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Kose C, Cao X, Dewey EB, Malkoç M, Adebali O, Sekelsky J, Lindsey-Boltz LA, Sancar A. Cross-species investigation into the requirement of XPA for nucleotide excision repair. Nucleic Acids Res 2024; 52:677-689. [PMID: 37994737 PMCID: PMC10810185 DOI: 10.1093/nar/gkad1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023] Open
Abstract
After reconstitution of nucleotide excision repair (excision repair) with XPA, RPA, XPC, TFIIH, XPF-ERCC1 and XPG, it was concluded that these six factors are the minimal essential components of the excision repair machinery. All six factors are highly conserved across diverse organisms spanning yeast to humans, yet no identifiable homolog of the XPA gene exists in many eukaryotes including green plants. Nevertheless, excision repair is reported to be robust in the XPA-lacking organism, Arabidopsis thaliana, which raises a fundamental question of whether excision repair could occur without XPA in other organisms. Here, we performed a phylogenetic analysis of XPA across all species with annotated genomes and then quantitatively measured excision repair in the absence of XPA using the sensitive whole-genome qXR-Seq method in human cell lines and two model organisms, Caenorhabditis elegans and Drosophila melanogaster. We find that although the absence of XPA results in inefficient excision repair and UV-sensitivity in humans, flies, and worms, excision repair of UV-induced DNA damage is detectable over background. These studies have yielded a significant discovery regarding the evolution of XPA protein and its mechanistic role in nucleotide excision repair.
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Affiliation(s)
- Cansu Kose
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Xuemei Cao
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Evan B Dewey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mustafa Malkoç
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Türkiye
| | - Ogün Adebali
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Türkiye
- Department of Computational Science-Biological Sciences, TÜBITAK Research Institute for Fundamental Sciences, Gebze, Türkiye
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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Alzahrani SM, Ebert PR. Attenuation of radiation toxicity by the phosphine resistance factor dihydrolipoamide dehydrogenase (DLD). Sci Rep 2019; 9:6455. [PMID: 31015501 PMCID: PMC6478721 DOI: 10.1038/s41598-019-42678-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 04/01/2019] [Indexed: 11/12/2022] Open
Abstract
Phosphine gas is an excellent fumigant for disinfesting stored grain of insect pests, but heavy reliance on phosphine has led to resistance in grain pests that threatens its efficacy. Phosphine-resistance was previously reported to be mediated by the enzyme DLD. Here we explore the relationship between phosphine toxicity and genotoxic treatments with the goal of understanding how phosphine works. Specifically, we utilized mutant lines either sensitive or resistant to phosphine, gamma irradiation or UV exposure. The phosphine-resistance mutation in the enzyme of energy metabolism, dihydrolipoamide dehydrogenase exhibited cross-resistance to UV and ionizing radiation. Two radiation-sensitive mutants that are defective in DNA repair as well as a mutant that is defective in the activation of the DAF-16 stress response transcription factor all exhibit sensitivity to phosphine that exceeds the sensitivity of the wild type control. A radiation resistance mutation in cep-1, the p53 orthologue, that is deficient in double strand break repair of DNA and is also deficient in apoptosis causes radiation-resistance results but sensitivity toward phosphine.
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Affiliation(s)
- Saad M Alzahrani
- The University of Queensland, School of Biological Sciences, St Lucia, QLD, 4072, Australia
- King Abdulaziz City for Science and Technology (KACST), Nuclear Science Research Institute (NSRI), P. O. Box 6086, Riyadh, 11442, Saudi Arabia
| | - Paul R Ebert
- The University of Queensland, School of Biological Sciences, St Lucia, QLD, 4072, Australia.
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Stress pre-conditioning with temperature, UV and gamma radiation induces tolerance against phosphine toxicity. PLoS One 2018; 13:e0195349. [PMID: 29672544 PMCID: PMC5909616 DOI: 10.1371/journal.pone.0195349] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/20/2018] [Indexed: 11/19/2022] Open
Abstract
Phosphine is the only general use fumigant for the protection of stored grain, though its long-term utility is threatened by the emergence of highly phosphine-resistant pests. Given this precarious situation, it is essential to identify factors, such as stress preconditioning, that interfere with the efficacy of phosphine fumigation. We used Caenorhabditis elegans as a model organism to test the effect of pre-exposure to heat and cold shock, UV and gamma irradiation on phosphine potency. Heat shock significantly increased tolerance to phosphine by 3-fold in wild-type nematodes, a process that was dependent on the master regulator of the heat shock response, HSF-1. Heat shock did not, however, increase the resistance of a strain carrying the phosphine resistance mutation, dld-1(wr4), and cold shock did not alter the response to phosphine of either strain. Pretreatment with the LD50 of UV (18 J cm-2) did not alter phosphine tolerance in wild-type nematodes, but the LD50 (33 J cm-2) of the phosphine resistant strain (dld-1(wr4)) doubled the level of resistance. In addition, exposure to a mild dose of gamma radiation (200 Gy) elevated the phosphine tolerance by ~2-fold in both strains.
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Lans H, Vermeulen W. Nucleotide Excision Repair in Caenorhabditis elegans. Mol Biol Int 2011; 2011:542795. [PMID: 22091407 PMCID: PMC3195855 DOI: 10.4061/2011/542795] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/18/2011] [Indexed: 01/23/2023] Open
Abstract
Nucleotide excision repair (NER) plays an essential role in many organisms across life domains to preserve and faithfully transmit DNA to the next generation. In humans, NER is essential to prevent DNA damage-induced mutation accumulation and cell death leading to cancer and aging. NER is a versatile DNA repair pathway that repairs many types of DNA damage which distort the DNA helix, such as those induced by solar UV light. A detailed molecular model of the NER pathway has emerged from in vitro and live cell experiments, particularly using model systems such as bacteria, yeast, and mammalian cell cultures. In recent years, the versatility of the nematode C. elegans to study DNA damage response (DDR) mechanisms including NER has become increasingly clear. In particular, C. elegans seems to be a convenient tool to study NER during the UV response in vivo, to analyze this process in the context of a developing and multicellular organism, and to perform genetic screening. Here, we will discuss current knowledge gained from the use of C. elegans to study NER and the response to UV-induced DNA damage.
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Affiliation(s)
- Hannes Lans
- Department of Genetics, Medical Genetics Center, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Medical Genetics Center, Erasmus MC, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
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Involvement of global genome repair, transcription coupled repair, and chromatin remodeling in UV DNA damage response changes during development. PLoS Genet 2010; 6:e1000941. [PMID: 20463888 PMCID: PMC2865526 DOI: 10.1371/journal.pgen.1000941] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Accepted: 04/06/2010] [Indexed: 01/22/2023] Open
Abstract
Nucleotide Excision Repair (NER), which removes a variety of helix-distorting lesions from DNA, is initiated by two distinct DNA damage-sensing mechanisms. Transcription Coupled Repair (TCR) removes damage from the active strand of transcribed genes and depends on the SWI/SNF family protein CSB. Global Genome Repair (GGR) removes damage present elsewhere in the genome and depends on damage recognition by the XPC/RAD23/Centrin2 complex. Currently, it is not well understood to what extent both pathways contribute to genome maintenance and cell survival in a developing organism exposed to UV light. Here, we show that eukaryotic NER, initiated by two distinct subpathways, is well conserved in the nematode Caenorhabditis elegans. In C. elegans, involvement of TCR and GGR in the UV-induced DNA damage response changes during development. In germ cells and early embryos, we find that GGR is the major pathway contributing to normal development and survival after UV irradiation, whereas in later developmental stages TCR is predominantly engaged. Furthermore, we identify four ISWI/Cohesin and four SWI/SNF family chromatin remodeling factors that are implicated in the UV damage response in a developmental stage dependent manner. These in vivo studies strongly suggest that involvement of different repair pathways and chromatin remodeling proteins in UV-induced DNA repair depends on developmental stage of cells.
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Boyd WA, Crocker TL, Rodriguez AM, Leung MCK, Lehmann DW, Freedman JH, Van Houten B, Meyer JN. Nucleotide excision repair genes are expressed at low levels and are not detectably inducible in Caenorhabditis elegans somatic tissues, but their function is required for normal adult life after UVC exposure. Mutat Res 2010; 683:57-67. [PMID: 19879883 PMCID: PMC2799044 DOI: 10.1016/j.mrfmmm.2009.10.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 10/06/2009] [Accepted: 10/16/2009] [Indexed: 04/09/2023]
Abstract
We performed experiments to characterize the inducibility of nucleotide excision repair (NER) in Caenorhabditis elegans, and to examine global gene expression in NER-deficient and -proficient strains as well as germline vs. somatic tissues, with and without genotoxic stress. We also carried out experiments to elucidate the importance of NER in the adult life of C. elegans under genotoxin-stressed and control conditions. Adult lifespan was not detectably different between wild-type and NER-deficient xpa-1 nematodes under control conditions. However, exposure to 6J/m(2)/day of ultraviolet C radiation (UVC) decreased lifespan in xpa-1 nematodes more than a dose of 100 J/m(2)/day in wild-type. Similar differential sensitivities were observed for adult size and feeding. Remarkably, global gene expression was nearly identical in young adult wild-type and xpa-1 nematodes, both in control conditions and 3h after exposure to 50 J/m(2) UVC. Neither NER genes nor repair activity were detectably inducible in young adults that lacked germ cells and developing embryos (glp-1 strain). However, expression levels of dozens of NER and other DNA damage response genes were much (5-30-fold) lower in adults lacking germ cells and developing embryos, suggesting that somatic and post-mitotic cells have a much lower DNA repair ability. Finally, we describe a refinement of our DNA damage assay that allows damage measurement in single nematodes.
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Affiliation(s)
- Windy A. Boyd
- Biomolecular Screening Branch, National Toxicology Program, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Tracey L. Crocker
- Nicholas School of the Environment, Duke University, Durham, NC 27708
| | - Ana M. Rodriguez
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | | | - D. Wade Lehmann
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jonathan H. Freedman
- Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Ben Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Joel N. Meyer
- Nicholas School of the Environment, Duke University, Durham, NC 27708
- Address correspondence to: Joel N. Meyer
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Leung MCK, Williams PL, Benedetto A, Au C, Helmcke KJ, Aschner M, Meyer JN. Caenorhabditis elegans: an emerging model in biomedical and environmental toxicology. Toxicol Sci 2008; 106:5-28. [PMID: 18566021 PMCID: PMC2563142 DOI: 10.1093/toxsci/kfn121] [Citation(s) in RCA: 662] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 06/10/2008] [Indexed: 12/21/2022] Open
Abstract
The nematode Caenorhabditis elegans has emerged as an important animal model in various fields including neurobiology, developmental biology, and genetics. Characteristics of this animal model that have contributed to its success include its genetic manipulability, invariant and fully described developmental program, well-characterized genome, ease of maintenance, short and prolific life cycle, and small body size. These same features have led to an increasing use of C. elegans in toxicology, both for mechanistic studies and high-throughput screening approaches. We describe some of the research that has been carried out in the areas of neurotoxicology, genetic toxicology, and environmental toxicology, as well as high-throughput experiments with C. elegans including genome-wide screening for molecular targets of toxicity and rapid toxicity assessment for new chemicals. We argue for an increased role for C. elegans in complementing other model systems in toxicological research.
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Affiliation(s)
- Maxwell C. K. Leung
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27750
| | - Phillip L. Williams
- Department of Environmental Health Science, College of Public University of Georgia, Athens, Georgia 30602
| | - Alexandre Benedetto
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Catherine Au
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Kirsten J. Helmcke
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Michael Aschner
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37240
| | - Joel N. Meyer
- Nicholas School of the Environment, Duke University, Durham, North Carolina 27750
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8
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Astin JW, O'Neil NJ, Kuwabara PE. Nucleotide excision repair and the degradation of RNA pol II by the Caenorhabditis elegans XPA and Rsp5 orthologues, RAD-3 and WWP-1. DNA Repair (Amst) 2007; 7:267-80. [PMID: 18053776 DOI: 10.1016/j.dnarep.2007.10.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 09/07/2007] [Accepted: 10/12/2007] [Indexed: 01/06/2023]
Abstract
The Caenorhabditis elegans rad-3 gene was identified in a genetic screen for radiation sensitive (rad) mutants. Here, we report that the UV sensitivity of rad-3 mutants is caused by a nonsense mutation in the C. elegans orthologue of the human nucleotide excision repair gene XPA. We have used the xpa-1/rad-3 mutant to examine how a defect in nucleotide excision repair (NER) perturbs development. We find that C. elegans carrying a mutation in xpa-1/rad-3 are hypersensitive and hypermutable in response to UV irradiation, but do not display hypersensitivity to oxidative stress or show obvious developmental abnormalities in the absence of UV exposure. Consistent with these observations, non-irradiated xpa-1 mutants have a similar lifespan as wild type. We further show that UV irradiated xpa-1 mutants undergo a stage-dependent decline in growth and survival, which is associated with a loss in transcriptional competence. Surprisingly, transcriptionally quiescent dauer stage larvae are able to survive a dose of UV irradiation, which is otherwise lethal to early stage larvae. We show that the loss of transcriptional competence in UV irradiated xpa-1 mutants is associated with the degradation of the large RNA polymerase II (RNA pol II) subunit, AMA-1, and have identified WWP-1 as the putative E3 ubiquitin ligase mediating this process. The absence of wwp-1 by itself does not cause sensitivity to UV irradiation, but it acts synergistically with a mutation in xpa-1 to enhance UV hypersensitivity.
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Affiliation(s)
- Jonathan W Astin
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, UK
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Kim SH, Holway AH, Wolff S, Dillin A, Michael WM. SMK-1/PPH-4.1-mediated silencing of the CHK-1 response to DNA damage in early C. elegans embryos. ACTA ACUST UNITED AC 2007; 179:41-52. [PMID: 17908915 PMCID: PMC2064732 DOI: 10.1083/jcb.200705182] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During early embryogenesis in Caenorhabditis elegans, the ATL-1-CHK-1 (ataxia telangiectasia mutated and Rad3 related-Chk1) checkpoint controls the timing of cell division in the future germ line, or P lineage, of the animal. Activation of the CHK-1 pathway by its canonical stimulus DNA damage is actively suppressed in early embryos so that P lineage cell divisions may occur on schedule. We recently found that the rad-2 mutation alleviates this checkpoint silent DNA damage response and, by doing so, causes damage-dependent delays in early embryonic cell cycle progression and subsequent lethality. In this study, we report that mutations in the smk-1 gene cause the rad-2 phenotype. SMK-1 is a regulatory subunit of the PPH-4.1 (protein phosphatase 4) protein phosphatase, and we show that SMK-1 recruits PPH-4.1 to replicating chromatin, where it silences the CHK-1 response to DNA damage. These results identify the SMK-1-PPH-4.1 complex as a critical regulator of the CHK-1 pathway in a developmentally relevant context.
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Affiliation(s)
- Seung-Hwan Kim
- The Biological Laboratories, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Antonia H. Holway
- The Biological Laboratories, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Suzanne Wolff
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Andrew Dillin
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - W. Matthew Michael
- The Biological Laboratories, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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Meyer JN, Boyd WA, Azzam GA, Haugen AC, Freedman JH, Van Houten B. Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans. Genome Biol 2007; 8:R70. [PMID: 17472752 PMCID: PMC1929140 DOI: 10.1186/gb-2007-8-5-r70] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 11/03/2006] [Accepted: 05/01/2007] [Indexed: 11/29/2022] Open
Abstract
Repair of UVC-induced DNA damage in Caenorhabditis elegans is similar kinetically and genetically to repair in humans, and it slows significantly in aging C. elegans. Background Caenorhabditis elegans is an important model for the study of DNA damage and repair related processes such as aging, neurodegeneration, and carcinogenesis. However, DNA repair is poorly characterized in this organism. We adapted a quantitative polymerase chain reaction assay to characterize repair of DNA damage induced by ultraviolet type C (UVC) radiation in C. elegans, and then tested whether DNA repair rates were affected by age in adults. Results UVC radiation induced lesions in young adult C. elegans, with a slope of 0.4 to 0.5 lesions per 10 kilobases of DNA per 100 J/m2, in both nuclear and mitochondrial targets. L1 and dauer larvae were more than fivefold more sensitive to lesion formation than were young adults. Nuclear repair kinetics in a well expressed nuclear gene were biphasic in nongravid adult nematodes: a faster, first order (half-life about 16 hours) phase lasting approximately 24 hours and resulting in removal of about 60% of the photoproducts was followed by a much slower phase. Repair in ten nuclear DNA regions was 15% and 50% higher in more actively transcribed regions in young and aging adults, respectively. Finally, repair was reduced by 30% to 50% in each of the ten nuclear regions in aging adults. However, this decrease in repair could not be explained by a reduction in expression of nucleotide excision repair genes, and we present a plausible mechanism, based on gene expression data, to account for this decrease. Conclusion Repair of UVC-induced DNA damage in C. elegans is similar kinetically and genetically to repair in humans. Furthermore, this important repair process slows significantly in aging C. elegans, the first whole organism in which this question has been addressed.
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Affiliation(s)
- Joel N Meyer
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Windy A Boyd
- Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Gregory A Azzam
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Astrid C Haugen
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jonathan H Freedman
- Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Bennett Van Houten
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Alexander Drive, Research Triangle Park, NC 27709, USA
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Holway AH, Kim SH, La Volpe A, Michael WM. Checkpoint silencing during the DNA damage response in Caenorhabditis elegans embryos. ACTA ACUST UNITED AC 2006; 172:999-1008. [PMID: 16549501 PMCID: PMC2063758 DOI: 10.1083/jcb.200512136] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In most cells, the DNA damage checkpoint delays cell division when replication is stalled by DNA damage. In early Caenorhabditis elegans embryos, however, the checkpoint responds to developmental signals that control the timing of cell division, and checkpoint activation by nondevelopmental inputs disrupts cell cycle timing and causes embryonic lethality. Given this sensitivity to inappropriate checkpoint activation, we were interested in how embryos respond to DNA damage. We demonstrate that the checkpoint response to DNA damage is actively silenced in embryos but not in the germ line. Silencing requires rad-2, gei-17, and the polh-1 translesion DNA polymerase, which suppress replication fork stalling and thereby eliminate the checkpoint-activating signal. These results explain how checkpoint activation is restricted to developmental signals during embryogenesis and insulated from DNA damage. They also show that checkpoint activation is not an obligatory response to DNA damage and that pathways exist to bypass the checkpoint when survival depends on uninterrupted progression through the cell cycle.
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Affiliation(s)
- Antonia H Holway
- The Biological Laboratories, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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12
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Jin SW, Kimble J, Ellis RE. Regulation of cell fate in Caenorhabditis elegans by a novel cytoplasmic polyadenylation element binding protein. Dev Biol 2001; 229:537-53. [PMID: 11150246 DOI: 10.1006/dbio.2000.9993] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The fog-1 gene of Caenorhabditis elegans specifies that germ cells differentiate as sperm rather than as oocytes. We cloned fog-1 through a combination of transformation rescue experiments, RNA-mediated inactivation, and mutant analyses. Our results show that fog-1 produces two transcripts, both of which are found in germ cells but not in the soma. Furthermore, two deletion mutants alter these transcripts and are likely to eliminate fog-1 activity. The larger transcript is expressed under the control of sex-determination genes, is necessary for fog-1 activity, and is sufficient to rescue a fog-1 mutant. This transcript encodes a novel member of the CPEB family of RNA-binding proteins. Because CPEB proteins in Xenopus and Drosophila regulate gene expression at the level of translation, we propose that FOG-1 controls germ cell fates by regulating the translation of specific messenger RNAs.
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Affiliation(s)
- S W Jin
- Department of Biology, University of Michigan, Ann Arbor, Michigan, 48109
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13
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Yanase S, Hartman PS, Ito A, Ishii N. Oxidative stress pretreatment increases the X-radiation resistance of the nematode Caenorhabditis elegans. Mutat Res 1999; 426:31-9. [PMID: 10320748 DOI: 10.1016/s0027-5107(99)00079-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pre-exposure of wild-type Caenorhabditis elegans to oxygen conferred a protective effect against the lethality imposed by subsequent X-irradiation. In contrast, two mutants (rad-1 and rad-2) that are UV and ionizing radiation hypersensitive but not oxygen sensitive, did not exhibit this adaptive response. To explore the molecular basis of protection, the expression of several key genes was examined using Northern blot analyses to measure mRNA levels. In the wild-type, expression of the heat shock protein genes, hsp16-1 and hsp16-48, increased dramatically after incubation under high oxygen. Expression of two superoxide dismutase genes (sod-1 and sod-3) was relatively unaffected. Unlike the wild-type, the basal levels of these four genes were significantly lower in the rad-1 and rad-2 mutants under atmospheric conditions. These genes were partially induced in response to oxidative stress. These data suggest that at least a portion of the hypersensitive phenotype of rad-1 and rad-2 may be attributed to inappropriate gene expression.
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Affiliation(s)
- S Yanase
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
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14
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Mills DK, Hartman PS. Lethal Consequences of Simulated Solar Radiation on the Nematode Caenorhabditis elegans in the Presence and Absence of Photosensitizers. Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb05289.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Hartman P, Goldstein P, Algarra M, Hubbard D, Mabery J. The nematode Caenorhabditis elegans is up to 39 times more sensitive to gamma radiation generated from 137Cs than from 60Co. Mutat Res 1996; 363:201-8. [PMID: 8765161 DOI: 10.1016/0921-8777(96)00012-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Survival after gamma irradiation (generated from either a 137Cs or 60Co source) was determined for two strains of the nematode Caenorhabditis elegans. Animals were between 1.3 and 39 times more sensitive to cesium than to cobalt. The magnitude of this differential sensitivity was dependent upon the strain, developmental stage and sex tested. Several control experiments eliminated trivial explanations for this difference. Since cobalt- and cesium-generated gamma particles have nearly identical energy depositions, the differential sensitivity likely reflects different mechanisms of processing the slightly different spectra of DNA damage induced by these two radiations. Sex-specific differences in radiation sensitivity were also noted and were likely due to the fact that males possess a single X chromosome rather than two, as do hermaphrodites.
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Affiliation(s)
- P Hartman
- Department of Biology, Texas Christian University, Fort Worth 76129, USA.
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16
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Abstract
Replication continues in wild-type (but not rad mutant) Caenorhabditis elegans embryos even after exposure to massive fluences of UV radiation. It is of interest to elucidate the mechanism(s) for this "damage-resistant" DNA synthesis. In this study, DNA from unirradiated and UV-irradiated wild-type embryos was examined using the electron microscope. Large fluences of UV radiation (180 J m-2) had little effect on either replication bubble size or distances between bubbles in wild-type embryos, indicating that the damage-resistant DNA synthesis was not grossly aberrant. Conversely, UV irradiation significantly decreased center-to-center distances between bubbles in excision-repair-deficient rad-3 embryos. This suggests that the decreased DNA synthesis observed after UV irradiation in rad-3 embryos is due largely to blockage of elongation of DNA synthesis.
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Affiliation(s)
- C A Jones
- Department of Biology, Texas Christian University, Fort Worth 76129, USA
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Hartman PS, De Wilde D, Dwarakanath VN. Genetic and molecular analyses of UV radiation-induced mutations in the fem-3 gene of Caenorhabditis elegans. Photochem Photobiol 1995; 61:607-14. [PMID: 7568407 DOI: 10.1111/j.1751-1097.1995.tb09876.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The utility of a new target gene (fem-3) is described for investigating the molecular nature of mutagenesis in the nematode Caenorhabditis elegans. As a principal attribute, this system allows for the selection, maintenance and molecular analysis of any type of mutation that disrupts the gene, including deletions. In this study, 86 mutant strains were isolated, of which 79 proved to have mutations in fem-3. Twenty of these originally tested as homozygous inviable. Homozygous inviability was expected, as Stewart and coworkers had previously observed that, unlike in other organisms, most UV radiation-induced mutations in C. elegans are chromosomal rearrangements of deficiencies (Mutat. Res. 249, 37-54, 1991). However, additional data, including Southern blot analyses on 48 of the strains, indicated that most of the UV radiation-induced fem-3 mutations were not deficiencies, as originally inferred from their homozygous inviability. Instead, the lethals were most likely "coincident mutations" in linked, essential genes that were concomitantly induced. As such, they were lost owing to genetic recombination during stock maintenance. As in mammalian cells, yeast and bacteria, the frequency of coincident mutations was much higher than would be predicted by chance.
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Affiliation(s)
- P S Hartman
- Department of Biology, Texas Christian University, Fort Worth 76129, USA
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Hartman PS, Marshall A. Inactivation of wild-type and rad mutant Caenorhabditis elegans by 8-methoxypsoralen and near ultraviolet radiation. Photochem Photobiol 1992; 55:103-11. [PMID: 1603841 DOI: 10.1111/j.1751-1097.1992.tb04215.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Survival of wild-type and four radiation-sensitive (rad) mutants of the nematode Caenorhabditis elegans was determined after near-UV irradiation in the presence of 8-methoxypsoralen (8-MOP). Three sets of inactivation profiles were generated for each strain by irradiating synchronous populations of either early embryos, late embryos or first-stage larvae (L1s). Late embryos were consistently the most sensitive. Curiously, none of the four rad mutants were even moderately hypersensitive. Split-dose experiments indicated that DNA-DNA crosslinks were primarily responsible for lethality. Crosslink induction and repair were determined using two different assays. In both cases, little if any repair was observed in wild-type. This lack of repair thus explains why the rad mutants were not hypersensitive to 8-MOP photoinactivation. Since early embryos undergo extensive cell cycling, their resistance to 8-MOP photoinactivation suggests that replication is highly refractory to both monoadducts and crosslinks, as has been demonstrated previously for UV radiation-induced photoproducts (Hartman et al., 1991, Mutat. Res., 255, pp. 163-173).
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Affiliation(s)
- P S Hartman
- Department of Biology, Texas Christian University, Fort Worth 76129
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Ishii N, Suzuki K. X-ray inactivation of Caenorhabditis elegans embryos or larvae. Int J Radiat Biol 1990; 58:827-33. [PMID: 1977826 DOI: 10.1080/09553009014552201] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The lethal effects of X-irradiation were examined in staged populations of Caenorhabditis elegans embryos or larvae. Radiation resistance decreased slightly throughout the first, proliferative phase of embryogenesis. This might be due to the increase in target size, since most cells in C. elegans are autonomously determined. Animals irradiated in the second half of embryogenesis were about 40-fold more resistant to the lethal effects of X-rays. This is probably due to the absence of cell divisions during this time. The radiation resistance increased still more with advancing larval stages. A radiation hypersensitive mutant, rad-1, irradiated in the first half of embryogenesis, is about 30-fold more sensitive than wild-type, but in the second half it is the same as wild-type.
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Affiliation(s)
- N Ishii
- Department of Molecular Biology, Tokai University School of Medicine, Kanagawa, Japan
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Sadaie T, Sadaie Y. Rad-2-dependent repair of radiation-induced chromosomal aberrations in Caenorhabditis elegans. Mutat Res 1989; 218:25-31. [PMID: 2747711 DOI: 10.1016/0921-8777(89)90043-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A method involving light microscopy was developed and utilized for the observation of gamma- or ultraviolet-induced aberrations of the chromosomes of Caenorhabditis elegans var. Bristol (N2). Gravid worms were irradiated and the chromosomes were examined in the early embryos derived from eggs fertilized after the irradiation. The frequency of gamma-induced aberrations in the early embryonic cells of C. elegans increased proportionally with the dosage of gamma-rays. It decreased greatly following incubation of the irradiated gravid worms for 2 days. This decrease was blocked by the rad-2 mutation but not by the rad-1 mutation of the same epistasis group. Both mutations make worms sensitive to radiation and chemicals. In addition, the hatchability of eggs laid by the rad-2 mutant after irradiation was restored very quickly as was that of the wild-type strain. Ultraviolet irradiation, on the other hand, induced few aberrations in both the wild-type and rad-1 strains, but it caused an elevated frequency of aberrations in the rad-2 strain. Ultraviolet irradiation strongly blocked the separation of chromosomes of the rad-2 strain. Furthermore, hatchability was very low in eggs laid by ultraviolet-irradiated rad-2 worms. These results suggest the existence of a rad-2-dependent mechanism for gonadal repair of chromosomal aberrations, including chromosomal non-separation, and indicate that gamma-induced chromosome aberrations are not fatal to the hatching of Caenorhabditis elegans which has holocentric chromosomes.
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Affiliation(s)
- T Sadaie
- Radioisotope Center, National Institute of Genetics, Japan
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Abstract
The (6-4) photoproduct is an important determinant of the lethal and mutagenic effects of UV irradiation of biological systems. The removal of this lesion appears to correlate closely with the early DNA repair responses of mammalian cells, including DNA incision events, repair synthesis and removal of replication blocks. The processing of (6-4) photoproducts and cyclobutane dimers appears to be enzymatically coupled in bacteria and most mammalian cell lines examined (i.e. a mutation affecting the repair of one lesion also often affects the other), although exceptions exist in which repair capacity may be evident for one photoproduct and not the other (e.g. UV61 and the XP revertant cell line). These differences in the processing of the two photoproducts in some cell lines of human and rodent origin suggest that in mammalian cells, different pathways for the repair of (6-4) photoproducts and cyclobutane dimers may be used. This observation is further supported by pleiotropic repair phenotypes such as those observed in CHO complementation class 2 mutants (e.g., UV5, UVL-1, UVL-13, and V-H1). Indirect data, from HCR of UV irradiated reported genes and the cytotoxic responses of UV61, suggest that the (6-4) photoproduct is cytotoxic in mammalian cells and may account for 20 to 30% of the cell killing after UV irradiation of rodent cells. Cytotoxicity of the (6-4) photoproduct may be important in the etiology of sunlight-induced carcinogenesis, affecting mutagenesis as well as tumorigenesis. The intricate photochemistry of the (6-4) photoproduct, its formation and photoisomerization, is in itself extremely interesting and may also be relevant to sunlight carcinogenesis. The data reviewed in this article support the notion that the (6-4) photoproduct and its Dewar photoisomer are important cytotoxic determinants of UV light. The idea that the (6-4) photoproduct is an important component in the spectrum of UV-induced cytotoxic damage may help clarify our understanding of why rodent cells survive the effects of UV irradiation as well as human cells, without apparent cyclobutane dimer repair in the bulk of their DNA. The preferential repair of cyclobutane dimers in essential genes has been proposed to account for this observation (Bohr et al., 1985, 1986; Mellon et al., 1986). The data reviewed here suggest that understanding the repair of a prominent type of noncyclobutane dimer damage, the (6-4) photoproduct, may also be important in resolving this paradox.
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Coohill T, Marshall T, Schubert W, Nelson G. Ultraviolet mutagenesis of radiation-sensitive (rad) mutants of the nematode Caenorhabditis elegans. Mutat Res 1988; 209:99-106. [PMID: 3193983 DOI: 10.1016/0165-7992(88)90025-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A mutational tester strain (JP10) of the nematode C. elegans was used to capture recessive lethal mutations in a balanced 300 essential gene autosomal region. The probability of converting a radiation interaction into a lethal mutation was measured in young gravid adults after exposure to fluences of 254-nm ultraviolet radiation (UV) ranging from 0 to 300 Jm-2. Mutation frequencies as high as 5% were observed. In addition, three different radiation-hypersensitive mutations, rad-1, rad-3 and rad-7 were incorporated into the JP10 background genotype, which allowed us to measure mutation frequencies in radiation-sensitive animals. The strain homozygous for rad-3 was hypermutable to UV while strains homozygous for rad-1 and rad-7 were hypomutable. Data showing the effects of UV on larval development and fertility for the rad mutants is also shown and compared for wild-type and JP10 backgrounds.
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Affiliation(s)
- T Coohill
- Department of Physics and Astronomy, Western Kentucky University, Bowling Green 42101
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Hartman PS, Simpson VJ, Johnson T, Mitchell D. Radiation sensitivity and DNA repair in Caenorhabditis elegans strains with different mean life spans. Mutat Res 1988; 208:77-82. [PMID: 3380112 DOI: 10.1016/s0165-7992(98)90003-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The sensitivities to three DNA damaging agents (UV and gamma-radiation, methyl methanesulfonate) were measured in four recombinant inbred (RI) strains of Caenorhabditis elegans with mean life spans ranging from 13 to 30.9 days, as well as in the wild-type strains used to derive these RI's. Sensitivities at several stages in the developmental cycle were tested. There were no significant correlations between mean life span and the lethal effects of these 3 agents. Excision of two UV-radiation-induced DNA photoproducts was also measured. Long-lived strains were no more repair competent than shorter-lived strains. These data indicate that DNA repair plays at best a minor role in the aging process of C. elegans.
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Affiliation(s)
- P S Hartman
- Department of Biology, Texas Christian University, Fort Worth 76129
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Keller CI, Calkins J, Hartman PS, Rupert CS. UV photobiology of the nematode Caenorhabditis elegans: action spectra, absence of photoreactivation and effects of caffeine. Photochem Photobiol 1987; 46:483-8. [PMID: 3423121 DOI: 10.1111/j.1751-1097.1987.tb04799.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Abstract
SummaryWild-typeCaenorhabditis elegansfails to reach adulthood if L1 larvae are incubated in the presence of 30 mM or greater concentrations of caffeine. Eleven mutants have been isolated in which caffeine has a less pronounced effect on development. The mutations are recessive, define two genes, and have been mapped. The mechanism(s) of resistance is unknown.
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Hartman PS. Effects of age and liquid holding on the UV-radiation sensitivities of wild-type and mutant Caenorhabditis elegans dauer larvae. Mutat Res 1984; 132:95-9. [PMID: 6493262 DOI: 10.1016/0167-8817(84)90003-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The dauer larva is a facultative developmental stage in the life cycle of the nematode Caenorhabditis elegans. Dauer larvae, which can survive under starvation for over 60 days, resume normal development when feeding is resumed. Wild-type (N2) and 4 radiation-sensitive (rad) mutant dauer larvae were tested for their abilities to develop into adults after UV-irradiation. The rad-3 mutant was over 30 times as sensitive as N2; rad-1, rad-2 and rad-7 mutants were not hypersensitive. Irradiation also delayed development in survivors. Wild-type dauer larvae did not differ in radiation sensitivity from 0 through 50 days of age. There was no liquid holding recovery (LHR); that is, survival did not increase when wild-type dauer larvae were held in buffer after irradiation.
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