newton MD, Boulton SJ, Lilley DMJ, Rueda DS. Search and processing of Holliday junctions within long DNA by junction-resolving enzymes. Nat Commun 2022; 13:5921. [PMID: 36207294 PMCID: PMC9547003 DOI: 10.1038/s41467-022-33503-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.
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Affiliation(s)
- Artur P Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
| | | | - Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David M J Lilley
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK.
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Odiba AS, Ezechukwu CS, Liao G, Li S, Chen Z, Liu X, Fang W, Jin C, Wang B. Loss of NSE-4 Perturbs Genome Stability and DNA Repair in Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms23137202. [PMID: 35806213 PMCID: PMC9266361 DOI: 10.3390/ijms23137202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
The Structural Maintenance of Chromosomes (SMC) complex plays an important role in maintaining chromosome integrity, in which the SMC5/6 complex occupies a central position by facilitating mitotic and meiotic processes as well as DNA repair. NSE-4 Kleisin is critical for both the organization and function of the SMC5/6 complex, bridging NSE1 and NSE3 (MAGE related) with the head domains of the SMC5 and SMC6 proteins. Despite the conservation in protein sequence, no functional relevance of the NSE-4 homologous protein (NSE-4) in Caenorhabditis elegans has been reported. Here, we demonstrated the essential role of C. elegans NSE-4 in genome maintenance and DNA repair. Our results showed that NSE-4 is essential for the maintenance of chromosomal structure and repair of a range of chemically induced DNA damage. Furthermore, NSE-4 is involved in inter-sister repair during meiosis. NSE-4 localizes on the chromosome and is indispensable for the localization of NSE-1. Collectively, our data from this study provide further insight into the evolutionary conservation and diversification of NSE-4 function in the SMC-5/6 complex.
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Affiliation(s)
- Arome Solomon Odiba
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Genetics and Biotechnology, University of Nigeria, Nsukka 410001, Nigeria
| | - Chiemekam Samuel Ezechukwu
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- Department of Zoology and Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Guiyan Liao
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- Correspondence: (G.L.); (B.W.)
| | - Siqiao Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
| | - Zhongliang Chen
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (Z.C.); (X.L.)
| | - Xihui Liu
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (Z.C.); (X.L.)
| | - Wenxia Fang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
| | - Cheng Jin
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (A.S.O.); (C.S.E.); (S.L.); (W.F.); (C.J.)
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (Z.C.); (X.L.)
- Correspondence: (G.L.); (B.W.)
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5
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Carreira R, Aguado FJ, Hurtado-Nieves V, Blanco MG. Canonical and novel non-canonical activities of the Holliday junction resolvase Yen1. Nucleic Acids Res 2021; 50:259-280. [PMID: 34928393 PMCID: PMC8754655 DOI: 10.1093/nar/gkab1225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/12/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
Yen1 and GEN1 are members of the Rad2/XPG family of nucleases that were identified as the first canonical nuclear Holliday junction (HJ) resolvases in budding yeast and humans due to their ability to introduce two symmetric, coordinated incisions on opposite strands of the HJ, yielding nicked DNA products that could be readily ligated. While GEN1 has been extensively characterized in vitro, much less is known about the biochemistry of Yen1. Here, we have performed the first in-depth characterization of purified Yen1. We confirmed that Yen1 resembles GEN1 in many aspects, including range of substrates targeted, position of most incisions they produce or the increase in the first incision rate by assembly of a dimer on a HJ, despite minor differences. However, we demonstrate that Yen1 is endowed with additional nuclease activities, like a nick-specific 5′-3′ exonuclease or HJ arm-chopping that could apparently blur its classification as a canonical HJ resolvase. Despite this, we show that Yen1 fulfils the requirements of a canonical HJ resolvase and hypothesize that its wider array of nuclease activities might contribute to its function in the removal of persistent recombination or replication intermediates.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Vanesa Hurtado-Nieves
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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Mechanism of mitotic recombination: insights from C. elegans. Curr Opin Genet Dev 2021; 71:10-18. [PMID: 34186335 PMCID: PMC8683258 DOI: 10.1016/j.gde.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/18/2021] [Accepted: 06/07/2021] [Indexed: 11/23/2022]
Abstract
Homologous recombination (HR) plays a critical role in largely error-free repair of mitotic and meiotic DNA double-strand breaks (DSBs). DSBs are one of the most deleterious DNA lesions, which are repaired by non-homologous end joining (NHEJ), homologous recombination (HR) or, if compromised, micro-homology mediated end joining (MMEJ). If left unrepaired, DSBs can lead to cell death or if repaired incorrectly can result in chromosome rearrangements that drive cancer development. Here, we describe recent advances in the field of mitotic HR made using Caenorhabditis elegans roundworm, as a model system.
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7
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Meier B, Volkova NV, Wang B, González-Huici V, Bertolini S, Campbell PJ, Gerstung M, Gartner A. C. elegans genome-wide analysis reveals DNA repair pathways that act cooperatively to preserve genome integrity upon ionizing radiation. PLoS One 2021; 16:e0258269. [PMID: 34614038 PMCID: PMC8494335 DOI: 10.1371/journal.pone.0258269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
Ionizing radiation (IR) is widely used in cancer therapy and accidental or environmental exposure is a major concern. However, little is known about the genome-wide effects IR exerts on germ cells and the relative contribution of DNA repair pathways for mending IR-induced lesions. Here, using C. elegans as a model system and using primary sequencing data from our recent high-level overview of the mutagenic consequences of 11 genotoxic agents, we investigate in detail the genome-wide mutagenic consequences of exposing wild-type and 43 DNA repair and damage response defective C. elegans strains to a Caesium (Cs-137) source, emitting γ-rays. Cs-137 radiation induced single nucleotide variants (SNVs) at a rate of ~1 base substitution per 3 Gy, affecting all nucleotides equally. In nucleotide excision repair mutants, this frequency increased 2-fold concurrently with increased dinucleotide substitutions. As observed for DNA damage induced by bulky DNA adducts, small deletions were increased in translesion polymerase mutants, while base changes decreased. Structural variants (SVs) were augmented with dose, but did not arise with significantly higher frequency in any DNA repair mutants tested. Moreover, 6% of all mutations occurred in clusters, but clustering was not significantly altered in any DNA repair mutant background. Our data is relevant for better understanding how DNA repair pathways modulate IR-induced lesions.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Nadezda V. Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Bin Wang
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Víctor González-Huici
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Peter J. Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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8
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Zhang X, Tian S, Beese-Sims SE, Chen J, Shin N, Colaiácovo MP, Kim HM. Histone demethylase AMX-1 is necessary for proper sensitivity to interstrand crosslink DNA damage. PLoS Genet 2021; 17:e1009715. [PMID: 34329293 PMCID: PMC8357103 DOI: 10.1371/journal.pgen.1009715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/11/2021] [Accepted: 07/14/2021] [Indexed: 01/02/2023] Open
Abstract
Histone methylation is dynamically regulated to shape the epigenome and adjust central nuclear processes including transcription, cell cycle control and DNA repair. Lysine-specific histone demethylase 2 (LSD2) has been implicated in multiple types of human cancers. However, its functions remain poorly understood. This study investigated the histone demethylase LSD2 homolog AMX-1 in C. elegans and uncovered a potential link between H3K4me2 modulation and DNA interstrand crosslink (ICL) repair. AMX-1 is a histone demethylase and mainly localizes to embryonic cells, the mitotic gut and sheath cells. Lack of AMX-1 expression resulted in embryonic lethality, a decreased brood size and disorganized premeiotic tip germline nuclei. Expression of AMX-1 and of the histone H3K4 demethylase SPR-5 is reciprocally up-regulated upon lack of each other and the mutants show increased H3K4me2 levels in the germline, indicating that AMX-1 and SPR-5 regulate H3K4me2 demethylation. Loss of AMX-1 function activates the CHK-1 kinase acting downstream of ATR and leads to the accumulation of RAD-51 foci and increased DNA damage-dependent apoptosis in the germline. AMX-1 is required for the proper expression of mismatch repair component MutL/MLH-1 and sensitivity against ICLs. Interestingly, formation of ICLs lead to ubiquitination-dependent subcellular relocalization of AMX-1. Taken together, our data suggest that AMX-1 functions in ICL repair in the germline.
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Affiliation(s)
- Xiaojuan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Sisi Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Sara E. Beese-Sims
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jingjie Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Nara Shin
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Monica P. Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hyun-Min Kim
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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9
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Thakur M, Mohan D, Singh AK, Agarwal A, Gopal B, Muniyappa K. Novel insights into ATP-Stimulated Cleavage of branched DNA and RNA Substrates through Structure-Guided Studies of the Holliday Junction Resolvase RuvX. J Mol Biol 2021; 433:167014. [PMID: 33933468 DOI: 10.1016/j.jmb.2021.167014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022]
Abstract
Much of our understanding of the homologous recombination (HR) machinery hinges on studies using Escherichia coli as a model organism. Interestingly enough, studies on the HR machinery in different bacterial species casts doubt on the universality of the E. coli paradigm. The human pathogen Mycobacterium tuberculosis encodes two Holliday junction (HJ)-resolvase paralogues, namely RuvC and RuvX; however, insights into their structural features and functional relevance is still limited. Here, we report on structure-guided functional studies of the M. tuberculosis RuvX HJ resolvase (MtRuvX). The crystalline MtRuvX is a dimer in the asymmetric unit, and each monomer has a RNAse H fold vis-à-vis RuvC-like nucleases. Interestingly, MtRuvX also contains some unique features, including the residues essential for ATP binding/coordination of Mg2+ ions. Indeed, MtRuvX exhibited an intrinsic, robust ATPase activity, which was further accentuated by DNA cofactors. Structure-guided substitutions of single residues at the ATP binding/Mg2+coordination sites while markedly attenuating the ATPase activity completely abrogated HJ cleavage, indicating an unanticipated relationship between ATP hydrolysis and DNA cleavage. However, the affinity of ATPase-deficient mutants for the HJ was not impaired. Contrary to RuvC, MtRuvX exhibits relaxed substrate specificity, cleaving a variety of branched DNA/RNA substrates. Notably, ATP hydrolysis plays a regulatory role, rendering MtRuvX from a canonical HJ resolvase to a DNA/RNA non-sequence specific endonuclease, indicating a link between HJ resolvase and nucleic acid metabolism. These findings provide novel insights into the structure and dual-functional activities of MtRuvX, and suggest that it may play an important role in DNA/RNA metabolism.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Disha Mohan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankur Kumar Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ankit Agarwal
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | | | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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10
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Meier B, Volkova NV, Hong Y, Bertolini S, González-Huici V, Petrova T, Boulton S, Campbell PJ, Gerstung M, Gartner A. Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation. PLoS One 2021; 16:e0250291. [PMID: 33905417 PMCID: PMC8078821 DOI: 10.1371/journal.pone.0250291] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Maintaining genome integrity is particularly important in germ cells to ensure faithful transmission of genetic information across generations. Here we systematically describe germ cell mutagenesis in wild-type and 61 DNA repair mutants cultivated over multiple generations. ~44% of the DNA repair mutants analysed showed a >2-fold increased mutagenesis with a broad spectrum of mutational outcomes. Nucleotide excision repair deficiency led to higher base substitution rates, whereas polh-1(Polη) and rev-3(Polζ) translesion synthesis polymerase mutants resulted in 50-400 bp deletions. Signatures associated with defective homologous recombination fall into two classes: 1) brc-1/BRCA1 and rad-51/RAD51 paralog mutants showed increased mutations across all mutation classes, 2) mus-81/MUS81 and slx-1/SLX1 nuclease, and him-6/BLM, helq-1/HELQ or rtel-1/RTEL1 helicase mutants primarily accumulated structural variants. Repetitive and G-quadruplex sequence-containing loci were more frequently mutated in specific DNA repair backgrounds. Tandem duplications embedded in inverted repeats were observed in helq-1 helicase mutants, and a unique pattern of 'translocations' involving homeologous sequences occurred in rip-1 recombination mutants. atm-1/ATM checkpoint mutants harboured structural variants specifically enriched in subtelomeric regions. Interestingly, locally clustered mutagenesis was only observed for combined brc-1 and cep-1/p53 deficiency. Our study provides a global view of how different DNA repair pathways contribute to prevent germ cell mutagenesis.
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Affiliation(s)
- Bettina Meier
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Nadezda V. Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | - Simone Bertolini
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Tsvetana Petrova
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
| | | | - Peter J. Campbell
- Cancer, Ageing and Somatic Mutation Program, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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11
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Gartner A, Engebrecht J. DNA repair, recombination, and damage signaling. Genetics 2021; 220:6522877. [PMID: 35137093 PMCID: PMC9097270 DOI: 10.1093/genetics/iyab178] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.
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Affiliation(s)
- Anton Gartner
- Department for Biological Sciences, IBS Center for Genomic Integrity, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea,Corresponding author: (A.G.); (J.E.)
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA,Corresponding author: (A.G.); (J.E.)
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12
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Santonicola P, Germoglio M, d'Abbusco DS, Adamo A. Functional characterization of Caenorhabditis elegans cbs-2 gene during meiosis. Sci Rep 2020; 10:20913. [PMID: 33262405 PMCID: PMC7708620 DOI: 10.1038/s41598-020-78006-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
Cystathionine β-synthase (CBS) is a eukaryotic enzyme that maintains the cellular homocysteine homeostasis and catalyzes the conversion of homocysteine to L-cystathionine and Hydrogen sulfide, via the trans-sulfuration pathway. In Caenorhabditis elegans, two cbs genes are present: cbs-1 functions similarly as to human CBS, and cbs-2, whose roles are instead unknown. In the present study we performed a phenotypic characterization of the cbs-2 mutant. The null cbs-2 mutant is viable, fertile and shows the wild-type complement of six bivalents in most oocyte nuclei, which is indicative of a correct formation of crossover recombination. In absence of synaptonemal complex formation (syp-2 mutant), loss of cbs-2 leads to chromosome fragmentation, suggesting that cbs-2 is essential during inter-sister repair. Interestingly, although proficient in the activation of the DNA damage checkpoint after exposure to genotoxic stress, the cbs-2 mutant is defective in DNA damage-induced apoptosis in meiotic germ cells. These results suggest possible functions for CBS-2 in meiosis, distinct from a role in the trans-sulfuration pathway. We propose that the C. elegans CBS-2 protein is required for both inter-sister repair and execution of DNA damage-induced apoptosis.
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Affiliation(s)
- Pamela Santonicola
- Institute of Biosciences and BioResources, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Marcello Germoglio
- Institute of Biosciences and BioResources, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Domenico Scotto d'Abbusco
- Institute of Biosciences and BioResources, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Adele Adamo
- Institute of Biosciences and BioResources, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy.
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13
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Song J, Freeman AD, Knebel A, Gartner A, Lilley DM. Human ANKLE1 Is a Nuclease Specific for Branched DNA. J Mol Biol 2020; 432:5825-5834. [PMID: 32866453 PMCID: PMC7610144 DOI: 10.1016/j.jmb.2020.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 12/02/2022]
Abstract
All physical connections between sister chromatids must be broken before cells can divide, and eukaryotic cells have evolved multiple ways in which to process branchpoints connecting DNA molecules separated both spatially and temporally. A single DNA link between chromatids has the potential to disrupt cell cycle progression and genome integrity, so it is highly likely that cells require a nuclease that can process remaining unresolved and hemi-resolved DNA junctions and other branched species at the very late stages of mitosis. We argue that ANKLE1 probably serves this function in human cells (LEM-3 in Caenorhabditis elegans). LEM-3 has previously been shown to be located at the cell mid-body, and we show here that human ANKLE1 is a nuclease that cleaves a range of branched DNA species. It thus has the substrate selectivity consistent with an enzyme required to process a variety of unresolved and hemi-resolved branchpoints in DNA. Our results suggest that ANKLE1 acts as a catch-all enzyme of last resort that allows faithful chromosome segregation and cell division to occur.
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Affiliation(s)
- Junfang Song
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
| | - Alasdair D.J. Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Axel Knebel
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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14
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Bailly AP, Perrin A, Serrano-Macia M, Maghames C, Leidecker O, Trauchessec H, Martinez-Chantar ML, Gartner A, Xirodimas DP. The Balance between Mono- and NEDD8-Chains Controlled by NEDP1 upon DNA Damage Is a Regulatory Module of the HSP70 ATPase Activity. Cell Rep 2020; 29:212-224.e8. [PMID: 31577950 PMCID: PMC6899524 DOI: 10.1016/j.celrep.2019.08.070] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin and ubiquitin-like chains are finely balanced by conjugating and de-conjugating enzymes. Alterations in this balance trigger the response to stress conditions and are often observed in pathologies. How such changes are detected is not well understood. We identify the HSP70 chaperone as a sensor of changes in the balance between mono- and poly-NEDDylation. Upon DNA damage, the induction of the de-NEDDylating enzyme NEDP1 restricts the formation of NEDD8 chains, mainly through lysines K11/K48. This promotes APAF1 oligomerization and apoptosis induction, a step that requires the HSP70 ATPase activity. HSP70 binds to NEDD8, and, in vitro, the conversion of NEDD8 chains into mono-NEDD8 stimulates HSP70 ATPase activity. This effect is independent of NEDD8 conjugation onto substrates. The study indicates that the NEDD8 cycle is a regulatory module of HSP70 function. These findings may be important in tumorigenesis, as we find decreased NEDP1 levels in hepatocellular carcinoma with concomitant accumulation of NEDD8 conjugates. Restriction of NEDD8 chains by NEDP1 is required for DNA damage-induced apoptosis The HSP70 chaperone is a sensor of the balance between mono- and NEDD8 chains Mono-NEDD8 stimulates HSP70 activity, which allows the formation of the apoptosome NEDP1 levels are downregulated in mouse hepatocellular carcinoma
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Affiliation(s)
- Aymeric P Bailly
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France.
| | - Aurelien Perrin
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Marina Serrano-Macia
- Liver Disease Laboratory, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Chantal Maghames
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Orsolya Leidecker
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Helene Trauchessec
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - M L Martinez-Chantar
- Liver Disease Laboratory, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Anton Gartner
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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15
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Carranza-García E, Navarro RE. Insights Into the Hypometabolic Stage Caused by Prolonged Starvation in L4-Adult Caenorhabditis elegans Hermaphrodites. Front Cell Dev Biol 2020; 8:124. [PMID: 32211406 PMCID: PMC7057233 DOI: 10.3389/fcell.2020.00124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 02/12/2020] [Indexed: 11/24/2022] Open
Abstract
Animals alter their reproductive cycles in response to changing nutritional conditions, to ensure that offspring production only occurs under favorable circumstances. These adaptive strategies include reversible hypometabolic states of dormancy such as “arrest” and “diapause.” The free-living nematode Caenorhabditis elegans can arrest its life cycle during some larval stages without modifying its anatomy and physiology until conditions improve but it can also modify its morphological and physiological features to cope with harsh conditions and transition into diapause. The well-defined “dauer” diapause was described more than 40 years ago and has been the subject of comprehensive investigations. The existence of another hypometabolic state, termed adult reproductive diapause (ARD), has been debated after it was first described 10 years ago. Here, we review the current knowledge regarding the effect of food deprivation during the pre-reproductive larval and adult stages on overall organismal homeostasis, highlighting the implications on germ cell maintenance and fertility preservation.
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Affiliation(s)
- E Carranza-García
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosa E Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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16
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Zheleva A, Gómez-Orte E, Sáenz-Narciso B, Ezcurra B, Kassahun H, de Toro M, Miranda-Vizuete A, Schnabel R, Nilsen H, Cabello J. Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes.
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Affiliation(s)
- Angelina Zheleva
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Eva Gómez-Orte
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | | | - Begoña Ezcurra
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Henok Kassahun
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María de Toro
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, Germany
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Juan Cabello
- CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
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17
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Nuclear and cytoplasmic WDR-23 isoforms mediate differential effects on GEN-1 and SKN-1 substrates. Sci Rep 2019; 9:11783. [PMID: 31409866 PMCID: PMC6692315 DOI: 10.1038/s41598-019-48286-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/01/2019] [Indexed: 01/14/2023] Open
Abstract
Maintaining a healthy cellular environment requires the constant control of proteostasis. E3 ubiquitin ligase complexes facilitate the post-translational addition of ubiquitin, which based on the quantity and specific lysine linkages, results in different outcomes. Our studies reveal the CUL4-DDB1 substrate receptor, WDR23, as both a positive and a negative regulator in cellular stress responses. These opposing roles are mediated by two distinct isoforms: WDR-23A in the cytoplasm and WDR-23B in the nucleus. C. elegans expressing only WDR-23A display activation of SKN-1 and enhanced survival to oxidative stress, whereas animals with restricted WDR-23B expression do not. Additionally, we identify GEN-1, a Holliday junction resolvase, as an evolutionarily conserved WDR-23 substrate and find that the nuclear and cytoplasmic isoforms of WDR-23 differentially affect double-strand break repair. Our results suggest that through differential ubiquitination, nuclear WDR-23B inhibits the activity of substrates, most likely by promoting protein turnover, while cytoplasmic WDR-23A performs a proteasome-independent role. Together, our results establish a cooperative role between two spatially distinct isoforms of WDR-23 in ensuring proper regulation of WDR-23 substrates.
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18
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Carranza-García E, Navarro RE. Apoptosis contributes to protect germ cells from the oogenic germline starvation response but is not essential for the gonad shrinking or recovery observed during adult reproductive diapause in C. elegans. PLoS One 2019; 14:e0218265. [PMID: 31194813 PMCID: PMC6564024 DOI: 10.1371/journal.pone.0218265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/29/2019] [Indexed: 12/18/2022] Open
Abstract
When C. elegans hermaphrodites are deprived of food during the mid-L4 larval stage and throughout adulthood, they enter an alternative stage termed "adult reproductive diapause (ARD)" in which they halt reproduction and extend their lifespan. During ARD, germ cell proliferation stops; oogenesis is slowed; and the gonad shrinks progressively, which has been described as the "oogenic germline starvation response". Upon refeeding, the shrunken gonad is regenerated, and animals recover fertility and live out their remaining lifespan. Little is known about the effects of ARD on oocyte quality after ARD. Thus, the aim of this study was to determine how oocyte quality is affected after ARD by measuring brood size and embryonic lethality as a reflection of defective oocyte production. We found that ARD affects reproductive capacity. The oogenic germline starvation response protects oogenic germ cells by slowing oogenesis to prevent prolonged arrest in diakinesis. In contrast to a previous report, we found that germ cell apoptosis is not the cause of gonad shrinkage; instead, we propose that ovulation contributes to gonad shrinkage during the oogenic germline starvation response. We show that germ cell apoptosis increases and continues during ARD via lin-35/Rb and an unknown mechanism. Although apoptosis contributes to maintain germ cell quality during ARD, we demonstrated that apoptosis is not essential to preserve animal fertility. Finally, we show that IIS signaling inactivation partially participates in the oogenic germline starvation response.
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Affiliation(s)
- E. Carranza-García
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - R. E. Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail:
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19
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Qu M, Qiu Y, Lv R, Yue Y, Liu R, Yang F, Wang D, Li Y. Exposure to MPA-capped CdTe quantum dots causes reproductive toxicity effects by affecting oogenesis in nematode Caenorhabditis elegans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 173:54-62. [PMID: 30769203 DOI: 10.1016/j.ecoenv.2019.02.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/27/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Quantum dots (QDs), considered as a type of excellent semiconductor nanomaterial, are widely employed and have a number of important applications. However, QDs have the potential to produce adverse effects and toxicity with the underlying molecular mechanisms not well understood. Herein, Caenorhabditis elegans was used for in vivo toxicity assessment to detect the reproductive toxicity of CdTe QDs. We found that exposure to CdTe QDs particles (≥ 50 mg/L) resulted in a defect in reproductive capacity, dysfunctional proliferation and differentiation, as well as an imbalance in oogenesis by reducing the number of cells in pachytene and diakinesis. Further, we identified a SPO-11 and PCH-2 mediated toxic mechanism and a GLP-1/Notch mediated protective mechanism in response to CdTe QDs particles (≥ 50 mg/L). Taken together, these results demonstrate the potential adverse impact of CdTe QDs (≥ 50 mg/L) exposure on oogenesis and provide valuable data and guidelines for evaluation of QD biocompatibility.
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Affiliation(s)
- Man Qu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yuexiu Qiu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Rongrong Lv
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Ying Yue
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, 110 Xiangya Road, Changsha 410078, China
| | - Dayong Wang
- Medical School, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yunhui Li
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu 210009, China.
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20
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Kuzmic M, Galas S, Lecomte-Pradines C, Dubois C, Dubourg N, Frelon S. Interplay between ionizing radiation effects and aging in C. elegans. Free Radic Biol Med 2019; 134:657-665. [PMID: 30743047 DOI: 10.1016/j.freeradbiomed.2019.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/26/2022]
Abstract
Living species are chronically exposed to environmental ionizing radiations from sources that can be overexpressed by nuclear accidents. In invertebrates, reproduction is the most radiosensitive studied endpoint, likely to be connected with aging. Surprisingly, aging is a sparsely investigated endpoint after chronic ionizing radiation, whereas understanding it is of fundamental interest in biology and medicine. Indeed, aging and aging-related diseases (e.g., cancer and degenerative diseases) cause about 90% of deaths in developed countries. Therefore, glp-1 sterile Caenorhabditis elegans nematode was used to assess the impact of chronic gamma irradiation on the lifespan. Analyses were performed, at the individual level, on aging and, in order to delve deeper into the mechanisms, at the molecular level, on oxidative damage (carbonylation), biomolecules (lipids, proteins and nucleic acids) and their colocalization. We observed that ionizing radiation accelerates aging (whatever the duration (3-19 days)/dose (0.5-24 Gy)/dose rate (7 and 52 mGy h-1) tested) leading to a longevity value equivalent to that of wt nematode (∼25-30 days). Moreover, the level of protein oxidative damage (carbonylation) turned out to be good cellular biomarker of aging, since it increases with age. Conversely, chronic radiation treatments reduced carbonylation levels and induced neutral lipid catabolism whatever the dose rate and the final delivered dose. Finally, under some conditions a lipid-protein colocalization without any carbonyl was observed; this could be linked to yolk accumulation in glp-1 nematodes. To conclude, we noticed through this study a link between chronic gamma exposure, lifespan shortening and lipid level decrease associated with a decrease in the overall carbonylation.
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Affiliation(s)
- Mira Kuzmic
- Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, 13115, Saint Paul Lez Durance Cedex, France
| | - Simon Galas
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Catherine Lecomte-Pradines
- Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, 13115, Saint Paul Lez Durance Cedex, France
| | - Cécile Dubois
- Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, 13115, Saint Paul Lez Durance Cedex, France
| | - Nicolas Dubourg
- Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, 13115, Saint Paul Lez Durance Cedex, France
| | - Sandrine Frelon
- Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, 13115, Saint Paul Lez Durance Cedex, France.
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21
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Falquet B, Rass U. Structure-Specific Endonucleases and the Resolution of Chromosome Underreplication. Genes (Basel) 2019; 10:E232. [PMID: 30893921 PMCID: PMC6470701 DOI: 10.3390/genes10030232] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Complete genome duplication in every cell cycle is fundamental for genome stability and cell survival. However, chromosome replication is frequently challenged by obstacles that impede DNA replication fork (RF) progression, which subsequently causes replication stress (RS). Cells have evolved pathways of RF protection and restart that mitigate the consequences of RS and promote the completion of DNA synthesis prior to mitotic chromosome segregation. If there is entry into mitosis with underreplicated chromosomes, this results in sister-chromatid entanglements, chromosome breakage and rearrangements and aneuploidy in daughter cells. Here, we focus on the resolution of persistent replication intermediates by the structure-specific endonucleases (SSEs) MUS81, SLX1-SLX4 and GEN1. Their actions and a recently discovered pathway of mitotic DNA repair synthesis have emerged as important facilitators of replication completion and sister chromatid detachment in mitosis. As RS is induced by oncogene activation and is a common feature of cancer cells, any advances in our understanding of the molecular mechanisms related to chromosome underreplication have important biomedical implications.
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Affiliation(s)
- Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
- Faculty of Natural Sciences, University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland.
| | - Ulrich Rass
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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22
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Bae W, Hong S, Park MS, Jeong HK, Lee MH, Koo HS. Single-strand annealing mediates the conservative repair of double-strand DNA breaks in homologous recombination-defective germ cells of Caenorhabditis elegans. DNA Repair (Amst) 2019; 75:18-28. [PMID: 30710866 DOI: 10.1016/j.dnarep.2019.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 11/25/2022]
Abstract
A missense mutation in C. elegans RAD-54, a homolog of RAD54 that operates in the homologous recombination (HR) pathway, was found to decrease ATPase activity in vitro. The hypomorphic mutation caused hypersensitivity of C. elegans germ cells to double-strand DNA breaks (DSBs). Although the formation of RAD-51 foci at DSBs was normal in both the mutant and knockdown worms, their subsequent dissipation was slow. The rad-54-deficient phenotypes were greatly aggravated when combined with an xpf-1 mutation, suggesting a conservative role of single-strand annealing (SSA) for DSB repair in HR-defective worms. The phenotypes of doubly-deficient rad-54;xpf-1 worms were partially suppressed by a mutation of lig-4, a nonhomologous end-joining (NHEJ) factor. In summary, RAD-54 is required for the dissociation of RAD-51 from DSB sites in C. elegans germ cells. Also, NHEJ and SSA exert negative and positive effects, respectively, on genome stability when HR is defective.
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Affiliation(s)
- Woori Bae
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 03772, Seoul, Republic of Korea
| | - Seokbong Hong
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 03772, Seoul, Republic of Korea
| | - Mi So Park
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 03772, Seoul, Republic of Korea
| | - Ha-Kyeong Jeong
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 03772, Seoul, Republic of Korea
| | - Myon-Hee Lee
- Department of Medicine, Hematology/Oncology Division, Brody School of Medicine at East Carolina University, Greenville, NC, 27834, United States
| | - Hyeon-Sook Koo
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 03772, Seoul, Republic of Korea.
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23
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Liu Y, Freeman ADJ, Déclais AC, Lilley DMJ. A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1. Nucleic Acids Res 2018; 46:11089-11098. [PMID: 30247722 PMCID: PMC6237754 DOI: 10.1093/nar/gky863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 01/07/2023] Open
Abstract
GEN1 is a member of the FEN/EXO family of structure-selective nucleases that cleave 1 nt 3' to a variety of branchpoints. For each, the H2TH motif binds a monovalent ion and plays an important role in binding one helical arm of the substrates. We investigate here the importance of this metal ion on substrate specificity and GEN1 structure. In the presence of K+ ions the substrate specificity is wider than in Na+, yet four-way junctions remain the preferred substrate. In a combination of K+ and Mg2+ second strand cleavage is accelerated 17-fold, ensuring bilateral cleavage of the junction. We have solved crystal structures of Chaetomium thermophilum GEN1 with Cs+, K+ and Na+ bound. With bound Cs+ the loop of the H2TH motif extends toward the active site so that D199 coordinates a Mg2+, buttressed by an interaction of the adjacent Y200. With the lighter ions bound the H2TH loop changes conformation and retracts away from the active site. We hypothesize this conformational change might play a role in second strand cleavage acceleration.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alasdair DJ Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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24
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Hong Y, Velkova M, Silva N, Jagut M, Scheidt V, Labib K, Jantsch V, Gartner A. The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans. PLoS Genet 2018; 14:e1007453. [PMID: 29879106 PMCID: PMC6007928 DOI: 10.1371/journal.pgen.1007453] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 06/19/2018] [Accepted: 05/29/2018] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination is essential for crossover (CO) formation and accurate chromosome segregation during meiosis. It is of considerable importance to work out how recombination intermediates are processed, leading to CO and non-crossover (NCO) outcome. Genetic analysis in budding yeast and Caenorhabditis elegans indicates that the processing of meiotic recombination intermediates involves a combination of nucleases and DNA repair enzymes. We previously reported that in C. elegans meiotic joint molecule resolution is mediated by two redundant pathways, conferred by the SLX-1 and MUS-81 nucleases, and by the HIM-6 Bloom helicase in conjunction with the XPF-1 endonuclease, respectively. Both pathways require the scaffold protein SLX-4. However, in the absence of all these enzymes, residual processing of meiotic recombination intermediates still occurs and CO formation is reduced but not abolished. Here we show that the LEM-3 nuclease, mutation of which by itself does not have an overt meiotic phenotype, genetically interacts with slx-1 and mus-81 mutants, the respective double mutants displaying 100% embryonic lethality. The combined loss of LEM-3 and MUS-81 leads to altered processing of recombination intermediates, a delayed disassembly of foci associated with CO designated sites, and the formation of univalents linked by SPO-11 dependent chromatin bridges (dissociated bivalents). However, LEM-3 foci do not colocalize with ZHP-3, a marker that congresses into CO designated sites. In addition, neither CO frequency nor distribution is altered in lem-3 single mutants or in combination with mus-81 or slx-4 mutations. Finally, we found persistent chromatin bridges during meiotic divisions in lem-3; slx-4 double mutants. Supported by the localization of LEM-3 between dividing meiotic nuclei, this data suggest that LEM-3 is able to process erroneous recombination intermediates that persist into the second meiotic division.
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Affiliation(s)
- Ye Hong
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Maria Velkova
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Nicola Silva
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Marlène Jagut
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Viktor Scheidt
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Austria
| | - Anton Gartner
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, United Kingdom
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25
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Turcotte CA, Sloat SA, Rigothi JA, Rosenkranse E, Northrup AL, Andrews NP, Checchi PM. Maintenance of Genome Integrity by Mi2 Homologs CHD-3 and LET-418 in Caenorhabditis elegans. Genetics 2018; 208:991-1007. [PMID: 29339410 PMCID: PMC5844346 DOI: 10.1534/genetics.118.300686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/10/2018] [Indexed: 02/06/2023] Open
Abstract
Meiotic recombination depends upon the tightly coordinated regulation of chromosome dynamics and is essential for the production of haploid gametes. Central to this process is the formation and repair of meiotic double-stranded breaks (DSBs), which must take place within the constraints of a specialized chromatin architecture. Here, we demonstrate a role for the nucleosome remodeling and deacetylase (NuRD) complex in orchestrating meiotic chromosome dynamics in Caenorhabditis elegans Our data reveal that the conserved Mi2 homologs Chromodomain helicase DNA-binding protein (CHD-3) and its paralog LET-418 facilitate meiotic progression by ensuring faithful repair of DSBs through homologous recombination. We discovered that loss of either CHD-3 or LET-418 results in elevated p53-dependent germ line apoptosis, which relies on the activation of the conserved checkpoint kinase CHK-1 Consistent with these findings, chd-3 and let-418 mutants produce a reduced number of offspring, indicating a role for Mi2 in forming viable gametes. When Mi2 function is compromised, persisting recombination intermediates are detected in late pachytene nuclei, indicating a failure in the timely repair of DSBs. Intriguingly, our data indicate that in Mi2 mutant germ lines, a subset of DSBs are repaired by nonhomologous end joining, which manifests as chromosomal fusions. We find that meiotic defects are exacerbated in Mi2 mutants lacking CKU-80, as evidenced by increased recombination intermediates, corpses, and defects in chromosomal integrity. Taken together, our findings support a model wherein the C. elegans Mi2 complex maintains genomic integrity through reinforcement of a chromatin landscape suitable for homology-driven repair mechanisms.
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Affiliation(s)
| | - Solomon A Sloat
- Department of Biology, Marist College, Poughkeepsie, New York 12601
| | - Julia A Rigothi
- Department of Biology, Marist College, Poughkeepsie, New York 12601
| | | | | | | | - Paula M Checchi
- Department of Biology, Marist College, Poughkeepsie, New York 12601
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26
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Liu Y, Freeman A, Déclais AC, Gartner A, Lilley DMJ. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes. Methods Enzymol 2018; 600:543-568. [PMID: 29458774 DOI: 10.1016/bs.mie.2017.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Four-way Holliday junctions in DNA are the central intermediates of genetic recombination and must be processed into regular duplex species. One mechanism for achieving this is called resolution, brought about by structure-selective nucleases. GEN1 is an important junction-resolving enzyme in eukaryotic cells, a member of the FEN1/EXO1 superfamily of nucleases. While human GEN1 is difficult to work with because of aggregation, orthologs from thermophilic fungi have been identified using bioinformatics and have proved to have excellent properties. Here, the expression and purification of this enzyme from Chaetomium thermophilum is described, together with the means of investigating its biochemical properties. The enzyme is quite similar to junction-resolving enzymes from lower organisms, binding to junctions in dimeric form, introducing symmetrical bilateral cleavages, the second of which is accelerated to promote productive resolution. Crystallization of C. thermophilum GEN1 is described, and the structure of a DNA-product complex. Juxtaposition of complexes in the crystal lattice suggests how the structure of a dimeric enzyme with an intact junction is organized.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Alasdair Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom.
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27
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Abstract
Successful chromosome segregation depends on the timely removal of DNA recombination and replication intermediates that interlink sister chromatids. These intermediates are acted upon by structure-selective endonucleases that promote incisions close to the junction point. GEN1, a member of the Rad2/XPG endonuclease family, was identified on the basis of its ability to cleave Holliday junction recombination intermediates. Resolution occurs by a nick and counter-nick mechanism in strands that are symmetrically related across the junction point, leading to the formation of ligatable nicked duplex products. The actions of GEN1 are, however, not restricted to HJs, as 5'-flaps and replication fork structures also serve as excellent in vitro substrates for the nuclease. In the cellular context, GEN1 activity is observed late in the cell cycle, as most of the protein is excluded from the nucleus, such that it gains access to DNA intermediates after the breakdown of nuclear envelope. Nuclear exclusion ensures the protection of replication forks and other DNA secondary structures important for normal metabolic processes. In this chapter, we describe the purification of recombinant GEN1 and detail biochemical assays involving the use of synthetic DNA substrates and cruciform-containing plasmids.
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28
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Wang H, Zhang C, Wang X, Lian Y, Guo B, Han M, Zhang X, Zhu X, Xu S, Guo Z, Bi Y, Shen Q, Wang X, Liu J, Zhuang Y, Ni T, Xu H, Wu X. Disruption of Gen1 Causes Congenital Anomalies of the Kidney and Urinary Tract in Mice. Int J Biol Sci 2018; 14:10-20. [PMID: 29483821 PMCID: PMC5821045 DOI: 10.7150/ijbs.22768] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/02/2017] [Indexed: 01/20/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are among the most common developmental defects in humans. Despite of several known CAKUT-related loci (HNF1B, PAX2, EYA1, etc.), the genetic etiology of CAKUT remains to be elucidated for most patients. In this study, we report that disruption of the Holliday Junction resolvase gene Gen1 leads to renal agenesis, duplex kidney, hydronephrosis, and vesicoureteral reflux (VUR) in mice. GEN1 interacts with SIX1 and enhances the transcriptional activity of SIX1/EYA1, a key regulatory complex of the GDNF morphogen. Gen1 mutation impairs Grem1 and Gdnf expression, resulting in excessive ureteric bud formation and defective ureteric bud branching during early kidney development. These results revealed an unidentified role of GEN1 in kidney development and suggested its contribution to CAKUT.
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Affiliation(s)
- Herui Wang
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China.,Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chi Zhang
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Xiaowen Wang
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China.,Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430000, China
| | - Yaru Lian
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200433, China
| | - Bin Guo
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Miao Han
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200433, China
| | - Xiaoe Zhang
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaoting Zhu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Sixian Xu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zengli Guo
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yunli Bi
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Qian Shen
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiang Wang
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Jiaojiao Liu
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Yuan Zhuang
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ting Ni
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200433, China
| | - Hong Xu
- Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xiaohui Wu
- State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai 201102, China
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29
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Caenorhabditis elegans BUB-3 and SAN-1/MAD3 Spindle Assembly Checkpoint Components Are Required for Genome Stability in Response to Treatment with Ionizing Radiation. G3-GENES GENOMES GENETICS 2017; 7:3875-3885. [PMID: 29046436 PMCID: PMC5714485 DOI: 10.1534/g3.117.1122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Relatively little is known about the cross-talk between the spindle assembly checkpoint and the DNA damage response, especially in multicellular organisms. We performed a Caenorhabditis elegans forward genetic screen to uncover new genes involved in the repair of DNA damage induced by ionizing radiation. We isolated a mutation, gt2000, which confers hypersensitivity to ionizing radiation and showed that gt2000 introduces a premature stop in bub-3. BUB-3 is a key component of the spindle assembly checkpoint. We provide evidence that BUB-3 acts during development and in the germline; irradiated bub-3(gt2000) larvae are developmentally retarded and form abnormal vulvae. Moreover, bub-3(gt2000) embryos sired from irradiated worms show increased levels of lethality. Both bub-3 and san-1 (the C. elegans homolog of MAD3) deletion alleles confer hypersensitivity to ionizing radiation, consistent with the notion that the spindle assembly checkpoint pathway is required for the DNA damage response. bub-3(gt2000) is moderately sensitive to the cross-linking drug cisplatin but not to ultraviolet light or methyl methanesulfonate. This is consistent with a role in dealing with DNA double-strand breaks and not with base damage. Double mutant analysis revealed that bub-3 does not act within any of the three major pathways involved in the repair of double-strand breaks. Finally, the cdc-20 gain-of-function mutant cdc-20/fzy-1(av15), which is refractory to the cell cycle delay conferred by the spindle checkpoint, showed phenotypes similar to bub-3 and san-1 mutants. We speculate that BUB-3 is involved in the DNA damage response through regulation of cell cycle timing.
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30
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Herbette M, Mercier M, Michal F, Cluet D, Burny C, Yvert G, Robert V, Palladino F. The C. elegans SET-2/SET1 histone H3 Lys4 (H3K4) methyltransferase preserves genome stability in the germline. DNA Repair (Amst) 2017; 57:139-150. [DOI: 10.1016/j.dnarep.2017.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
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31
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González-Huici V, Wang B, Gartner A. A Role for the Nonsense-Mediated mRNA Decay Pathway in Maintaining Genome Stability in Caenorhabditis elegans. Genetics 2017; 206:1853-1864. [PMID: 28634159 PMCID: PMC5560793 DOI: 10.1534/genetics.117.203414] [Citation(s) in RCA: 10] [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: 04/28/2017] [Accepted: 06/05/2017] [Indexed: 12/31/2022] Open
Abstract
Ionizing radiation (IR) is commonly used in cancer therapy and is a main source of DNA double-strand breaks (DSBs), one of the most toxic forms of DNA damage. We have used Caenorhabditis elegans as an invertebrate model to identify novel factors required for repair of DNA damage inflicted by IR. We have performed an unbiased genetic screen, finding that smg-1 mutations confer strong hyper-sensitivity to IR. SMG-1 is a phosphoinositide-3 kinase (PI3K) involved in mediating nonsense-mediated mRNA decay (NMD) of transcripts containing premature stop codons and related to the ATM and ATR kinases which are at the apex of DNA damage signaling pathways. Hyper-sensitivity to IR also occurs when other genes mediating NMD are mutated. The hyper-sensitivity to bleomycin, a drug known to induce DSBs, further supports that NMD pathway mutants are defective in DSB repair. Hyper-sensitivity was not observed upon treatment with alkylating agents or UV irradiation. We show that SMG-1 mainly acts in mitotically dividing germ cells, and during late embryonic and larval development. Based on epistasis experiments, SMG-1 does not appear to act in any of the three major pathways known to mend DNA DSBs, namely homologous recombination (HR), nonhomologous end-joining (NHEJ), and microhomology-mediated end-joining (MMEJ). We speculate that SMG-1 kinase activity could be activated following DNA damage to phosphorylate specific DNA repair proteins and/or that NMD inactivation may lead to aberrant mRNAs leading to synthesis of malfunctioning DNA repair proteins.
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Affiliation(s)
- Víctor González-Huici
- School of Life Sciences, Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
| | - Bin Wang
- School of Life Sciences, Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
| | - Anton Gartner
- School of Life Sciences, Centre for Gene Regulation and Expression, University of Dundee, DD1 5EH, UK
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32
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Lilley DMJ. Holliday junction-resolving enzymes-structures and mechanisms. FEBS Lett 2017; 591:1073-1082. [PMID: 27990631 DOI: 10.1002/1873-3468.12529] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Holliday junction-resolving enzymes are nucleases that are highly specific for the structure of the junction, to which they bind in dimeric form. Two symmetrically disposed cleavages are made. These are not simultaneous, but the second cleavage is accelerated relative to the first, so ensuring that bilateral cleavage occurs during the lifetime of the DNA-protein complex. In eukaryotic cells there are two known junction-resolving activities. GEN1 is similar to enzymes from lower organisms. A crystallographic structure of a fungal GEN1 bound to the product of resolution has been determined. These complexes are dimerized within the crystal lattice such that the strands of the products may be simply reconnected to form a junction. These structures suggest a trajectory for the resolution process.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, UK
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33
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Dehé PM, Gaillard PHL. Control of structure-specific endonucleases to maintain genome stability. Nat Rev Mol Cell Biol 2017; 18:315-330. [PMID: 28327556 DOI: 10.1038/nrm.2016.177] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-specific endonucleases (SSEs) have key roles in DNA replication, recombination and repair, and emerging roles in transcription. These enzymes have specificity for DNA secondary structure rather than for sequence, and therefore their activity must be precisely controlled to ensure genome stability. In this Review, we discuss how SSEs are controlled as part of genome maintenance pathways in eukaryotes, with an emphasis on the elaborate mechanisms that regulate the members of the major SSE families - including the xeroderma pigmentosum group F-complementing protein (XPF) and MMS and UV-sensitive protein 81 (MUS81)-dependent nucleases, and the flap endonuclease 1 (FEN1), XPG and XPG-like endonuclease 1 (GEN1) enzymes - during processes such as DNA adduct repair, Holliday junction processing and replication stress. We also discuss newly characterized connections between SSEs and other classes of DNA-remodelling enzymes and cell cycle control machineries, which reveal the importance of SSE scaffolds such as the synthetic lethal of unknown function 4 (SLX4) tumour suppressor for the maintenance of genome stability.
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Affiliation(s)
- Pierre-Marie Dehé
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
| | - Pierre-Henri L Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, CNRS, Aix Marseille Université, INSERM, Institut Paoli-Calmettes, 27 Boulevard Leï Roure, 13009 Marseille, France
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34
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Caenorhabditis elegans as a powerful alternative model organism to promote research in genetic toxicology and biomedicine. Arch Toxicol 2017; 91:2029-2044. [PMID: 28299394 DOI: 10.1007/s00204-017-1944-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/23/2017] [Indexed: 12/20/2022]
Abstract
In view of increased life expectancy the risk for disturbed integrity of genetic information increases. This inevitably holds the implication for higher incidence of age-related diseases leading to considerable cost increase in health care systems. To develop preventive strategies it is crucial to evaluate external and internal noxae as possible threats to our DNA. Especially the interplay of DNA damage response (DDR) and DNA repair (DR) mechanisms needs further deciphering. Moreover, there is a distinct need for alternative in vivo test systems for basic research and also risk assessment in toxicology. Especially the evaluation of combinational toxicity of environmentally present genotoxins and adverse effects of clinically used DNA damaging anticancer drugs is a major challenge for modern toxicology. This review focuses on the applicability of Caenorhabditis elegans as a model organism to unravel and tackle scientific questions related to the biological consequences of genotoxin exposure and highlights methods for studying DDR and DR. In this regard large-scale in vivo screens of mixtures of chemicals and extensive parallel sequencing are highlighted as unique advantages of C. elegans. In addition, concise information regarding evolutionary conserved molecular mechanisms of the DDR and DR as well as currently available data obtained from the use of prototypical genotoxins and preferential read-outs of genotoxin testing are discussed. The use of established protocols, which are already available in the community, is encouraged to facilitate and further improve the implementation of C. elegans as a powerful genetic model system in genetic toxicology and biomedicine.
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35
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Wang C, Higgins JD, He Y, Lu P, Zhang D, Liang W. Resolvase OsGEN1 Mediates DNA Repair by Homologous Recombination. PLANT PHYSIOLOGY 2017; 173:1316-1329. [PMID: 28049740 PMCID: PMC5291025 DOI: 10.1104/pp.16.01726] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/29/2016] [Indexed: 05/18/2023]
Abstract
Yen1/GEN1 are canonical Holliday junction resolvases that belong to the RAD2/XPG family. In eukaryotes, such as budding yeast, mice, worms, and humans, Yen1/GEN1 work together with Mus81-Mms4/MUS81-EME1 and Slx1-Slx4/SLX1-SLX4 in DNA repair by homologous recombination to maintain genome stability. In plants, the biological function of Yen1/GEN1 remains largely unclear. In this study, we characterized the loss of function mutants of OsGEN1 and OsSEND1, a pair of paralogs of Yen1/GEN1 in rice (Oryza sativa). We first investigated the role of OsGEN1 during meiosis and found a reduction in chiasma frequency by ∼6% in osgen1 mutants, compared to the wild type, suggesting a possible involvement of OsGEN1 in the formation of crossovers. Postmeiosis, OsGEN1 foci were detected in wild-type microspore nuclei, but not in the osgen1 mutant concomitant with an increase in double-strand breaks. Persistent double-strand breaks led to programmed cell death of the male gametes and complete male sterility. In contrast, depletion of OsSEND1 had no effects on plant development and did not enhance osgen1 defects. Our results indicate that OsGEN1 is essential for homologous recombinational DNA repair at two stages of microsporogenesis in rice.
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Affiliation(s)
- Chong Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - James D Higgins
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Yi He
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Pingli Lu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.)
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China (C.W., Y.H., D.Z., W.L.);
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom (J.D.H.);
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (P.L.); and
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia 5064, Australia (D.Z.)
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Amendola PG, Zaghet N, Ramalho JJ, Vilstrup Johansen J, Boxem M, Salcini AE. JMJD-5/KDM8 regulates H3K36me2 and is required for late steps of homologous recombination and genome integrity. PLoS Genet 2017; 13:e1006632. [PMID: 28207814 PMCID: PMC5336306 DOI: 10.1371/journal.pgen.1006632] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 03/03/2017] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
The eukaryotic genome is organized in a three-dimensional structure called chromatin, constituted by DNA and associated proteins, the majority of which are histones. Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes. Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair. Here, we show that the JMJD-5 regulates H3K36 di-methylation and it is required at late stages of double strand break repair mediated by homologous recombination. Loss of jmjd-5 results in hypersensitivity to ionizing radiation and in meiotic defects, and it is associated with aberrant retention of RAD-51 at sites of double strand breaks. Analyses of jmjd-5 genetic interactions with genes required for resolving recombination intermediates (rtel-1) or promoting the resolution of RAD-51 double stranded DNA filaments (rfs-1 and helq-1) suggest that jmjd-5 prevents the formation of stalled postsynaptic recombination intermediates and favors RAD-51 removal. As these phenotypes are all recapitulated by a catalytically inactive jmjd-5 mutant, we propose a novel role for H3K36me2 regulation during late steps of homologous recombination critical to preserve genome integrity.
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Affiliation(s)
- Pier Giorgio Amendola
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Nico Zaghet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - João J. Ramalho
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Mike Boxem
- Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
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Reichman R, Alleva B, Smolikove S. Prophase I: Preparing Chromosomes for Segregation in the Developing Oocyte. Results Probl Cell Differ 2017; 59:125-173. [PMID: 28247048 DOI: 10.1007/978-3-319-44820-6_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Formation of an oocyte involves a specialized cell division termed meiosis. In meiotic prophase I (the initial stage of meiosis), chromosomes undergo elaborate events to ensure the proper segregation of their chromosomes into gametes. These events include processes leading to the formation of a crossover that, along with sister chromatid cohesion, forms the physical link between homologous chromosomes. Crossovers are formed as an outcome of recombination. This process initiates with programmed double-strand breaks that are repaired through the use of homologous chromosomes as a repair template. The accurate repair to form crossovers takes place in the context of the synaptonemal complex, a protein complex that links homologous chromosomes in meiotic prophase I. To allow proper execution of meiotic prophase I events, signaling processes connect different steps in recombination and synapsis. The events occurring in meiotic prophase I are a prerequisite for proper chromosome segregation in the meiotic divisions. When these processes go awry, chromosomes missegregate. These meiotic errors are thought to increase with aging and may contribute to the increase in aneuploidy observed in advanced maternal age female oocytes.
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Affiliation(s)
- Rachel Reichman
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Benjamin Alleva
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Sarit Smolikove
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA.
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McClendon TB, Mainpal R, Amrit FRG, Krause MW, Ghazi A, Yanowitz JL. X Chromosome Crossover Formation and Genome Stability in Caenorhabditis elegans Are Independently Regulated by xnd-1. G3 (BETHESDA, MD.) 2016; 6:3913-3925. [PMID: 27678523 PMCID: PMC5144962 DOI: 10.1534/g3.116.035725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/21/2016] [Indexed: 01/19/2023]
Abstract
The germ line efficiently combats numerous genotoxic insults to ensure the high fidelity propagation of unaltered genomic information across generations. Yet, germ cells in most metazoans also intentionally create double-strand breaks (DSBs) to promote DNA exchange between parental chromosomes, a process known as crossing over. Homologous recombination is employed in the repair of both genotoxic lesions and programmed DSBs, and many of the core DNA repair proteins function in both processes. In addition, DNA repair efficiency and crossover (CO) distribution are both influenced by local and global differences in chromatin structure, yet the interplay between chromatin structure, genome integrity, and meiotic fidelity is still poorly understood. We have used the xnd-1 mutant of Caenorhabditis elegans to explore the relationship between genome integrity and crossover formation. Known for its role in ensuring X chromosome CO formation and germ line development, we show that xnd-1 also regulates genome stability. xnd-1 mutants exhibited a mortal germ line, high embryonic lethality, high incidence of males, and sensitivity to ionizing radiation. We discovered that a hypomorphic allele of mys-1 suppressed these genome instability phenotypes of xnd-1, but did not suppress the CO defects, suggesting it serves as a separation-of-function allele. mys-1 encodes a histone acetyltransferase, whose homolog Tip60 acetylates H2AK5, a histone mark associated with transcriptional activation that is increased in xnd-1 mutant germ lines, raising the possibility that thresholds of H2AK5ac may differentially influence distinct germ line repair events. We also show that xnd-1 regulated him-5 transcriptionally, independently of mys-1, and that ectopic expression of him-5 suppressed the CO defects of xnd-1 Our work provides xnd-1 as a model in which to study the link between chromatin factors, gene expression, and genome stability.
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Affiliation(s)
- T Brooke McClendon
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pennsylvania
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Services University of Pittsburgh School of Medicine, Pennsylvania 15213
| | - Rana Mainpal
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Services University of Pittsburgh School of Medicine, Pennsylvania 15213
| | - Francis R G Amrit
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pennsylvania 15224
| | - Michael W Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892
| | - Arjumand Ghazi
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pennsylvania 15224
| | - Judith L Yanowitz
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pennsylvania
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Services University of Pittsburgh School of Medicine, Pennsylvania 15213
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Ackermann L, Schell M, Pokrzywa W, Kevei É, Gartner A, Schumacher B, Hoppe T. E4 ligase-specific ubiquitination hubs coordinate DNA double-strand-break repair and apoptosis. Nat Struct Mol Biol 2016; 23:995-1002. [PMID: 27669035 PMCID: PMC5349472 DOI: 10.1038/nsmb.3296] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/19/2016] [Indexed: 12/26/2022]
Abstract
Multiple protein ubiquitination events at DNA double-strand breaks (DSBs) regulate damage recognition, signaling and repair. It has remained poorly understood how the repair process of DSBs is coordinated with the apoptotic response. Here, we identified the E4 ubiquitin ligase UFD-2 as a mediator of DNA-damage-induced apoptosis in a genetic screen in Caenorhabditis elegans. We found that, after initiation of homologous recombination by RAD-51, UFD-2 forms foci that contain substrate-processivity factors including the ubiquitin-selective segregase CDC-48 (p97), the deubiquitination enzyme ATX-3 (Ataxin-3) and the proteasome. In the absence of UFD-2, RAD-51 foci persist, and DNA damage-induced apoptosis is prevented. In contrast, UFD-2 foci are retained until recombination intermediates are removed by the Holliday-junction-processing enzymes GEN-1, MUS-81 or XPF-1. Formation of UFD-2 foci also requires proapoptotic CEP-1 (p53) signaling. Our findings establish a central role of UFD-2 in the coordination between the DNA-repair process and the apoptotic response.
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Affiliation(s)
- Leena Ackermann
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
| | - Michael Schell
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
| | - Wojciech Pokrzywa
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
| | - Éva Kevei
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
| | - Anton Gartner
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee Scotland
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
- CECAD Research Center and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and CECAD Research Center, University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
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40
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Wu Y, Qian Y, Zhou G, Lv J, Yan Q, Dong X. Effect of GEN1 interference on the chemosensitivity of the breast cancer MCF-7 and SKBR3 cell lines. Oncol Lett 2016; 11:3597-3604. [PMID: 27284361 PMCID: PMC4887781 DOI: 10.3892/ol.2016.4489] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/01/2016] [Indexed: 12/20/2022] Open
Abstract
Chemotherapy is a notable method for the treatment of breast cancer. Numerous genes associated with the sensitivity of cancer to chemotherapy have been found. In recent years, evidence has suggested that a particular structure termed Holliday junction (HJ) plays a crucial role in cancer chemosensitivity. Targeting HJ resolvases, such as structure-specific endonuclease subunit SLX4 (Slx4) and MUS81 structure-specific endonuclease subunit (Mus81), significantly increases the chemosensitivity of tumor cells. Flap endonuclease GEN homolog 1 (GEN1) is a HJ resolvase that belongs to the Rad2/xeroderma pigmentosum complementation group G nuclease family. Whether GEN1 affects the chemosensitivity of tumor cells in a similar manner to Slx4 and Mus81 remains unknown. The aim of the present study was to determine the effect of GEN1 interference on the chemosensitivity of breast cancer cell lines. The investigation of the function of GEN1 was performed using MCF-7 and SKBR3 cells. Short hairpin RNA was used to suppress the expression of GEN1, and western blot analysis and reverse transcription-quantitative polymerase chain reaction were used to detect gene expression. In addition, a cell counting kit-8 assay was performed to detect the viability of cells and flow cytometry was performed to test apoptosis levels. Suppression of GEN1 in SKBR3 cells effectively increased the sensitivity to the chemotherapeutic drug 5-fluorouracil (5-FU), while MCF-7 cells showed no significant change in sensitivity following GEN1 suppression. However, when GEN1 was targeted in addition to Mus81, the MCF-7 cells also demonstrated a significantly increased sensitivity to 5-FU. In addition, when the level of Mus81 was low, GEN1 expression was increased under a low concentration of 5-FU. The present results suggest that GEN1 may play different roles in different breast cancer cell lines. The function of GEN1 may be affected by the level of Mus81 in the cell line. In addition, GEN1 interference may improve the sensitivity to chemotherapy induced by targeting Mus81 alone.
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Affiliation(s)
- Yunlu Wu
- Clinical Laboratory Center, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang 312000, P.R. China; The Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ying Qian
- Clinical Laboratory Center, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang 312000, P.R. China
| | - Guozhong Zhou
- Clinical Laboratory Center, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang 312000, P.R. China
| | - Juan Lv
- Clinical Laboratory Center, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang 312000, P.R. China
| | - Qiuyue Yan
- Clinical Laboratory Center, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang 312000, P.R. China; The Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Xuejun Dong
- Clinical Laboratory Center, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang 312000, P.R. China; The Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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41
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Cinquin A, Chiang M, Paz A, Hallman S, Yuan O, Vysniauskaite I, Fowlkes CC, Cinquin O. Intermittent Stem Cell Cycling Balances Self-Renewal and Senescence of the C. elegans Germ Line. PLoS Genet 2016; 12:e1005985. [PMID: 27077385 PMCID: PMC4831802 DOI: 10.1371/journal.pgen.1005985] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/18/2016] [Indexed: 11/22/2022] Open
Abstract
Self-renewing organs often experience a decline in function in the course of aging. It is unclear whether chronological age or external factors control this decline, or whether it is driven by stem cell self-renewal—for example, because cycling cells exhaust their replicative capacity and become senescent. Here we assay the relationship between stem cell cycling and senescence in the Caenorhabditis elegans reproductive system, defining this senescence as the progressive decline in “reproductive capacity,” i.e. in the number of progeny that can be produced until cessation of reproduction. We show that stem cell cycling diminishes remaining reproductive capacity, at least in part through the DNA damage response. Paradoxically, gonads kept under conditions that preclude reproduction keep cycling and producing cells that undergo apoptosis or are laid as unfertilized gametes, thus squandering reproductive capacity. We show that continued activity is in fact beneficial inasmuch as gonads that are active when reproduction is initiated have more sustained early progeny production. Intriguingly, continued cycling is intermittent—gonads switch between active and dormant states—and in all likelihood stochastic. Other organs face tradeoffs whereby stem cell cycling has the beneficial effect of providing freshly-differentiated cells and the detrimental effect of increasing the likelihood of cancer or senescence; stochastic stem cell cycling may allow for a subset of cells to preserve proliferative potential in old age, which may implement a strategy to deal with uncertainty as to the total amount of proliferation to be undergone over an organism’s lifespan. Stem cell cycling is expected to be beneficial because it helps delay aging, by ensuring organ self-renewal. Yet stem cell cycling is best used sparingly: cycling likely causes mutation accumulation—increasing the likelihood of cancer—and may eventually cause stem cells to senesce and thus stop contributing to organ self renewal. It is unknown how self-renewing organs make tradeoffs between benefits and drawbacks of stem cell cycling. Here we use the C. elegans reproductive system as a model organ. We characterize benefits and drawbacks of stem cell cycling—which are keeping worms primed for reproduction, and reducing the number of future progeny worms may bear, respectively. We show that, under specific conditions of reproductive inactivity, stem cells switch back and forth between active and dormant states; the timing of these switches, whose genetic control we start delineating, appears random. This randomness may help explain why populations of aging, reproductively-inactive worms experience an increase in the variability of their reproductive capacity. Stochastic stem cell cycling may underlie tradeoffs between self-renewal and senescence in other organs.
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Affiliation(s)
- Amanda Cinquin
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Michael Chiang
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Adrian Paz
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Sam Hallman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California, Irvine, Irvine, California, United States of America
| | - Oliver Yuan
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Indre Vysniauskaite
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Charless C. Fowlkes
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California, Irvine, Irvine, California, United States of America
| | - Olivier Cinquin
- Department of Developmental & Cell Biology, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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42
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Wild P, Matos J. Cell cycle control of DNA joint molecule resolution. Curr Opin Cell Biol 2016; 40:74-80. [PMID: 26970388 DOI: 10.1016/j.ceb.2016.02.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/02/2016] [Accepted: 02/19/2016] [Indexed: 12/01/2022]
Abstract
The establishment of stable interactions between chromosomes underpins vital cellular processes such as recombinational DNA repair and bipolar chromosome segregation. On the other hand, timely disengagement of persistent connections is necessary to assure efficient partitioning of the replicated genome prior to cell division. Whereas great progress has been made in defining how cohesin-mediated chromosomal interactions are disengaged as cells prepare to undergo chromosome segregation, little is known about the metabolism of DNA joint molecules (JMs), generated during the repair of chromosomal lesions. Recent work on Mus81 and Yen1/GEN1, two conserved structure-selective endonucleases, revealed unforeseen links between JM-processing and cell cycle progression. Cell cycle kinases and phosphatases control Mus81 and Yen1/GEN1 to restrain deleterious JM-processing during S-phase, while safeguarding chromosome segregation during mitosis.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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43
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Olivier M, Da Ines O, Amiard S, Serra H, Goubely C, White CI, Gallego ME. The Structure-Specific Endonucleases MUS81 and SEND1 Are Essential for Telomere Stability in Arabidopsis. THE PLANT CELL 2016; 28:74-86. [PMID: 26704385 PMCID: PMC4746687 DOI: 10.1105/tpc.15.00898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/23/2015] [Indexed: 05/02/2023]
Abstract
Structure-specific endonucleases act to repair potentially toxic structures produced by recombination and DNA replication, ensuring proper segregation of the genetic material to daughter cells during mitosis and meiosis. Arabidopsis thaliana has two putative homologs of the resolvase (structure-specific endonuclease): GEN1/Yen1. Knockout of resolvase genes GEN1 and SEND1, individually or together, has no detectable effect on growth, fertility, or sensitivity to DNA damage. However, combined absence of the endonucleases MUS81 and SEND1 results in severe developmental defects, spontaneous cell death, and genome instability. A similar effect is not seen in mus81 gen1 plants, which develop normally and are fertile. Absence of RAD51 does not rescue mus81 send1, pointing to roles of these proteins in DNA replication rather than DNA break repair. The enrichment of S-phase histone γ-H2AX foci and a striking loss of telomeric DNA in mus81 send1 further support this interpretation. SEND1 has at most a minor role in resolution of the Holliday junction but acts as an essential backup to MUS81 for resolution of toxic replication structures to ensure genome stability and to maintain telomere integrity.
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Affiliation(s)
- Margaux Olivier
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Olivier Da Ines
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Simon Amiard
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Heïdi Serra
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Chantal Goubely
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
| | - Maria E Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, 63000 Clermont-Ferrand, France
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Liu Y, Freeman ADJ, Déclais AC, Wilson TJ, Gartner A, Lilley DMJ. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA. Cell Rep 2015; 13:2565-2575. [PMID: 26686639 PMCID: PMC4695337 DOI: 10.1016/j.celrep.2015.11.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/04/2015] [Accepted: 11/11/2015] [Indexed: 11/25/2022] Open
Abstract
We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. GEN1 crystallized with a resolution product containing two perpendicular DNA helices GEN1 shares the FEN1 superfamily fold, with a two-metal ion-containing active site GEN1 forms a dimer that juxtaposes two products in a substrate-like complex A resulting model of a GEN1-junction complex is supported by solution experiments
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alasdair D J Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anton Gartner
- Center for Gene Regulation and Expression, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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45
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Kim HM, Colaiácovo MP. DNA Damage Sensitivity Assays in Caenorhabditis elegans. Bio Protoc 2015; 5:e1487. [PMID: 26807430 PMCID: PMC4723109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
C. elegans has served as a genetically tractable multicellular model system to examine DNA damage-induced genotoxic stress which threatens genome integrity. Importantly, the high degree of conservation shared between worms and humans offers the advantage that findings about DNA damage-induced cell cycle arrest/checkpoint response and DNA double-strand break repair in worms are applicable to human studies. Here, we describe simple DNA damage sensitivity assays to quantify the response of C. elegans to diverse types of DNA damaging agents. These assays have provided important insights into the mechanisms of function for factors such as ZTF-8 that are involved in DNA damage repair and response in the C. elegans germline. These DNA damage sensitivity assays rely on the straightforward readouts of either egg or larval lethality and involve the use of various DNA damaging agents. We use γ-irradiation (γ-IR), which produces DNA double-strand breaks (DSBs), camptothecin (CPT), which induces single-strand breaks, nitrogen mustard (HN2), which produces interstrand crosslinks (ICLs), hydroxyurea (HU), which results in replication fork arrest thus preventing DNA synthesis, and UV-C, which causes photoproducts (pyrimidine dimers). See Table 1. Comparisons between the relative sensitivity/resistance observed in, for example, mutants compared to wild type, for various DNA damaging agents allows for inferences regarding potential repair pathways being affected.
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46
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Krol K, Brozda I, Skoneczny M, Bretne M, Skoneczna A. A genomic screen revealing the importance of vesicular trafficking pathways in genome maintenance and protection against genotoxic stress in diploid Saccharomyces cerevisiae cells. PLoS One 2015; 10:e0120702. [PMID: 25756177 PMCID: PMC4355298 DOI: 10.1371/journal.pone.0120702] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/25/2015] [Indexed: 11/30/2022] Open
Abstract
The ability to survive stressful conditions is important for every living cell. Certain stresses not only affect the current well-being of cells but may also have far-reaching consequences. Uncurbed oxidative stress can cause DNA damage and decrease cell survival and/or increase mutation rates, and certain substances that generate oxidative damage in the cell mainly act on DNA. Radiomimetic zeocin causes oxidative damage in DNA, predominantly by inducing single- or double-strand breaks. Such lesions can lead to chromosomal rearrangements, especially in diploid cells, in which the two sets of chromosomes facilitate excessive and deleterious recombination. In a global screen for zeocin-oversensitive mutants, we selected 133 genes whose deletion reduces the survival of zeocin-treated diploid Saccharomyces cerevisiae cells. The screen revealed numerous genes associated with stress responses, DNA repair genes, cell cycle progression genes, and chromatin remodeling genes. Notably, the screen also demonstrated the involvement of the vesicular trafficking system in cellular protection against DNA damage. The analyses indicated the importance of vesicular system integrity in various pathways of cellular protection from zeocin-dependent damage, including detoxification and a direct or transitional role in genome maintenance processes that remains unclear. The data showed that deleting genes involved in vesicular trafficking may lead to Rad52 focus accumulation and changes in total DNA content or even cell ploidy alterations, and such deletions may preclude proper DNA repair after zeocin treatment. We postulate that functional vesicular transport is crucial for sustaining an integral genome. We believe that the identification of numerous new genes implicated in genome restoration after genotoxic oxidative stress combined with the detected link between vesicular trafficking and genome integrity will reveal novel molecular processes involved in genome stability in diploid cells.
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Affiliation(s)
- Kamil Krol
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Izabela Brozda
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Maria Bretne
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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Freeman ADJ, Liu Y, Déclais AC, Gartner A, Lilley DMJ. GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes. J Mol Biol 2014; 426:3946-3959. [PMID: 25315822 PMCID: PMC4270448 DOI: 10.1016/j.jmb.2014.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/28/2022]
Abstract
Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1nt 3' to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1.
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Affiliation(s)
- Alasdair D J Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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Buisset-Goussen A, Goussen B, Della-Vedova C, Galas S, Adam-Guillermin C, Lecomte-Pradines C. Effects of chronic gamma irradiation: a multigenerational study using Caenorhabditis elegans. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2014; 137:190-197. [PMID: 25102824 DOI: 10.1016/j.jenvrad.2014.07.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 05/24/2023]
Abstract
The effects of chronic exposure to (137)Cs gamma radiation (dose rate ranging from 6.6 to 42.7 mGy h(-1)) on growth and reproductive ability were carried out over three generations of Caenorhabditis elegans (F0, F1, and F2). Exposure began at the egg stage for the first generation and was stopped at the end of laying of third-generation eggs (F2). At the same time, the two subsequent generations from parental exposure were returned to the control conditions (F1' and F2'). There was no radiation-induced significant effect on growth, hatchability, and cumulative number of larvae within generations. Moreover, no significant differences were found in growth parameters (hatching length, maximal length, and a constant related to growth rate) among the generations. However, a decrease in the cumulative number of larvae across exposed generations was observed between F0 and F2 at the highest dose rate (238.8 ± 15.4 and 171.2 ± 13.1 number of larvae per individual, respectively). Besides, the F1' generation was found to lay significantly fewer eggs than the F1 generation for tested dose rates 6.6, 8.1, 19.4, and 28.1 mGy h(-1). Our results confirmed that reproduction (here, cumulative number of larvae) is the most sensitive endpoint affected by chronic exposure to ionizing radiation. The results obtained revealed transgenerational effects from parental exposure in the second generation, and the second non-exposed generation was indeed more affected than the second exposed generation.
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Affiliation(s)
- Adeline Buisset-Goussen
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SERIS, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France.
| | - Benoit Goussen
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SERIS, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France; Unité Modèles pour l'Ecotoxicologie et la Toxicologie (METO), Institut National de l'Environnement Industriel et des Risques (INERIS), BP2, F-60550 Verneuil en Halatte, France
| | | | - Simon Galas
- Université Montpellier1, Faculté de Pharmacie, Laboratoire de Toxicologie, 15, Avenue Charles Flahault BP 14491, 34093 Montpellier Cedex 5, France
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SERIS, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France
| | - Catherine Lecomte-Pradines
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SERIS, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France
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Kim HM, Colaiácovo MP. ZTF-8 interacts with the 9-1-1 complex and is required for DNA damage response and double-strand break repair in the C. elegans germline. PLoS Genet 2014; 10:e1004723. [PMID: 25329393 PMCID: PMC4199516 DOI: 10.1371/journal.pgen.1004723] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/29/2014] [Indexed: 11/19/2022] Open
Abstract
Germline mutations in DNA repair genes are linked to tumor progression. Furthermore, failure in either activating a DNA damage checkpoint or repairing programmed meiotic double-strand breaks (DSBs) can impair chromosome segregation. Therefore, understanding the molecular basis for DNA damage response (DDR) and DSB repair (DSBR) within the germline is highly important. Here we define ZTF-8, a previously uncharacterized protein conserved from worms to humans, as a novel factor involved in the repair of both mitotic and meiotic DSBs as well as in meiotic DNA damage checkpoint activation in the C. elegans germline. ztf-8 mutants exhibit specific sensitivity to γ-irradiation and hydroxyurea, mitotic nuclear arrest at S-phase accompanied by activation of the ATL-1 and CHK-1 DNA damage checkpoint kinases, as well as accumulation of both mitotic and meiotic recombination intermediates, indicating that ZTF-8 functions in DSBR. However, impaired meiotic DSBR progression partially fails to trigger the CEP-1/p53-dependent DNA damage checkpoint in late pachytene, also supporting a role for ZTF-8 in meiotic DDR. ZTF-8 partially co-localizes with the 9-1-1 DDR complex and interacts with MRT-2/Rad1, a component of this complex. The human RHINO protein rescues the phenotypes observed in ztf-8 mutants, suggesting functional conservation across species. We propose that ZTF-8 is involved in promoting repair at stalled replication forks and meiotic DSBs by transducing DNA damage checkpoint signaling via the 9-1-1 pathway. Our findings define a conserved function for ZTF-8/RHINO in promoting genomic stability in the germline.
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Affiliation(s)
- Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Monica P. Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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Bauknecht M, Kobbe D. AtGEN1 and AtSEND1, two paralogs in Arabidopsis, possess holliday junction resolvase activity. PLANT PHYSIOLOGY 2014; 166:202-16. [PMID: 25037209 PMCID: PMC4149707 DOI: 10.1104/pp.114.237834] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/10/2014] [Indexed: 05/02/2023]
Abstract
Holliday junctions (HJs) are physical links between homologous DNA molecules that arise as central intermediary structures during homologous recombination and repair in meiotic and somatic cells. It is necessary for these structures to be resolved to ensure correct chromosome segregation and other functions. In eukaryotes, including plants, homologs of a gene called XPG-like endonuclease1 (GEN1) have been identified that process HJs in a manner analogous to the HJ resolvases of phages, archaea, and bacteria. Here, we report that Arabidopsis (Arabidopsis thaliana), a eukaryotic organism, has two functional GEN1 homologs instead of one. Like all known eukaryotic resolvases, AtGEN1 and Arabidopsis single-strand DNA endonuclease1 both belong to class IV of the Rad2/XPG family of nucleases. Their resolvase activity shares the characteristics of the Escherichia coli radiation and UV sensitive C paradigm for resolvases, which involves resolving HJs by symmetrically oriented incisions in two opposing strands. This leads to ligatable products without the need for further processing. The observation that the sequence context influences the cleavage by the enzymes can be interpreted as a hint for the existence of sequence specificity. The two Arabidopsis paralogs differ in their preferred sequences. The precise cleavage positions observed for the resolution of mobile nicked HJs suggest that these cleavage positions are determined by both the substrate structure and the sequence context at the junction point.
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Affiliation(s)
- Markus Bauknecht
- Botanical Institute II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Daniela Kobbe
- Botanical Institute II, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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