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Kutashev K, Meschichi A, Reeck S, Fonseca A, Sartori K, White CI, Sicard A, Rosa S. Differences in RAD51 transcriptional response and cell cycle dynamics reveal varying sensitivity to DNA damage among Arabidopsis thaliana root cell types. THE NEW PHYTOLOGIST 2024. [PMID: 38840557 DOI: 10.1111/nph.19875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024]
Abstract
Throughout their lifecycle, plants are subjected to DNA damage from various sources, both environmental and endogenous. Investigating the mechanisms of the DNA damage response (DDR) is essential to unravel how plants adapt to the changing environment, which can induce varying amounts of DNA damage. Using a combination of whole-mount single-molecule RNA fluorescence in situ hybridization (WM-smFISH) and plant cell cycle reporter lines, we investigated the transcriptional activation of a key homologous recombination (HR) gene, RAD51, in response to increasing amounts of DNA damage in Arabidopsis thaliana roots. The results uncover consistent variations in RAD51 transcriptional response and cell cycle arrest among distinct cell types and developmental zones. Furthermore, we demonstrate that DNA damage induced by genotoxic stress results in RAD51 transcription throughout the whole cell cycle, dissociating its traditional link with S/G2 phases. This work advances the current comprehension of DNA damage response in plants by demonstrating quantitative differences in DDR activation. In addition, it reveals new associations with the cell cycle and cell types, providing crucial insights for further studies of the broader response mechanisms in plants.
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Affiliation(s)
- Konstantin Kutashev
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Anis Meschichi
- Department of Biology, Institute of Molecular Plant Biology, Swiss Federal Institute of Technology Zürich, Zürich, 8092, Switzerland
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Research Park, Norwich, NR4 7UH, UK
| | - Alejandro Fonseca
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Kevin Sartori
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Charles I White
- Institut Génétique Reproduction et Développement (iGReD), Université Clermont Auvergne, UMR 6293, CNRS, U1103 INSERM, Clermont-Ferrand, 63001, France
| | - Adrien Sicard
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 756 51, Sweden
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Murthy HN, Joseph KS, Paek KY, Park SY. Production of specialized metabolites in plant cell and organo-cultures: the role of gamma radiation in eliciting secondary metabolism. Int J Radiat Biol 2024; 100:678-688. [PMID: 38451191 DOI: 10.1080/09553002.2024.2324469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE To provide an updated summary of recent advances in the application of gamma irradiation to elicit secondary metabolism and for induction of mutations in plant cell and organ cultures for the production of industrially important specialized metabolites (SMs). CONCLUSIONS Research on the application of gamma radiation with plants has contributed a lot to microbial decontamination of seeds, and the promotion of physiological processes such as seed germination, seedling vigor, plant growth, and development. Various studies have demonstrated the influence of gamma rays on the morphology, physiology, and biochemistry of plants. Recent research efforts have also shown that low-dose gamma (5-100 Gy) irradiation can be utilized as an expedient solution to alleviate the deleterious effect of abiotic stresses and to obtain better yields of plants. Inducing mutagenesis using gamma irradiation has also evolved as a better option for inducing genetic variability in crops, vegetables, medicinal and ornamentals for their genetic improvement. Plant SMs are gaining increasing importance as pharmaceutical, therapeutic, cosmetic, and agricultural products. Plant cell, tissue, and organ cultures represent an attractive alternative to conventional methods of procuring useful SMs. Among the varied approaches the elicitor-induced in vitro culture techniques are considered an efficient tool for studying and improving the production of SMs. This review focuses on the utilization of low-dose gamma irradiation in the production of high-value SMs such as phenolics, terpenoids, and alkaloids. Furthermore, we present varied successful examples of gamma-ray-induced mutations in the production of SMs.
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Affiliation(s)
- Hosakatte Niranjana Murthy
- Department of Botany, Karnatak University, Dharwad, India
- Department of Horticultural Science, Chungbuk National University, Cheongju, Republic of Korea
| | | | - Kee Yoeup Paek
- Department of Horticultural Science, Chungbuk National University, Cheongju, Republic of Korea
| | - So Young Park
- Department of Horticultural Science, Chungbuk National University, Cheongju, Republic of Korea
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3
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Sears RG, Rigoulot SB, Occhialini A, Morgan B, Kakeshpour T, Brabazon H, Barnes CN, Seaberry EM, Jacobs B, Brown C, Yang Y, Schimel TM, Lenaghan SC, Neal Stewart C. Engineered gamma radiation phytosensors for environmental monitoring. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1745-1756. [PMID: 37224108 PMCID: PMC10440981 DOI: 10.1111/pbi.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/13/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
Nuclear energy, already a practical solution for supplying energy on a scale similar to fossil fuels, will likely increase its footprint over the next several decades to meet current climate goals. Gamma radiation is produced during fission in existing nuclear reactors and thus the need to detect leakage from nuclear plants, and effects of such leakage on ecosystems will likely also increase. At present, gamma radiation is detected using mechanical sensors that have several drawbacks, including: (i) limited availability; (ii) reliance on power supply; and (iii) requirement of human presence in dangerous areas. To overcome these limitations, we have developed a plant biosensor (phytosensor) to detect low-dose ionizing radiation. The system utilizes synthetic biology to engineer a dosimetric switch into potato utilizing the plant's native DNA damage response (DDR) machinery to produce a fluorescent output. In this work, the radiation phytosensor was shown to respond to a wide range of gamma radiation exposure (10-80 Grey) producing a reporter signal that was detectable at >3 m. Further, a pressure test of the top radiation phytosensor in a complex mesocosm demonstrated full function of the system in a 'real world' scenario.
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Affiliation(s)
- Robert G. Sears
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Stephen B. Rigoulot
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - Britany Morgan
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Tayebeh Kakeshpour
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Holly Brabazon
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Caitlin N. Barnes
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Erin M. Seaberry
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Brianna Jacobs
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Chandler Brown
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Yongil Yang
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
| | - Tayler M. Schimel
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - Scott C. Lenaghan
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
- Department of Food ScienceThe University of TennesseeKnoxvilleTennesseeUSA
| | - C. Neal Stewart
- Department of Plant SciencesThe University of TennesseeKnoxvilleTennesseeUSA
- Center for Agricultural Synthetic BiologyThe University of Tennessee, KnoxvilleKnoxvilleTennesseeUSA
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Zhu M, Cheng Y, Wu S, Huang X, Qiu J. Deleterious mutations are characterized by higher genomic heterozygosity than other genic variants in plant genomes. Genomics 2022; 114:110290. [DOI: 10.1016/j.ygeno.2022.110290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/08/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
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Wolter F, Schindele P, Beying N, Scheben A, Puchta H. Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. THE PLANT CELL 2021; 33:3454-3469. [PMID: 34375428 PMCID: PMC8566284 DOI: 10.1093/plcell/koab204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/04/2021] [Indexed: 05/03/2023]
Abstract
In nature, single-strand breaks (SSBs) in DNA occur more frequently (by orders of magnitude) than double-strand breaks (DSBs). SSBs induced by the CRISPR/Cas9 nickase at a distance of 50-100 bp on opposite strands are highly mutagenic, leading to insertions/deletions (InDels), with insertions mainly occurring as direct tandem duplications. As short tandem repeats are overrepresented in plant genomes, this mechanism seems to be important for genome evolution. We investigated the distance at which paired 5'-overhanging SSBs are mutagenic and which DNA repair pathways are essential for insertion formation in Arabidopsis thaliana. We were able to detect InDel formation up to a distance of 250 bp, although with much reduced efficiency. Surprisingly, the loss of the classical nonhomologous end joining (NHEJ) pathway factors KU70 or DNA ligase 4 completely abolished tandem repeat formation. The microhomology-mediated NHEJ factor POLQ was required only for patch-like insertions, which are well-known from DSB repair as templated insertions from ectopic sites. As SSBs can also be repaired using homology, we furthermore asked whether the classical homologous recombination (HR) pathway is involved in this process in plants. The fact that RAD54 is not required for homology-mediated SSB repair demonstrates that the mechanisms for DSB- and SSB-induced HR differ in plants.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Patrick Schindele
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Natalja Beying
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Author for correspondence:
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Lee G, Ahmadi H, Quintana J, Syllwasschy L, Janina N, Preite V, Anderson JE, Pietzenuk B, Krämer U. Constitutively enhanced genome integrity maintenance and direct stress mitigation characterize transcriptome of extreme stress-adapted Arabidopsis halleri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:896-911. [PMID: 34669984 DOI: 10.1111/tpj.15544] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metal-rich toxic soils and ordinary soils are both natural habitats of Arabidopsis halleri, a diploid perennial and obligate outcrosser in the sister clade of the genetic model plant Arabidopsis thaliana. The molecular divergence underlying survival in sharply contrasting environments is unknown. Here we comparatively address metal physiology and transcriptomes of A. halleri originating from the most highly heavy metal-contaminated soil in Europe, Ponte Nossa, Italy (Noss), and from non-metalliferous (NM) soils. Plants from Noss exhibit enhanced hypertolerance and attenuated accumulation of cadmium (Cd), and their transcriptomic Cd responsiveness is decreased, compared to plants of NM soil origin. Among the condition-independent transcriptome characteristics of Noss, the most highly overrepresented functional class of 'meiotic cell cycle' comprises 21 transcripts with elevated abundance in vegetative tissues, in particular Argonaute 9 (AGO9) and the synaptonemal complex transverse filament protein-encoding ZYP1a/b. Increased AGO9 transcript levels in Noss are accompanied by decreased long terminal repeat retrotransposon expression. Similar to Noss, plants from other highly metalliferous sites in Poland and Germany share elevated somatic AGO9 transcript levels in comparison to plants originating from NM soils in their respective geographic regions. Transcript levels of Iron-Regulated Transporter 1 (IRT1) are very low and transcript levels of Heavy Metal ATPase 2 (HMA2) are strongly elevated in Noss, which can account for its altered Cd handling. We conclude that in plants adapted to the most extreme abiotic stress, broadly enhanced functions comprise genes with likely roles in somatic genome integrity maintenance, accompanied by few alterations in stress-specific functional networks.
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Affiliation(s)
- Gwonjin Lee
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Hassan Ahmadi
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Julia Quintana
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Lara Syllwasschy
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Nadežda Janina
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Veronica Preite
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Justin E Anderson
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Björn Pietzenuk
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, Bochum, Germany
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7
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Schulz E, Tohge T, Winkler JB, Albert A, Schäffner AR, Fernie AR, Zuther E, Hincha DK. Natural Variation among Arabidopsis Accessions in the Regulation of Flavonoid Metabolism and Stress Gene Expression by Combined UV Radiation and Cold. PLANT & CELL PHYSIOLOGY 2021; 62:502-514. [PMID: 33544865 PMCID: PMC8286136 DOI: 10.1093/pcp/pcab013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 01/20/2021] [Indexed: 05/20/2023]
Abstract
Plants are constantly exposed to stressful environmental conditions. Plant stress reactions were mainly investigated for single stress factors. However, under natural conditions plants may be simultaneously exposed to different stresses. Responses to combined stresses cannot be predicted from the reactions to the single stresses. Flavonoids accumulate in Arabidopsis thaliana during exposure to UV-A, UV-B or cold, but the interactions of these factors on flavonoid biosynthesis were unknown. We therefore investigated the interaction of UV radiation and cold in regulating the expression of well-characterized stress-regulated genes, and on transcripts and metabolites of the flavonoid biosynthetic pathway in 52 natural Arabidopsis accessions that differ widely in their freezing tolerance. The data revealed interactions of cold and UV on the regulation of stress-related and flavonoid biosynthesis genes, and on flavonoid composition. In many cases, plant reactions to a combination of cold and UV were unique under combined stress and not predictable from the responses to the single stresses. Strikingly, all correlations between expression levels of flavonoid biosynthesis genes and flavonol levels were abolished by UV-B exposure. Similarly, correlations between transcript levels of flavonoid biosynthesis genes or flavonoid contents, and freezing tolerance were lost in the presence of UV radiation, while correlations with the expression levels of cold-regulated genes largely persisted. This may indicate different molecular cold acclimation responses in the presence or absence of UV radiation.
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Affiliation(s)
- Elisa Schulz
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam 14476, Germany
- MetaSysX GmbH, Am Mühlenberg 11, Potsdam 14476, Germany
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam 14476, Germany
- Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Ikoma, 630-0192 Japan
| | - J Barbro Winkler
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Andreas Albert
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
- Deutsches Patent- und Markenamt, Zweibrückenstr. 12, München 80331, Germany
| | - Anton R Schäffner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam 14476, Germany
| | - Ellen Zuther
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam 14476, Germany
- Corresponding author: E-mail,
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam 14476, Germany
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8
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Amirikhah R, Etemadi N, Sabzalian MR, Nikbakht A, Eskandari A. Gamma radiation negatively impacted seed germination, seedling growth and antioxidant enzymes activities in tall fescue infected with Epichloë endophyte. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 216:112169. [PMID: 33826977 DOI: 10.1016/j.ecoenv.2021.112169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/19/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Plants and their accompanying microorganisms growing in contaminated sites with long-lived gamma-emitting radionuclides may be affected by radiation stress. The present study aimed to investigate the effects of gamma radiation on symbiotic relationship between Epichloë endophyte and Festuca arundinacea plant along with the radio-sensitivity of a pair of clones of tall fescue with (E+) and without (E-) symbiotic Epichloë endophyte exposed to different doses of gamma radiation including 25, 50, 75, 100, 150, 200, 300, and 400 Gray (Gy) from a Cobalt-60 source. Both irradiated and non-irradiated seeds of each status were grown under controlled conditions. Seed germination indices, seedling growth and certain physiological criteria associated with plant responses to oxidative stress were examined. The results revealed that low doses (up to 75 Gy) of gamma radiation stimulated seed germination indices and seedling growth. However, high doses (100-400 Gy) significantly reduced the final germination percentage, germination rate index, coefficient of velocity of germination, and the seed reserve depletion percentage, and enhanced the mean germination time. Further, high doses of radiation reduced root and shoot lengths, root and shoot fresh weights, and activities of antioxidant enzymes (especially catalase and superoxide dismutase), and increased the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) of the seedlings. The results showed that the endophyte was present in seeds after gamma ray irradiation. However, the presence of endophyte in seedlings started to be reduced significantly (18.45% reduction rather than the control) at 50 Gy of gamma radiation. High doses (100 Gy and above) dramatically declined the presence of endophyte down to zero in seedlings compared to the control. In this study, the E- clone had higher seed germination and seedling growth as well as lower H2O2 and MDA contents under radiation stress as compared with the E+ clone. Additionally, shoot tolerance index (STI) indicated more radiation tolerance in the E- clone. According to the results of the present study, it is concluded that biological impacts of gamma radiation stress and the harmful effects on endophyte viability may cause more radio-sensitivity and changes in the growth and physio-biochemical aspects of the host plant.
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Affiliation(s)
- Rahim Amirikhah
- Department of Horticultural Science, College of Agriculture, Isfahan University of Technology, 84156-83111 Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticultural Science, College of Agriculture, Isfahan University of Technology, 84156-83111 Isfahan, Iran.
| | - Mohammad R Sabzalian
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, 84156-83111 Isfahan, Iran
| | - Ali Nikbakht
- Department of Horticultural Science, College of Agriculture, Isfahan University of Technology, 84156-83111 Isfahan, Iran
| | - Ali Eskandari
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute, Karaj, Iran
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9
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Van Vu T, Thi Hai Doan D, Kim J, Sung YW, Thi Tran M, Song YJ, Das S, Kim J. CRISPR/Cas-based precision genome editing via microhomology-mediated end joining. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:230-239. [PMID: 33047464 PMCID: PMC7868975 DOI: 10.1111/pbi.13490] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 10/03/2020] [Indexed: 05/05/2023]
Abstract
Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteKm 02, Pham Van Dong RoadCo Nhue 1, Bac Tu Liem, Hanoi11917Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- Division of Life ScienceGyeongsang National University501 Jinju‐daeroJinju52828Republic of Korea
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10
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The Dark Side of UV-Induced DNA Lesion Repair. Genes (Basel) 2020; 11:genes11121450. [PMID: 33276692 PMCID: PMC7761550 DOI: 10.3390/genes11121450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
In their life cycle, plants are exposed to various unfavorable environmental factors including ultraviolet (UV) radiation emitted by the Sun. UV-A and UV-B, which are partially absorbed by the ozone layer, reach the surface of the Earth causing harmful effects among the others on plant genetic material. The energy of UV light is sufficient to induce mutations in DNA. Some examples of DNA damage induced by UV are pyrimidine dimers, oxidized nucleotides as well as single and double-strand breaks. When exposed to light, plants can repair major UV-induced DNA lesions, i.e., pyrimidine dimers using photoreactivation. However, this highly efficient light-dependent DNA repair system is ineffective in dim light or at night. Moreover, it is helpless when it comes to the repair of DNA lesions other than pyrimidine dimers. In this review, we have focused on how plants cope with deleterious DNA damage that cannot be repaired by photoreactivation. The current understanding of light-independent mechanisms, classified as dark DNA repair, indispensable for the maintenance of plant genetic material integrity has been presented.
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11
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Jaikumar NS, Dorn KM, Baas D, Wilke B, Kapp C, Snapp SS. Nucleic acid damage and DNA repair are affected by freezing stress in annual wheat (Triticum aestivum) and by plant age and freezing in its perennial relative (Thinopyrum intermedium). AMERICAN JOURNAL OF BOTANY 2020; 107:1693-1709. [PMID: 33340368 DOI: 10.1002/ajb2.1584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/27/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Nucleic acid integrity can be compromised under many abiotic stresses. To date, however, few studies have considered whether nucleic acid damage and damage repair play a role in cold-stress adaptation. A further insufficiently explored question concerns how age affects cold stress adaptation among mature perennials. As a plant ages, the optimal trade-off between growth and stress tolerance may shift. METHODS Oxidative damage to RNA and expression of genes involved in DNA repair were compared in multiple mature cohorts of Thinopyrum intermedium (an emerging perennial cereal) and in wheat and barley under intermittent freezing stress and under nonfreezing conditions. Activity of glutathione peroxidase (GPX) and four other antioxidative enzymes was also measured under these conditions. DNA repair genes included photolyases involved in repairing ultraviolet-induced damage and two genes involved in repairing oxidatively induced damage (ERCC1, RAD23). RESULTS Freezing stress was accompanied by large increases in photolyase expression and ERCC1 expression (in wheat and Thinopyrum) and in GPX and GR activity (particularly in Thinopyrum). This is the first report of DNA photolyases being overexpressed under freezing stress. Older Thinopyrum had lower photolyase expression and less freezing-induced overexpression of ERCC1. Younger Thinopyrum plants sustained more oxidative damage to RNA. CONCLUSIONS Overexpression of DNA repair genes is an important aspect of cold acclimation. When comparing adult cohorts, aging was associated with changes in the freezing stress response, but not with overall increases or decreases in stress tolerance.
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Affiliation(s)
- Nikhil S Jaikumar
- Institute for Genomic Biology, University of Illinois Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Kevin M Dorn
- United States Department of Agriculture, Agricultural Research Service, Soil Management and Sugarbeet Research Unit, 1701 Centre Ave, Fort Collins, CO, 80526, USA
| | - Dean Baas
- Michigan State University Extension, 612 E. Main Street, Centreville, MI, 49032, USA
| | - Brook Wilke
- Kellogg Biological Station, Michigan State University, 3700 East Gull Lake Drive, Hickory Corners, MI, 49060, USA
| | - Christian Kapp
- Upper Peninsula Research and Extension Center, Michigan State University, E3774 University Drive, Chatham, MI, 49816, USA
| | - Sieglinde S Snapp
- Department of Plant, Soil and Microbial Science, Michigan State University, 1066 Bogue St., East Lansing, MI, 48824, USA
- Center for Global Change and Earth Observations, Michigan State University, 1405 S Harrison Rd., East Lansing, MI, 48823, USA
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12
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Wang Y, Singh R, Tong E, Tang M, Zheng L, Fang H, Li R, Guo L, Song J, Srinivasan R, Sharma A, Lin L, Trujillo JA, Manshardt R, Chen LY, Ming R, Yu Q. Positional cloning and characterization of the papaya diminutive mutant reveal a truncating mutation in the CpMMS19 gene. THE NEW PHYTOLOGIST 2020; 225:2006-2021. [PMID: 31733154 DOI: 10.1111/nph.16325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
The papaya diminutive mutant exhibits miniature stature, retarded growth and reduced fertility. This undesirable mutation appeared in the variety 'Sunset', the progenitor of the transgenic line 'SunUp', and was accidentally carried forward into breeding populations. The diminutive mutation was mapped to chromosome 2 and fine mapped to scaffold 25. Sequencing of a bacterial artificial chromosome in the fine mapped region led to the identification of the target gene responsible for the diminutive mutant, a gene orthologous to MMS19 with a 36.8 kb deletion co-segregating with the diminutive mutant. The genomic sequence of CpMMS19 is 62 kb, consisting of 20 exons and 19 introns. It encodes a protein of 1143 amino acids while the diminutive allele encodes a truncated protein of 287 amino acids. Expression of the full-length CpMMS19 was able to complement the thermosensitive growth of the yeast mms19 deletion mutant while expression of the diminutive allele resulted in increased thermosensitivity. Over-expression of the diminutive allele in Arabidopsis met18 mutant results in a high frequency of seed abortion. The papaya diminutive phenotype is caused by an alteration in gene function rather than a loss-of-function mutation. SCAR (sequence characterized amplified region) markers were developed for rapid detection of the diminutive allele in breeding populations.
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Affiliation(s)
- Ying Wang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Eric Tong
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Min Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwei Zheng
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Hongkun Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruoyu Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Guo
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinjin Song
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rajeswari Srinivasan
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jorge A Trujillo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Richard Manshardt
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
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13
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Amirikhah R, Etemadi N, Sabzalian MR, Nikbakht A, Eskandari A. Physiological consequences of gamma ray irradiation in tall fescue with elimination potential of Epichloë fungal endophyte. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109412. [PMID: 31295658 DOI: 10.1016/j.ecoenv.2019.109412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 06/01/2019] [Accepted: 07/02/2019] [Indexed: 06/09/2023]
Abstract
Perennial plants and their associated microorganisms grow in the areas that may be contaminated with long-lived gamma-emitting radionuclides. This will induce gamma stress response in plants and their accompanying microorganisms. The present work investigated the growth and physiological responses of Epichloe endophyte infected tall fescue to gamma radiation, as well as whether the endophyte could persist and infect the host plant once exposed to gamma radiation. Seeds of Iranian native genotype of 75B+ of tall fescue were exposed to different doses, including 5.0, 10.0, 15.0, 20.0, 30.0 and 40.0 krad of gamma ray from a 60Co source. Irradiated and unirradiated seeds were sown in pots and grown under controlled conditions in the greenhouse. The growth and physiological parameters associated with plant tolerance to oxidative stress of host plants, as well as endophytic infection frequency (% of plants infected) and intensity (mean number of endophytic hyphae per the field of view), were examined in 3 months-old seedlings. The results indicated that all gamma radiation doses (except 5.0 kr) significantly reduced the height and survival percentage of the host plant. Days to the emergence of seedling increased gradually as gamma doses rose. A dose-rate dependent induction was seen for photosynthetic pigments and proline content. Malondialdehyde (MDA) content grew with elevation of irradiation doses. Depending on the dose and time, the activities of antioxidant enzymes in the host plant responded differently to gamma radiation. Gamma radiation altered the enzyme activities with sever decline in SOD and CAT activities. However, it had barely any effect on in APX and POD activities. The results also revealed that the persistence and intensity of endophyte were affected after gamma-ray irradiation. The initial percentage of tall fescue seeds infected with the endophyte was 91% in un-irradiated seeds. Presence of the viable endophyte started to decline significantly (23%) at 5.0 kr of gamma radiation. A dramatic reduction in the presence and intensity of endophyte occurred at 10.0 to 40.0 kr intensities. Gamma radiation × trait (GT)-biplot analysis indicated positive correlations between the endophyte symbiosis and antioxidant enzyme activities. Also, negative correlations were observed between the endophyte and MDA content in the host plant. Our results suggest that radiation stress (doses over 5.0 kr) caused reduction in the growth and antioxidant enzyme activities of the host plant that accompanied by a dramatic reduction in the persistence and intensity of endophyte fungi. Our findings have provided the basic information for future studies on the effect of gamma irradiation on the interaction between endophytic fungi and its host plant.
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Affiliation(s)
- Rahim Amirikhah
- Department of Horticultural Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticultural Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran.
| | - Mohammad R Sabzalian
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Ali Nikbakht
- Department of Horticultural Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran
| | - Ali Eskandari
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute, Karaj, Iran
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Guyon-Debast A, Rossetti P, Charlot F, Epert A, Neuhaus JM, Schaefer DG, Nogué F. The XPF-ERCC1 Complex Is Essential for Genome Stability and Is Involved in the Mechanism of Gene Targeting in Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2019; 10:588. [PMID: 31143199 PMCID: PMC6521618 DOI: 10.3389/fpls.2019.00588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
The XPF-ERCC1 complex, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair, and homologous recombination. XPF-ERCC1 incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here, we have examined the role of the XPF-ERCC1 complex in the model bryophyte Physcomitrella patens which exhibits uniquely high gene targeting frequencies. We undertook targeted knockout of the Physcomitrella ERCC1 and XPF genes. Mutant analysis shows that the endonuclease complex is essential for resistance to UV-B and to the alkylating agent MMS, and contributes to the maintenance of genome integrity but is also involved in gene targeting in this model plant. Using different constructs we determine whether the function of the XPF-ERCC1 endonuclease complex in gene targeting was removal of 3' non-homologous termini, similar to SSA, or processing of looped-out heteroduplex intermediates. Interestingly, our data suggest a role of the endonuclease in both pathways and have implications for the mechanism of targeted gene replacement in plants and its specificities compared to yeast and mammalian cells.
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Affiliation(s)
- Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Patricia Rossetti
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aline Epert
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Jean-Marc Neuhaus
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Didier G. Schaefer
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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15
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Kim JH, Ryu TH, Lee SS, Lee S, Chung BY. Ionizing radiation manifesting DNA damage response in plants: An overview of DNA damage signaling and repair mechanisms in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 278:44-53. [PMID: 30471728 DOI: 10.1016/j.plantsci.2018.10.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/30/2018] [Accepted: 10/16/2018] [Indexed: 05/23/2023]
Abstract
Plants orchestrate various DNA damage responses (DDRs) to overcome the deleterious impacts of genotoxic agents on genetic materials. Ionizing radiation (IR) is widely used as a potent genotoxic agent in plant DDR research as well as plant breeding and quarantine services for commercial uses. This review aimed to highlight the recent advances in cellular and phenotypic DDRs, especially those induced by IR. Various physicochemical genotoxic agents damage DNA directly or indirectly by inhibiting DNA replication. Among them, IR-induced DDRs are considerably more complicated. Many aspects of such DDRs and their initial transcriptomes are closely related to oxidative stress response. Although many key components of DDR signaling have been characterized in plants, DDRs in plant cells are not understood in detail to allow comparison with those in yeast and mammalian cells. Recent studies have revealed plant DDR signaling pathways including the key regulator SOG1. The SOG1 and its upstream key components ATM and ATR could be functionally characterized by analyzing their knockout DDR phenotypes after exposure to IR. Considering the potent genotoxicity of IR and its various DDR phenotypes, IR-induced DDR studies should help to establish an integrated model for plant DDR signaling pathways by revealing the unknown key components of various DDRs in plants.
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Affiliation(s)
- Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Tae Ho Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Sungbeom Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea; Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Byung Yeoup Chung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
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16
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Nikitaki Z, Holá M, Donà M, Pavlopoulou A, Michalopoulos I, Angelis KJ, Georgakilas AG, Macovei A, Balestrazzi A. Integrating plant and animal biology for the search of novel DNA damage biomarkers. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 775:21-38. [DOI: 10.1016/j.mrrev.2018.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
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17
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Boubriak I, Akimkina T, Polischuk V, Dmitriev A, McCready S, Grodzinsky D. Long term effects of Chernobyl contamination on DNA repair function and plant resistance to different biotic and abiotic stress factors. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716060049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Lytvyn DI, Raynaud C, Yemets AI, Bergounioux C, Blume YB. Involvement of Inositol Biosynthesis and Nitric Oxide in the Mediation of UV-B Induced Oxidative Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:430. [PMID: 27148278 PMCID: PMC4828445 DOI: 10.3389/fpls.2016.00430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/18/2016] [Indexed: 05/12/2023]
Abstract
The involvement of NO-signaling in ultraviolet B (UV-B) induced oxidative stress (OS) in plants is an open question. Inositol biosynthesis contributes to numerous cellular functions, including the regulation of plants tolerance to stress. This work reveals the involvement of inositol-3-phosphate synthase 1 (IPS1), a key enzyme for biosynthesis of myo-inositol and its derivatives, in the response to NO-dependent OS in Arabidopsis. Homozygous mutants deficient for IPS1 (atips1) and wild-type plants were transformed with a reduction- grx1-rogfp2 and used for the dynamic measurement of UV-B-induced and SNP (sodium nitroprusside)-mediated oxidative stresses by confocal microscopy. atips1 mutants displayed greater tissue-specific resistance to the action of UV-B than the wild type. SNP can act both as an oxidant or repairer depending on the applied concentration, but mutant plants were more tolerant than the wild type to nitrosative effects of high concentration of SNP. Additionally, pretreatment with low concentrations of SNP (10, 100 μM) before UV-B irradiation resulted in a tissue-specific protective effect that was enhanced in atips1. We conclude that the interplay between nitric oxide and inositol signaling can be involved in the mediation of UV-B-initiated oxidative stress in the plant cell.
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Affiliation(s)
- Dmytro I. Lytvyn
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of UkraineKyiv, Ukraine
- *Correspondence: Dmytro I. Lytvyn,
| | - Cécile Raynaud
- Laboratory of Cell Cycle Chromatin and Development, Institute of Plant Sciences Paris-Saclay IPS2, CNRS 9213, INRA 1403, Université Paris-Sud, Université Evry Val d’Essonne, Université Paris Diderot, Sorbonne Paris-Cite, Universite Paris-SaclayOrsay, France
| | - Alla I. Yemets
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of UkraineKyiv, Ukraine
| | - Catherine Bergounioux
- Laboratory of Cell Cycle Chromatin and Development, Institute of Plant Sciences Paris-Saclay IPS2, CNRS 9213, INRA 1403, Université Paris-Sud, Université Evry Val d’Essonne, Université Paris Diderot, Sorbonne Paris-Cite, Universite Paris-SaclayOrsay, France
| | - Yaroslav B. Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of UkraineKyiv, Ukraine
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19
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DNA damage and repair in plants under ultraviolet and ionizing radiations. ScientificWorldJournal 2015; 2015:250158. [PMID: 25729769 PMCID: PMC4333283 DOI: 10.1155/2015/250158] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/27/2014] [Accepted: 11/04/2014] [Indexed: 11/17/2022] Open
Abstract
Being sessile, plants are continuously exposed to DNA-damaging agents present in the environment such as ultraviolet (UV) and ionizing radiations (IR). Sunlight acts as an energy source for photosynthetic plants; hence, avoidance of UV radiations (namely, UV-A, 315–400 nm; UV-B, 280–315 nm; and UV-C, <280 nm) is unpreventable. DNA in particular strongly absorbs UV-B; therefore, it is the most important target for UV-B induced damage. On the other hand, IR causes water radiolysis, which generates highly reactive hydroxyl radicals (OH•) and causes radiogenic damage to important cellular components. However, to maintain genomic integrity under UV/IR exposure, plants make use of several DNA repair mechanisms. In the light of recent breakthrough, the current minireview (a) introduces UV/IR and overviews UV/IR-mediated DNA damage products and (b) critically discusses the biochemistry and genetics of major pathways responsible for the repair of UV/IR-accrued DNA damage. The outcome of the discussion may be helpful in devising future research in the current context.
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20
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Characterization of DNA repair deficient strains of Chlamydomonas reinhardtii generated by insertional mutagenesis. PLoS One 2014; 9:e105482. [PMID: 25144319 PMCID: PMC4140758 DOI: 10.1371/journal.pone.0105482] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022] Open
Abstract
While the mechanisms governing DNA damage response and repair are fundamentally conserved, cross-kingdom comparisons indicate that they differ in many aspects due to differences in life-styles and developmental strategies. In photosynthetic organisms these differences have not been fully explored because gene-discovery approaches are mainly based on homology searches with known DDR/DNA repair proteins. Here we performed a forward genetic screen in the green algae Chlamydomonas reinhardtii to identify genes deficient in DDR/DNA repair. We isolated five insertional mutants that were sensitive to various genotoxic insults and two of them exhibited altered efficiency of transgene integration. To identify genomic regions disrupted in these mutants, we established a novel adaptor-ligation strategy for the efficient recovery of the insertion flanking sites. Four mutants harbored deletions that involved known DNA repair factors, DNA Pol zeta, DNA Pol theta, SAE2/COM1, and two neighbouring genes encoding ERCC1 and RAD17. Deletion in the last mutant spanned two Chlamydomonas-specific genes with unknown function, demonstrating the utility of this approach for discovering novel factors involved in genome maintenance.
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21
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Missirian V, Conklin PA, Culligan KM, Huefner ND, Britt AB. High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core "DSB" response specific to clastogenic treatments. FRONTIERS IN PLANT SCIENCE 2014; 5:364. [PMID: 25136344 PMCID: PMC4117989 DOI: 10.3389/fpls.2014.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/08/2014] [Indexed: 05/19/2023]
Abstract
Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as "collateral" damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe(26+) high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the "DSB response" were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing "extended night." This response was not apparent in gamma-irradiated plants.
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Affiliation(s)
- Victor Missirian
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Phillip A. Conklin
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Kevin M. Culligan
- Department of Molecular, Cellular, and Biomedical Sciences, University of New HampshireDurham, NH, USA
| | - Neil D. Huefner
- Department of Plant Biology, University of California DavisDavis, CA, USA
| | - Anne B. Britt
- Department of Plant Biology, University of California DavisDavis, CA, USA
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22
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Fan J, Shi M, Huang JZ, Xu J, Wang ZD, Guo DP. Regulation of photosynthetic performance and antioxidant capacity by ⁶⁰Co γ-irradiation in Zizania latifolia plants. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2014; 129:33-42. [PMID: 24355402 DOI: 10.1016/j.jenvrad.2013.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 11/10/2013] [Accepted: 11/26/2013] [Indexed: 06/03/2023]
Abstract
The aim of the present work was to investigate the photosynthetic performance and antioxidant enzyme activities in response to γ-irradiation of an aquatic plant Zizania latifolia. The Z. latifolia seedlings at 6-leaf stage were exposed to 25, 50 and 100 Gy of γ rays from a (60)Co source. The growth parameters, chlorophyll contents, photosynthetic gas exchange, chlorophyll fluorescence, malondialdehyde (MDA) content, antioxidant enzyme activities and antioxidant contents were examined at 1-5 weeks post-irradiation (WPI). The results showed that plant height, leaf number and tiller (branch close to ground) number were significantly suppressed by 50 and 100 Gy irradiation at 5, 3-5 and 4-5 WPI, respectively, but they were not significantly different from control by 25 Gy irradiation. Chlorophyll a, chlorophyll b, and total chlorophyll contents were also found to be significantly decreased by irradiation. The net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci) and transpiration rate (Tr) generally declined in a dose-dependent manner. As for the chlorophyll fluorescence parameters, maximum quantum efficiency of PSII photochemistry (Fv/Fm), actual photochemical efficiency of PSII (Φ(PSII)) and photochemical quenching (qP) were observed to be significantly decreased compared to the control at 3 WPI, while non-photochemical quenching (NPQ) significantly increased by 100 Gy. γ-irradiation induced substantial increase in MDA content, ascorbate peroxidase (APX) activity, reduced ascorbate (AsA) content and reduced glutathione (GSH) content, suggesting a protective mechanism of Z. latifolia plant against oxidative stress when exposed to γ-irradiation.
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Affiliation(s)
- Jing Fan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Min Shi
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, PR China
| | - Jian-Zhong Huang
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou 310029, PR China.
| | - Jie Xu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - Zhi-Dan Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China
| | - De-Ping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.
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23
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Cheng Z, Lin J, Lin T, Xu M, Huang Z, Yang Z, Huang X, Zheng J. Genome-wide analysis of radiation-induced mutations in rice (Oryza sativa L. ssp. indica). MOLECULAR BIOSYSTEMS 2014; 10:795-805. [PMID: 24457353 DOI: 10.1039/c3mb70349e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Radiation has been efficiently used for rice germplasm innovation. However, the molecular mechanisms by which radiation induces mutations are still unclear. In this study, we performed whole genome sequencing to reveal the comprehensive mutations in rice treated with radiation. Red-1 (a rice rich in beneficial ingredients for human health) was derived from rice 9311 after γ-radiation. Solexa sequencing technology was applied to uncover the mutations. Compared with the 9311 genome, 9.19% of genome sequences were altered in the Red-1 genome. Among these alterations, there were 381,403 SNPs, 50,116 1-5 bp Indels, 1279 copy number variations, and 10,026 presence/absence variations. These alterations were located in 14,493 genes, the majority of which contained a kinase domain, leucine rich repeats, or Cyt_P450. Point mutations were the main type of variation in the Red-1 genome. Gene ontology clustering revealed that genes that are associated with cell components, binding function, catalytic activity and metabolic processes were susceptible to γ-radiation. It was also predicted that 8 mutated genes were involved in the biosynthetic pathways of beneficial products or pigment accumulation. We conclude that genome-wide analysis of mutations provides novel insights into the mechanisms by which radiation improves the beneficial ingredients in rice Red-1.
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Affiliation(s)
- Zuxin Cheng
- Crop Quality Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Differentially expressed genes in response to gamma-irradiation during the vegetative stage in Arabidopsis thaliana. Mol Biol Rep 2014; 41:2229-41. [PMID: 24442319 DOI: 10.1007/s11033-014-3074-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 01/04/2014] [Indexed: 10/25/2022]
Abstract
Biochemical and physiological processes in plants are affected by gamma-irradiation, which causes significant changes in gene transcripts and expression. To identify the differentially expressed Arabidopsis genes in response to gamma-irradiation, we performed a microarray analysis with rosette leaves during the vegetative stage. Arabidopsis plants were exposed to a wide spectrum doses of gamma ray (100, 200, 300, 400, 800, 1200, 1600 or 2000 Gy) for 24 h. At the dose range from 100 to 400 Gy, irradiated plants were found to be shorter than controls after 8 days of irradiation, while doses over 800 Gy caused severe growth retardation. Therefore, 100 and 800 Gy were selected as adequate doses for microarray analysis to identify differentially expressed genes. Among the 20,993 genes used as microarray probes, a total number of 496 and 1,042 genes were up-regulated and down-regulated by gamma-irradiation, respectively (P < 0.05). We identified the characteristics of the genes that were up-and down-regulated fourfold higher genes by gamma irradiation according to The arabidopsis information resource gene ontology. To confirm the microarray results, we performed a northern blot and quantitative real-time PCR with several selected genes that had a large difference in expression after irradiation. In particular, genes associated with lipid transfer proteins, histones and transposons were down-regulated by 100 and/or 800 Gy of gamma irradiation. The expression patterns of selected genes were generally in agreement with the microarray results, although there were quantitative differences in the expression levels.
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Abstract
Solar ultraviolet (UV) radiation, mainly UV-B (280-315 nm), is one of the most potent genotoxic agents that adversely affects living organisms by altering their genomic stability. DNA through its nucleobases has absorption maxima in the UV region and is therefore the main target of the deleterious radiation. The main biological relevance of UV radiation lies in the formation of several cytotoxic and mutagenic DNA lesions such as cyclobutane pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers (DEWs), as well as DNA strand breaks. However, to counteract these DNA lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, excision repair, and mismatch repair (MMR). Photoreactivation involving the enzyme photolyase is the most frequently used repair mechanism in a number of organisms. Excision repair can be classified as base excision repair (BER) and nucleotide excision repair (NER) involving a number of glycosylases and polymerases, respectively. In addition to this, double-strand break repair, SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms to ensure genomic stability. This review concentrates on the UV-induced DNA damage and the associated repair mechanisms as well as various damage detection methods.
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Affiliation(s)
- Richa
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, 221005, India
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Huefner ND, Yoshiyama K, Friesner JD, Conklin PA, Britt AB. Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2014; 5:206. [PMID: 24904606 PMCID: PMC4033213 DOI: 10.3389/fpls.2014.00206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
Low linear energy transfer (LET) gamma rays and high LET HZE (high atomic weight, high energy) particles act as powerful mutagens in both plants and animals. DNA damage generated by HZE particles is more densely clustered than that generated by gamma rays. To understand the genetic requirements for resistance to high versus low LET radiation, a series of Arabidopsis thaliana mutants were exposed to either 1GeV Fe nuclei or gamma radiation. A comparison of effects on the germination and subsequent growth of seedlings led us to conclude that the relative biological effectiveness (RBE) of the two types of radiation (HZE versus gamma) are roughly 3:1. Similarly, in wild-type lines, loss of somatic heterozygosity was induced at an RBE of about a 2:1 (HZE versus gamma). Checkpoint and repair defects, as expected, enhanced sensitivity to both agents. The "replication fork" checkpoint, governed by ATR, played a slightly more important role in resistance to HZE-induced mutagenesis than in resistance to gamma induced mutagenesis.
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Affiliation(s)
- Neil D. Huefner
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
| | - Kaoru Yoshiyama
- Department of Plant Biology, University of California at DavisDavis, CA, USA
| | - Joanna D. Friesner
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
| | - Phillip A. Conklin
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
| | - Anne B. Britt
- Department of Plant Biology, University of California at DavisDavis, CA, USA
- Graduate Program in Genetics, University of California at DavisDavis, CA, USA
- *Correspondence: Anne B. Britt, Department of Plant Biology, University of California at Davis, 1002 Life Sciences, One Shields Avenue, Davis, CA 95616, USA e-mail:
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Ly V, Hatherell A, Kim E, Chan A, Belmonte MF, Schroeder DF. Interactions between Arabidopsis DNA repair genes UVH6, DDB1A, and DDB2 during abiotic stress tolerance and floral development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 213:88-97. [PMID: 24157211 DOI: 10.1016/j.plantsci.2013.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 05/29/2023]
Abstract
Plants must protect themselves from a spectrum of abiotic stresses. For example, the sun is a source of heat, intense light, and DNA-damaging ultraviolet (UV) rays. Damaged DNA binding protein 1A (DDB1A), DDB2, and UV hypersensitive 6 (UVH6)/XPD are all involved in the repair of UV-damaged DNA - DDB1A and DDB2 in the initial damage recognition stage, while the UVH6/XPD helicase unwinds the damaged strand. We find that, as predicted, Arabidopsis ddb1a and ddb2 mutants do not affect uvh6/xpd UV tolerance. In addition, uvh6 is heat sensitive, and ddb1a and ddb2 weakly enhance this trait. The uvh6 ddb1a and uvh6 ddb2 double mutants also exhibit sensitivity to oxidative stress, suggesting a role for DDB1 complexes in heat and oxidative stress tolerance. Finally, we describe a new uvh6 phenotype, the low penetrance production of flowers with five petals and five sepals. ddb1a and ddb2 suppress this phenotype in uvh6 mutants. Interestingly, heat treatment also induces five-petalled flowers in the ddb1a and ddb2 single mutants. Thus UVH6, DDB1A, and DDB2 all contribute to UV tolerance, heat tolerance and floral patterning.
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Affiliation(s)
- Valentina Ly
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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28
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Stoilov L, Georgieva M, Manova V, Liu L, Gecheff K. Karyotype reconstruction modulates the sensitivity of barley genome to radiation-induced DNA and chromosomal damage. Mutagenesis 2012; 28:153-60. [DOI: 10.1093/mutage/ges065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Campi M, D’Andrea L, Emiliani J, Casati P. Participation of chromatin-remodeling proteins in the repair of ultraviolet-B-damaged DNA. PLANT PHYSIOLOGY 2012; 158:981-95. [PMID: 22170978 PMCID: PMC3271783 DOI: 10.1104/pp.111.191452] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/14/2011] [Indexed: 05/17/2023]
Abstract
The genome of plants is organized into chromatin, affecting the rates of transcription, DNA recombination, and repair. In this work, we have investigated the consequences of reduced expression of some chromatin-remodeling factors and histone acetylation in maize (Zea mays) and Arabidopsis (Arabidopsis thaliana) in their participation in DNA repair after ultraviolet (UV)-B irradiation. Plants deficient in NFC102/NFC4 or SDG102/SDG26 showed more damaged DNA than wild-type plants; however, the Arabidopsis chc1 mutant showed similar accumulation of cyclobutane pyrimidine dimers as wild-type plants, in contrast to the increased DNA damage measured in the maize chc101 RNA interference line. In Arabidopsis, plants deficient in chromatin remodeling are also affected in the accumulation of pigments by UV-B. Plants treated with an inhibitor of histone acetyltransferases, curcumin, previous to the UV-B treatment show deficiencies in DNA repair; in addition, the chromatin remodeling-deficient plants have altered levels of acetylated histones after the UV-B treatment, demonstrating that histone acetylation is important during DNA repair in these two plant species. Arabidopsis mutants ham1 and ham2 also showed increased DNA damage after UV-B, suggesting that the role of these proteins in DNA damage repair has been conserved through evolution. However, cyclobutane pyrimidine dimer accumulation was higher in ham1 than in ham2; suggesting that HAM1 has a major role in DNA repair after UV-B. In summary, in this work, we have demonstrated that chromatin remodeling, and histone acetylation in particular, is important during DNA repair by UV-B, demonstrating that both genetic and epigenetic effects control DNA repair in plants.
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Affiliation(s)
| | | | | | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, 2000 Rosario, Argentina
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Dumont M, Massot S, Doutriaux MP, Gratias A. Characterization of Brca2-deficient plants excludes the role of NHEJ and SSA in the meiotic chromosomal defect phenotype. PLoS One 2011; 6:e26696. [PMID: 22039535 PMCID: PMC3198793 DOI: 10.1371/journal.pone.0026696] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/02/2011] [Indexed: 12/22/2022] Open
Abstract
In somatic cells, three major pathways are involved in the repair of DNA double-strand breaks (DBS): Non-Homologous End Joining (NHEJ), Single-Strand Annealing (SSA) and Homologous Recombination (HR). In somatic and meiotic HR, DNA DSB are 5′ to 3′ resected, producing long 3′ single-stranded DNA extensions. Brca2 is essential to load the Rad51 recombinase onto these 3′ overhangs. The resulting nucleofilament can thus invade a homologous DNA sequence to copy and restore the original genetic information. In Arabidopsis, the inactivation of Brca2 specifically during meiosis by an RNAi approach results in aberrant chromosome aggregates, chromosomal fragmentation and missegregation leading to a sterility phenotype. We had previously suggested that such chromosomal behaviour could be due to NHEJ. In this study, we show that knock-out plants affected in both BRCA2 genes show the same meiotic phenotype as the RNAi-inactivated plants. Moreover, it is demonstrated that during meiosis, neither NHEJ nor SSA compensate for HR deficiency in BRCA2-inactivated plants. The role of the plant-specific DNA Ligase6 is also excluded. The possible mechanism(s) involved in the formation of these aberrant chromosomal bridges in the absence of HR during meiosis are discussed.
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Affiliation(s)
- Marilyn Dumont
- Institut de Biologie des Plantes, CNRS UMR8618, Université Paris Sud-11, Orsay, France
| | - Sophie Massot
- Institut de Biologie des Plantes, CNRS UMR8618, Université Paris Sud-11, Orsay, France
| | | | - Ariane Gratias
- Institut de Biologie des Plantes, CNRS UMR8618, Université Paris Sud-11, Orsay, France
- * E-mail:
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Zhang Y, Rohde LH, Wu H. Involvement of nucleotide excision and mismatch repair mechanisms in double strand break repair. Curr Genomics 2011; 10:250-8. [PMID: 19949546 PMCID: PMC2709936 DOI: 10.2174/138920209788488544] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/28/2009] [Accepted: 03/30/2009] [Indexed: 11/25/2022] Open
Abstract
Living organisms are constantly threatened by environmental DNA-damaging agents, including UV and ionizing radiation (IR). Repair of various forms of DNA damage caused by IR is normally thought to follow lesion-specific repair pathways with distinct enzymatic machinery. DNA double strand break is one of the most serious kinds of damage induced by IR, which is repaired through double strand break (DSB) repair mechanisms, including homologous recombination (HR) and non-homologous end joining (NHEJ). However, recent studies have presented increasing evidence that various DNA repair pathways are not separated, but well interlinked. It has been suggested that non-DSB repair mechanisms, such as Nucleotide Excision Repair (NER), Mismatch Repair (MMR) and cell cycle regulation, are highly involved in DSB repairs. These findings revealed previously unrecognized roles of various non-DSB repair genes and indicated that a successful DSB repair requires both DSB repair mechanisms and non-DSB repair systems. One of our recent studies found that suppressed expression of non-DSB repair genes, such as XPA, RPA and MLH1, influenced the yield of IR induced micronuclei formation and/or chromosome aberrations, suggesting that these genes are highly involved in DSB repair and DSB-related cell cycle arrest, which reveals new roles for these gene products in the DNA repair network. In this review, we summarize current progress on the function of non-DSB repair-related proteins, especially those that participate in NER and MMR pathways, and their influence on DSB repair. In addition, we present our developing view that the DSB repair mechanisms are more complex and are regulated by not only the well known HR/NHEJ pathways, but also a systematically coordinated cellular network.
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Affiliation(s)
- Ye Zhang
- NASA Johnson Space Center, Houston, Texas 77058
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32
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Gregg SQ, Robinson AR, Niedernhofer LJ. Physiological consequences of defects in ERCC1-XPF DNA repair endonuclease. DNA Repair (Amst) 2011; 10:781-91. [PMID: 21612988 DOI: 10.1016/j.dnarep.2011.04.026] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ERCC1-XPF is a structure-specific endonuclease required for nucleotide excision repair, interstrand crosslink repair, and the repair of some double-strand breaks. Mutations in ERCC1 or XPF cause xeroderma pigmentosum, XFE progeroid syndrome or cerebro-oculo-facio-skeletal syndrome, characterized by increased risk of cancer, accelerated aging and severe developmental abnormalities, respectively. This review provides a comprehensive overview of the health impact of ERCC1-XPF deficiency, based on these rare diseases and mouse models of them. This offers an understanding of the tremendous health impact of DNA damage derived from environmental and endogenous sources.
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Affiliation(s)
- Siobhán Q Gregg
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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33
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Rastogi RP, Richa, Kumar A, Tyagi MB, Sinha RP. Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucleic Acids 2010; 2010:592980. [PMID: 21209706 PMCID: PMC3010660 DOI: 10.4061/2010/592980] [Citation(s) in RCA: 589] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/15/2010] [Accepted: 09/28/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280-315 nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms.
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Affiliation(s)
- Rajesh P Rastogi
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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34
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Singh SK, Roy S, Choudhury SR, Sengupta DN. DNA repair and recombination in higher plants: insights from comparative genomics of Arabidopsis and rice. BMC Genomics 2010; 11:443. [PMID: 20646326 PMCID: PMC3091640 DOI: 10.1186/1471-2164-11-443] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 07/21/2010] [Indexed: 11/13/2022] Open
Abstract
Background The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them. Results We identified genes potentially involved in DRR mechanisms in Arabidopsis and rice using similarity searches and conserved domain analysis against proteins known to be involved in DRR in human, yeast and E. coli. As expected, many of DRR genes are very similar to those found in other eukaryotes. Beside these eukaryotes specific genes, several prokaryotes specific genes were also found to be well conserved in plants. In Arabidopsis, several functionally important DRR gene duplications are present, which do not occur in rice. Among DRR proteins, we found that proteins belonging to the nucleotide excision repair pathway were relatively more conserved than proteins needed for the other DRR pathways. Sub-cellular localization studies of DRR gene suggests that these proteins are mostly reside in nucleus while gene drain in between nucleus and cell organelles were also found in some cases. Conclusions The similarities and dissimilarities in between plants and other organisms' DRR pathways are discussed. The observed differences broaden our knowledge about DRR in the plants world, and raises the potential question of whether differentiated functions have evolved in some cases. These results, altogether, provide a useful framework for further experimental studies in these organisms.
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Affiliation(s)
- Sanjay K Singh
- Department of Botany, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700 009, India.
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Al Khateeb WM, Schroeder DF. Overexpression of Arabidopsis damaged DNA binding protein 1A (DDB1A) enhances UV tolerance. PLANT MOLECULAR BIOLOGY 2009; 70:371-83. [PMID: 19288212 DOI: 10.1007/s11103-009-9479-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 02/27/2009] [Indexed: 05/19/2023]
Abstract
Damaged DNA Binding protein 1 (DDB1) is a conserved protein and a component of multiple cellular complexes. Arabidopsis has two homologues of DDB1: DDB1A and DDB1B. In this study we examine the role of DDB1A in Arabidopsis UV tolerance and DNA repair using a DDB1A null mutant (ddb1a) and overexpression lines. DDB1A overexpression lines showed higher levels of UV-resistance than wild-type in a range of assays as well as faster DNA repair. However a significant difference between wild-type plants and ddb1a mutants was only observed immediately following UV treatment in root length and photoproduct repair assays. DDB1A and DDB1B mRNA levels increased 3 h after UV exposure and DDB1A is required for UV regulation of DDB1B and DDB2 mRNA levels. In conclusion, while DDB1A is sufficient to increase Arabidopsis UV tolerance, it is only necessary for immediate response to UV damage.
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Affiliation(s)
- Wesam M Al Khateeb
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
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Suppressor of gamma response 1 (SOG1) encodes a putative transcription factor governing multiple responses to DNA damage. Proc Natl Acad Sci U S A 2009; 106:12843-8. [PMID: 19549833 DOI: 10.1073/pnas.0810304106] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Arabidopsis sog1-1 (suppressor of gamma response) mutant was originally isolated as a second-site suppressor of the radiosensitive phenotype of seeds defective in the repair endonuclease XPF. Here, we report that SOG1 encodes a putative transcription factor. This gene is a member of the NAC domain [petunia NAM (no apical meristem) and Arabidopsis ATAF1, 2 and CUC2] family (a family of proteins unique to land plants). Hundreds of genes are normally up-regulated in Arabidopsis within an hour of treatment with ionizing radiation; the induction of these genes requires the damage response protein kinase ATM, but not the related kinase ATR. Here, we find that SOG1 is also required for this transcriptional up-regulation. In contrast, the SOG1-dependent checkpoint response observed in xpf mutant seeds requires ATR, but does not require ATM. Thus, phenotype of the sog1-1 mutant mimics aspects of the phenotypes of both atr and atm mutants in Arabidopsis, suggesting that SOG1 participates in pathways governed by both of these sensor kinases. We propose that, in plants, signals related to genomic stress are processed through a single, central transcription factor, SOG1.
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Repair and tolerance of oxidative DNA damage in plants. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2009; 681:169-179. [DOI: 10.1016/j.mrrev.2008.07.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/11/2008] [Accepted: 07/17/2008] [Indexed: 11/19/2022]
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Vannier JB, Depeiges A, White C, Gallego ME. ERCC1/XPF protects short telomeres from homologous recombination in Arabidopsis thaliana. PLoS Genet 2009; 5:e1000380. [PMID: 19214203 PMCID: PMC2632759 DOI: 10.1371/journal.pgen.1000380] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Accepted: 01/13/2009] [Indexed: 12/17/2022] Open
Abstract
Many repair and recombination proteins play essential roles in telomere function and chromosome stability, notwithstanding the role of telomeres in "hiding" chromosome ends from DNA repair and recombination. Among these are XPF and ERCC1, which form a structure-specific endonuclease known for its essential role in nucleotide excision repair and is the subject of considerable interest in studies of recombination. In contrast to observations in mammalian cells, we observe no enhancement of chromosomal instability in Arabidopsis plants mutated for either XPF (AtRAD1) or ERCC1 (AtERCC1) orthologs, which develop normally and show wild-type telomere length. However, in the absence of telomerase, mutation of either of these two genes induces a significantly earlier onset of chromosomal instability. This early appearance of telomere instability is not due to a general acceleration of telomeric repeat loss, but is associated with the presence of dicentric chromosome bridges and cytologically visible extrachromosomal DNA fragments in mitotic anaphase. Such extrachromosomal fragments are not observed in later-generation single-telomerase mutant plants presenting similar frequencies of anaphase bridges. Extensive FISH analyses show that these DNAs are broken chromosomes and correspond to two specific chromosome arms. Analysis of the Arabidopsis genome sequence identified two extensive blocks of degenerate telomeric repeats, which lie at the bases of these two arms. Our data thus indicate a protective role of ERCC1/XPF against 3' G-strand overhang invasion of interstitial telomeric repeats. The fact that the Atercc1 (and Atrad1) mutants dramatically potentiate levels of chromosome instability in Attert mutants, and the absence of such events in the presence of telomerase, have important implications for models of the roles of recombination at telomeres and is a striking illustration of the impact of genome structure on the outcomes of equivalent recombination processes in different organisms.
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Affiliation(s)
- Jean-Baptiste Vannier
- Génétique, Reproduction et Développement, UMR CNRS 6247, Clermont Université, INSERM U931, Aubière, France
| | - Annie Depeiges
- Génétique, Reproduction et Développement, UMR CNRS 6247, Clermont Université, INSERM U931, Aubière, France
| | - Charles White
- Génétique, Reproduction et Développement, UMR CNRS 6247, Clermont Université, INSERM U931, Aubière, France
| | - Maria Eugenia Gallego
- Génétique, Reproduction et Développement, UMR CNRS 6247, Clermont Université, INSERM U931, Aubière, France
- * E-mail:
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Yang G, Mei T, Yuan H, Zhang W, Chen L, Xue J, Wu L, Wang Y. Bystander/abscopal effects induced in intact Arabidopsis seeds by low-energy heavy-ion radiation. Radiat Res 2008; 170:372-80. [PMID: 18763864 DOI: 10.1667/rr1324.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 03/02/2008] [Indexed: 11/03/2022]
Abstract
To date, radiation-induced bystander effects have been observed largely in in vitro single-cell systems; verification of both the effects and the mechanisms in multicellular systems in vivo is important. Previously we showed that bystander/ abscopal effects can be induced by irradiating the shoot apical meristem cells in Arabidopsis embryos. In this study, we investigated the in vivo effects induced by 30 keV 40Ar ions in intact Arabidopsis seeds and traced the postembryonic development of both irradiated and nonirradiated shoot apical meristem and root apical meristem cells. Since the range of 30 keV 40Ar ions in water is about 0.07 microm, which is less than the distance from the testa to shoot apical meristem and root apical meristem in Arabidopsis seeds (about 100 microm), the incident low-energy heavy ions generally stop in the proximal surface. Our results showed that, after the 30 keV 40Ar-ion irradiation of shielded and nonshielded Arabidopsis seeds at a fluence of 1.5 x 10(17) ions/cm2, short- and long-term postembryonic development, including germination, root hair differentiation, primary root elongation, lateral root initiation and survival, was significantly inhibited. Since shoot apical meristem and root apical meristem cells were not damaged directly by radiation, the results suggested that a damage signal(s) is transferred from the irradiated cells to shoot apical meristem and root apical meristem cells and causes the ultimate developmental alterations, indicating that long-distance bystander/ abscopal effects exist in the intact seed. A further study of mechanisms showed that the effects are associated with either enhanced generation of reactive oxygen species (ROS) or decreased auxin-dependent transcription in postembryonic development. Treatment with the ROS scavenger dimethyl sulfoxide (DMSO) or synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) can significantly reverse both the alterations in postembryonic development and auxin-dependent transcription, suggesting that ROS and auxin-dependent transcription processes play essential roles in the low-energy heavy-ion radiation-induced long-distance bystander/abscopal effects in the intact organism.
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Affiliation(s)
- Gen Yang
- State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871, People's Republic of China
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Abstract
The Saccharomyces cerevisiae RAD54 gene has critical roles in DNA double-strand break repair, homologous recombination, and gene targeting. Previous results show that the yeast gene enhances gene targeting when expressed in Arabidopsis thaliana. In this work we address the trans-species compatibility of Rad54 functions. We show that overexpression of yeast RAD54 in Arabidopsis enhances DNA damage resistance severalfold. Thus, the yeast gene is active in the Arabidopsis homologous-recombination repair system. Moreover, we have identified an A. thaliana ortholog of yeast RAD54, named AtRAD54. This gene, with close sequence similarity to RAD54, complements methylmethane sulfonate (MMS) sensitivity but not UV sensitivity or gene targeting defects of rad54Delta mutant yeast cells. Overexpression of AtRAD54 in Arabidopsis leads to enhanced resistance to DNA damage. This gene's assignment as a RAD54 ortholog is further supported by the interaction of AtRad54 with AtRad51 and the interactions between alien proteins (i.e., yeast Rad54 with AtRAD51 and yeast Rad51 with AtRad54) in a yeast two-hybrid experiment. These interactions hint at the molecular nature of this interkingdom complementation, although the stronger effect of the yeast Rad54 in plants than AtRad54 in yeast might be explained by an ability of the Rad54 protein to act alone, independently of its interaction with Rad51.
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Abstract
ERCC1-XPF endonuclease is required for nucleotide excision repair (NER) of helix-distorting DNA lesions. However, mutations in ERCC1 or XPF in humans or mice cause a more severe phenotype than absence of NER, prompting a search for novel repair activities of the nuclease. In Saccharomyces cerevisiae, orthologs of ERCC1-XPF (Rad10-Rad1) participate in the repair of double-strand breaks (DSBs). Rad10-Rad1 contributes to two error-prone DSB repair pathways: microhomology-mediated end joining (a Ku86-independent mechanism) and single-strand annealing. To determine if ERCC1-XPF participates in DSB repair in mammals, mutant cells and mice were screened for sensitivity to gamma irradiation. ERCC1-XPF-deficient fibroblasts were hypersensitive to gamma irradiation, and gammaH2AX foci, a marker of DSBs, persisted in irradiated mutant cells, consistent with a defect in DSB repair. Mutant mice were also hypersensitive to irradiation, establishing an essential role for ERCC1-XPF in protecting against DSBs in vivo. Mice defective in both ERCC1-XPF and Ku86 were not viable. However, Ercc1(-/-) Ku86(-/-) fibroblasts were hypersensitive to gamma irradiation compared to single mutants and accumulated significantly greater chromosomal aberrations. Finally, in vitro repair of DSBs with 3' overhangs led to large deletions in the absence of ERCC1-XPF. These data support the conclusion that, as in yeast, ERCC1-XPF facilitates DSB repair via an end-joining mechanism that is Ku86 independent.
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Ricaud L, Proux C, Renou JP, Pichon O, Fochesato S, Ortet P, Montané MH. ATM-mediated transcriptional and developmental responses to gamma-rays in Arabidopsis. PLoS One 2007; 2:e430. [PMID: 17487278 PMCID: PMC1855986 DOI: 10.1371/journal.pone.0000430] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 04/19/2007] [Indexed: 11/19/2022] Open
Abstract
ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of γ-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed.
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Affiliation(s)
- Lilian Ricaud
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Caroline Proux
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Jean-Pierre Renou
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Olivier Pichon
- Unité de Recherche en Génomique Végétale, UMR INRA 1165 - CNRS 8114 - UEVE, Evry, France
| | - Sylvain Fochesato
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Philippe Ortet
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
| | - Marie-Hélène Montané
- CEA, DSV, Institut de Biologie Environnementale et de Biotechnologie (iBEB), Service de biologie végétale et de microbiologie environnementales (SBVME), Cadarache, Saint Paul-lez-Durance, France
- * To whom correspondence should be addressed. E-mail:
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43
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Hartung F, Suer S, Bergmann T, Puchta H. The role of AtMUS81 in DNA repair and its genetic interaction with the helicase AtRecQ4A. Nucleic Acids Res 2006; 34:4438-48. [PMID: 16945961 PMCID: PMC1636358 DOI: 10.1093/nar/gkl576] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The endonuclease MUS81 has been shown in a variety of organisms to be involved in DNA repair in mitotic and meiotic cells. Homologues of the MUS81 gene exist in the genomes of all eukaryotes, pointing to a conserved role of the protein. However, the biological role of MUS81 varies between different eukaryotes. For example, while loss of the gene results in strongly impaired fertility in Saccharomyces cerevisiae and nearly complete sterility in Schizosaccharomyces pombe, it is not essential for meiosis in mammals. We identified a functional homologue (AtMUS81/At4g30870) in the genome of Arabidopsis thaliana and isolated a full-length cDNA of this gene. Analysing two independent T-DNA insertion lines of AtMUS81, we found that they are sensitive to the mutagens MMS and MMC. Both mutants have a deficiency in homologous recombination in somatic cells but only after induction by genotoxic stress. In contrast to yeast, no meiotic defect of AtMUS81 mutants was detectable and the mutants are viable. Crosses with a hyperrecombinogenic mutant of the AtRecQ4A helicase resulted in synthetic lethality in the double mutant. Thus, the nuclease AtMUS81 and the helicase AtRecQ4A seem to be involved in two alternative pathways of resolution of replicative DNA structures in somatic cells.
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Affiliation(s)
| | | | | | - H. Puchta
- To whom correspondence should be addressed. Tel: +49 721 6088894; Fax: +49 721 6084874;
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44
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Affiliation(s)
- Seisuke Kimura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda-shi, Chiba, Japan
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45
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Shaked H, Avivi-Ragolsky N, Levy AA. Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics 2006; 173:985-94. [PMID: 16547115 PMCID: PMC1526515 DOI: 10.1534/genetics.105.051664] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The genome of plants, like that of other eukaryotes, is organized into chromatin, a compact structure that reduces the accessibility of DNA to machineries such as transcription, replication, and DNA recombination and repair. Plant genes, which contain the characteristic ATPase/helicase motifs of the chromatin remodeling Swi2/Snf2 family of proteins, have been thoroughly studied, but their role in homologous recombination or DNA repair has received limited attention. We have searched for homologs of the yeast RAD54 gene, whose role in recombination and repair and in chromatin remodeling is well established. Forty Arabidopsis SWI2/SNF2 genes were identified and the function of a selected group of 14 was analyzed. Mutant analysis and/or RNAi-mediated silencing showed that 11 of the 14 genes tested played a role in response to DNA damage. Two of the 14 genes were involved in homologous recombination between inverted repeats. The putative ortholog of RAD54 and close homologs of ERCC6/RAD26 were involved in DNA damage response, suggesting functional conservation across kingdoms. In addition, genes known for their role in development, such as PICKLE/GYMNOS and PIE1, or in silencing, such as DDM1, turned out to also be involved in DNA damage response. A comparison of ddm1 and met1 mutants suggests that DNA damage response is affected essentially by chromatin structure and that cytosine methylation is less critical. These results emphasize the broad involvement of the SWI2/SNF2 family, and thus of chromatin remodeling, in genome maintenance and the link between epigenetic and genetic processes.
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Affiliation(s)
- Hezi Shaked
- Plant Sciences Department, Weizmann Institute of Science, Rehovot, 76100 Israel
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46
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Wijeratne AJ, Chen C, Zhang W, Timofejeva L, Ma H. The Arabidopsis thaliana PARTING DANCERS gene encoding a novel protein is required for normal meiotic homologous recombination. Mol Biol Cell 2006; 17:1331-43. [PMID: 16394097 PMCID: PMC1382321 DOI: 10.1091/mbc.e05-09-0902] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Recent studies of meiotic recombination in the budding yeast and the model plant Arabidopsis thaliana indicate that meiotic crossovers (COs) occur through two genetic pathways: the interference-sensitive pathway and the interference-insensitive pathway. However, few genes have been identified in either pathway. Here, we describe the identification of the PARTING DANCERS (PTD) gene, as a gene with an elevated expression level in meiocytes. Analysis of two independently generated transferred DNA insertional lines in PTD showed that the mutants had reduced fertility. Further cytological analysis of male meiosis in the ptd mutants revealed defects in meiosis, including reduced formation of chiasmata, the cytological appearance of COs. The residual chiasmata in the mutants were distributed randomly, indicating that the ptd mutants are defective for CO formation in the interference-sensitive pathway. In addition, transmission electron microscopic analysis of the mutants detected no obvious abnormality of synaptonemal complexes and apparently normal late recombination nodules at the pachytene stage, suggesting that the mutant's defects in bivalent formation were postsynaptic. Comparison to other genes with limited sequence similarity raises the possibility that PTD may present a previously unknown function conserved in divergent eukaryotic organisms.
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Affiliation(s)
- Asela J Wijeratne
- Intercollege Graduate Program in Plant Physiology, The Pennsylvania State University, University Park, PA 16802, USA
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47
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Kunz BA, Cahill DM, Mohr PG, Osmond MJ, Vonarx EJ. Plant responses to UV radiation and links to pathogen resistance. INTERNATIONAL REVIEW OF CYTOLOGY 2006; 255:1-40. [PMID: 17178464 DOI: 10.1016/s0074-7696(06)55001-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Increased incident ultraviolet (UV) radiation due to ozone depletion has heightened interest in plant responses to UV because solar UV wavelengths can reduce plant genome stability, growth, and productivity. These detrimental effects result from damage to cell components including nucleic acids, proteins, and membrane lipids. As obligate phototrophs, plants must counter the onslaught of cellular damage due to prolonged exposure to sunlight. They do so by attenuating the UV dose received through accumulation of UV-absorbing secondary metabolites, neutralizing reactive oxygen species produced by UV, monomerizing UV-induced pyrimidine dimers by photoreactivation, extracting UV photoproducts from DNA via nucleotide excision repair, and perhaps transiently tolerating the presence of DNA lesions via replicative bypass of the damage. The signaling mechanisms controlling these responses suggest that UV exposure also may be beneficial to plants by increasing cellular immunity to pathogens. Indeed, pathogen resistance can be enhanced by UV treatment, and recent experiments suggest DNA damage and its processing may have a role.
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Affiliation(s)
- Bernard A Kunz
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3217, Australia
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48
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Bray CM, West CE. DNA repair mechanisms in plants: crucial sensors and effectors for the maintenance of genome integrity. THE NEW PHYTOLOGIST 2005; 168:511-28. [PMID: 16313635 DOI: 10.1111/j.1469-8137.2005.01548.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As obligate phototrophs, plants harness energy from sunlight to split water, producing oxygen and reducing power. This lifestyle exposes plants to particularly high levels of genotoxic stress that threatens genomic integrity, leading to mutation, developmental arrest and cell death. Plants, which with algae are the only photosynthetic eukaryotes, have evolved very effective pathways for DNA damage signalling and repair, and this review summarises our current understanding of these processes in the responses of plants to genotoxic stress. We also identify how the use of new and emerging technologies can complement established physiological and ecological studies to progress the application of this knowledge in biotechnology.
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Affiliation(s)
- Clifford M Bray
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
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49
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Gallego ME, White CI. DNA repair and recombination functions in Arabidopsis telomere maintenance. Chromosome Res 2005; 13:481-91. [PMID: 16132813 DOI: 10.1007/s10577-005-0995-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this review, we discuss recent advances in the knowledge of plant telomere maintenance, focusing on the model plant Arabidopsis thaliana and, in particular, on the roles of proteins involved in DNA repair and recombination. The question of the interrelationships between DNA repair and recombination pathways and proteins with telomere function and maintenance is of increasing interest and has been the subject of a number of recent reviews (Cech 2004, d'Adda di Fagagna et al. 2004, Hande 2004, Harrington 2004, Maser and DePinho 2004). Understanding of telomere biology, DNA repair and recombination in plants has rapidly progressed over the last decade, substantially due to genetic approaches in Arabidopsis, and we feel that this is an appropriate time to review current knowledge in this field. A number of recent reviews have dealt more generally with the subject of plant telomere structure and evolution (Riha et al. 2001, McKnight et al. 2002, Riha and Shippen 2003b, McKnight and Shippen 2004, Fajkus et al. 2005) and we thus focus specifically on plant telomere biology in the context of DNA repair and recombination in Arabidopsis.
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Affiliation(s)
- Maria E Gallego
- UMR 6547 CNRS, Université Blaise Pascal, 24 avenue des Landais, 63177 Aubière, France
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50
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Sahr T, Voigt G, Schimmack W, Paretzke HG, Ernst D. Low-level radiocaesium exposure alters gene expression in roots of Arabidopsis. THE NEW PHYTOLOGIST 2005; 168:141-8. [PMID: 16159328 DOI: 10.1111/j.1469-8137.2005.01485.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Radiocaesium is one of the main anthropogenic sources of internal and external exposure to beta- and gamma-radiation (e.g. from global fallout of atmospheric atomic bomb testing and from the Chernobyl reactor accident). Here we investigated gene expression by suppression subtractive hybridization (SSH) and reverse transcription-polymerase chain reaction (RT-PCR) in Arabidopsis thaliana, which was induced by the root uptake of 134Cs. SSH analysis resulted in the isolation of 46 clones that were differentially expressed at 30 Bq cm(-3) 134Cs. Most of the expressed sequence tags identified belonged to genes encoding proteins that were involved in cell growth, cell division and the development of plants, and in proteins controlling translation, general metabolism and stress defence, including a DNA excision repair protein. The accumulation of caesium in plant material was measured in plants grown for 5 wk on agar contaminated by up to 60 Bq cm(-3) 134Cs. 134Cs was found to accumulate, in particular, in leaf rosettes and was dependent on the activity concentration in the growth media. The data indicate that low-level ionizing radiation influences important cellular responses, resulting in a changed gene-expression profile.
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Affiliation(s)
- Tobias Sahr
- Institute of Biochemical Plant Pathology, GSF - National Research Center for Environment and Health, D-85764 Neuherberg, Germany
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