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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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2
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Kawaguchi K, Kazama M, Hata T, Matsuo M, Obokata J, Satoh S. Inducible Expression of the Restriction Enzyme Uncovered Genome-Wide Distribution and Dynamic Behavior of Histones H4K16ac and H2A.Z at DNA Double-Strand Breaks in Arabidopsis. PLANT & CELL PHYSIOLOGY 2024; 65:142-155. [PMID: 37930797 DOI: 10.1093/pcp/pcad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
DNA double-strand breaks (DSBs) are among the most serious types of DNA damage, causing mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed in mammals. However, this DSB induction system is unsuitable for investigating chromatin remodeling during and after DSB repair, and such an approach has not been performed in plants. Here, we established a transgenic Arabidopsis plant harboring a restriction enzyme gene Sbf I driven by a heat-inducible promoter. Using this transgenic line, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated the dynamics of these histone marks around the endogenous 623 Sbf I recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by the ChIP-seq procedure. From the results, Sbf I-induced DSBs were detected at 360 loci, which induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs in Arabidopsis.
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Affiliation(s)
- Kohei Kawaguchi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Mei Kazama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Takayuki Hata
- Graduate School of Medicine, Hirosaki University, Hirosaki, Aomori 036-8560, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
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3
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Cseh A, Lenykó-Thegze A, Makai D, Szabados F, Hamow KÁ, Gulyás Z, Kiss T, Karsai I, Moncsek B, Mihók E, Sepsi A. Meiotic instability and irregular chromosome pairing underpin heat-induced infertility in bread wheat carrying the Rht-B1b or Rht-D1b Green Revolution genes. THE NEW PHYTOLOGIST 2024; 241:180-196. [PMID: 37691304 DOI: 10.1111/nph.19256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/12/2023] [Indexed: 09/12/2023]
Abstract
Mutations in the Rht-B1a and Rht-D1a genes of wheat (Triticum aestivum; resulting in Rht-B1b and Rht-D1b alleles) cause gibberellin-insensitive dwarfism and are one of the most important elements of increased yield introduced during the 'Green Revolution'. We measured the effects of a short period of heat imposed during the early reproductive stage on near-isogenic lines carrying Rht-B1b or Rht-D1b alleles, with respect to the wild-type (WT). The temperature shift caused a significant fertility loss within the ears of Rht-B1b and Rht-D1b wheats, greater than that observed for the WT. Defects in chromosome synapsis, reduced homologous recombination and a high frequency of chromosome mis-segregation were associated with reduced fertility. The transcription of TaGA3ox gene involved in the final stage of gibberellic acid (GA) biosynthesis was activated and ultra-performance liquid chromatography-tandem mass spectrometry identified GA1 as the dominant bioactive GA in developing ears, but levels were unaffected by the elevated temperature. Rht-B1b and Rht-D1b mutants were inclined to meiotic errors under optimal temperatures and showed a higher susceptibility to heat than their tall counterparts. Identification and introduction of new dwarfing alleles into modern breeding programmes is invaluable in the development of climate-resilient wheat varieties.
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Affiliation(s)
- András Cseh
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Andrea Lenykó-Thegze
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Egyetem tér 1-3, Budapest, 1053, Hungary
| | - Diána Makai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Fanni Szabados
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Kamirán Áron Hamow
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Zsolt Gulyás
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Tibor Kiss
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eszterházy tér 1, Eger, 3300, Hungary
| | - Ildikó Karsai
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Blanka Moncsek
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Edit Mihók
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
| | - Adél Sepsi
- HUN-REN, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2, Hungary
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4
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Li Q, Zhou J, Li S, Zhang W, Du Y, Li K, Wang Y, Sun Q. DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis. Nat Commun 2023; 14:7763. [PMID: 38012183 PMCID: PMC10682485 DOI: 10.1038/s41467-023-43680-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
Genome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA topoisomerase 1 (TOP1i) triggers the global increase of R-loops (called topoR-loops) and DNA damages, which are exacerbated in the DNA damage repair-compromised mutant atm. A suppressor screen identifies a mutation in POL2A, the catalytic subunit of DNA polymerase ε, rescuing the TOP1i-induced topoR-loop accumulation and genome instability in atm. Importantly we find that a highly conserved junction domain between the exonuclease and polymerase domains in POL2A is required for modulating topoR-loops near DNA replication origins and facilitating faithful DNA replication. Our results suggest that DNA replication acts in concert with genome topological states to fine-tune R-loops and thereby maintain genome integrity, revealing a likely conserved regulatory mechanism of TOP1i resistance in chemotherapy for ATM-deficient cancers.
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Affiliation(s)
- Qin Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Shuai Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yingxue Du
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Yingxiang Wang
- College of Life Science, South China Agricultural University, Guangdong Laboratory for Lingnan Morden Agriculture, Guangzhou, 510642, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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5
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Nisa M, Eekhout T, Bergis C, Pedroza-Garcia JA, He X, Mazubert C, Vercauteren I, Cools T, Brik-Chaouche R, Drouin-Wahbi J, Chmaiss L, Latrasse D, Bergounioux C, Vandepoele K, Benhamed M, De Veylder L, Raynaud C. Distinctive and complementary roles of E2F transcription factors during plant replication stress responses. MOLECULAR PLANT 2023; 16:1269-1282. [PMID: 37415334 DOI: 10.1016/j.molp.2023.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Survival of living organisms is fully dependent on their maintenance of genome integrity, being permanently threatened by replication stress in proliferating cells. Although the plant DNA damage response (DDR) regulator SOG1 has been demonstrated to cope with replication defects, accumulating evidence points to other pathways functioning independent of SOG1. Here, we report the roles of the Arabidopsis E2FA and EF2B transcription factors, two well-characterized regulators of DNA replication, in plant response to replication stress. Through a combination of reverse genetics and chromatin immunoprecipitation approaches, we show that E2FA and E2FB share many target genes with SOG1, providing evidence for their involvement in the DDR. Analysis of double- and triple-mutant combinations revealed that E2FB, rather than E2FA, plays the most prominent role in sustaining plant growth in the presence of replication defects, either operating antagonistically or synergistically with SOG1. Conversely, SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants. Collectively, our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.
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Affiliation(s)
- Maherun Nisa
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Clara Bergis
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Jose-Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Christelle Mazubert
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Toon Cools
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Rim Brik-Chaouche
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Jeannine Drouin-Wahbi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Layla Chmaiss
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
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6
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Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol 2023; 24:65. [PMID: 37016448 PMCID: PMC10074895 DOI: 10.1186/s13059-023-02908-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
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Affiliation(s)
- Lihua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuting Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yating Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuwen Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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7
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Fan T, Kang H, Wu D, Zhu X, Huang L, Wu J, Zhu Y. Arabidopsis γ-H2A.X-INTERACTING PROTEIN participates in DNA damage response and safeguards chromatin stability. Nat Commun 2022; 13:7942. [PMID: 36572675 PMCID: PMC9792525 DOI: 10.1038/s41467-022-35715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Upon the occurrence of DNA double strand breaks (DSB), the proximal histone variant H2A.X is phosphorylated as γ-H2A.X, a critical signal for consequent DSB signaling and repair pathways. Although γ-H2A.X-triggered DNA damage response (DDR) has been well-characterized in yeast and animals, the corresponding pathways in plant DDR are less well understood. Here, we show that an Arabidopsis protein γ-H2A.X-INTERACTING PROTEIN (XIP) can interact with γ-H2A.X. Its C-terminal dual-BRCT-like domain contributes to its specific interaction with γ-H2A.X. XIP-deficient seedlings display smaller meristems, inhibited growth, and higher sensitivity to DSB-inducing treatment. Loss-of-function in XIP causes transcriptome changes mimicking wild-type plants subject to replicative or genotoxic stresses. After genotoxic bleomycin treatment, more proteins with upregulated phosphorylation modifications, more DNA fragments and cell death were found in xip mutants. Moreover, XIP physically interacts with RAD51, the key recombinase in homologous recombination (HR), and somatic HR frequency is significantly reduced in xip mutants. Collectively, XIP participates in plant response to DSB and contributes to chromatin stability.
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Affiliation(s)
- Tianyi Fan
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Huijia Kang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China ,grid.8547.e0000 0001 0125 2443Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Di Wu
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Xinyu Zhu
- grid.12527.330000 0001 0662 3178Department of Chemical Engineering (Tanwei College), Tsinghua University, Beijing, China
| | - Lin Huang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jiabing Wu
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yan Zhu
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
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8
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Muñoz-Díaz E, Sáez-Vásquez J. Nuclear dynamics: Formation of bodies and trafficking in plant nuclei. FRONTIERS IN PLANT SCIENCE 2022; 13:984163. [PMID: 36082296 PMCID: PMC9445803 DOI: 10.3389/fpls.2022.984163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.
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Affiliation(s)
- Eduardo Muñoz-Díaz
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
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9
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Foroozani M, Holder DH, Deal RB. Histone Variants in the Specialization of Plant Chromatin. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:149-172. [PMID: 35167758 PMCID: PMC9133179 DOI: 10.1146/annurev-arplant-070221-050044] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.
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Affiliation(s)
| | - Dylan H Holder
- Department of Biology, Emory University, Atlanta, Georgia, USA;
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia, USA;
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10
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De S, Jose J, Pal A, Roy Choudhury S, Roy S. Exposure to Low UV-B Dose Induces DNA Double-Strand Breaks Mediated Onset of Endoreduplication in Vigna radiata (L.) R. Wilczek Seedlings. PLANT & CELL PHYSIOLOGY 2022; 63:463-483. [PMID: 35134223 DOI: 10.1093/pcp/pcac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Multiple lines of evidence indicate that solar UV-B light acts as an important environmental signal in plants, regulating various cellular and metabolic activities, gene expression, growth and development. Here, we show that low levels of UV-B (4.0 kJ m-2) significantly influence plant response during early seedling development in the tropical legume crop Vigna radiata (L.) R. Wilczek. Exposure to low doses of UV-B showed relatively less growth inhibition yet remarkably enhanced lateral root formation in seedlings. Both low and high (8.0 kJ m-2) doses of UV-B treatment induced DNA double-strand breaks and activated the SOG1-related ATM-ATR-mediated DNA damage response pathway. These effects led to G2-M-phase arrest with a compromised expression of the key cell cycle regulators, including CDKB1;1, CDKB2;1 and CYCB1;1, respectively. However, along with these effects, imbibitional exposure of seeds to a low UV-B dose resulted in enhanced accumulation of FZR1/CCS52A, E2Fa and WEE1 kinase and prominent induction of endoreduplication in 7-day-old seedlings. Low dose of UV-B mediated phenotypical responses, while the onset of endoreduplication appeared to be regulated at least in part via UV-B induced reactive oxygen species accumulation. Transcriptome analyses further revealed a network of co-regulated genes associated with DNA repair, cell cycle regulation and oxidative stress response pathways that are activated upon exposure to low doses of UV-B.
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Affiliation(s)
- Sayanti De
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, West Bengal 713104, India
| | - Jismon Jose
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, West Bengal 700054, India
| | - Swarup Roy Choudhury
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, West Bengal 713104, India
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11
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Pedroza-Garcia JA, Xiang Y, De Veylder L. Cell cycle checkpoint control in response to DNA damage by environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:490-507. [PMID: 34741364 DOI: 10.1111/tpj.15567] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Being sessile organisms, plants are ubiquitously exposed to stresses that can affect the DNA replication process or cause DNA damage. To cope with these problems, plants utilize DNA damage response (DDR) pathways, consisting of both highly conserved and plant-specific elements. As a part of this DDR, cell cycle checkpoint control mechanisms either pause the cell cycle, to allow DNA repair, or lead cells into differentiation or programmed cell death, to prevent the transmission of DNA errors in the organism through mitosis or to its offspring via meiosis. The two major DDR cell cycle checkpoints control either the replication process or the G2/M transition. The latter is largely overseen by the plant-specific SOG1 transcription factor, which drives the activity of cyclin-dependent kinase inhibitors and MYB3R proteins, which are rate limiting for the G2/M transition. By contrast, the replication checkpoint is controlled by different players, including the conserved kinase WEE1 and likely the transcriptional repressor RBR1. These checkpoint mechanisms are called upon during developmental processes, in retrograde signaling pathways, and in response to biotic and abiotic stresses, including metal toxicity, cold, salinity, and phosphate deficiency. Additionally, the recent expansion of research from Arabidopsis to other model plants has revealed species-specific aspects of the DDR. Overall, it is becoming evidently clear that the DNA damage checkpoint mechanisms represent an important aspect of the adaptation of plants to a changing environment, hence gaining more knowledge about this topic might be helpful to increase the resilience of plants to climate change.
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Affiliation(s)
- José Antonio Pedroza-Garcia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Yanli Xiang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
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12
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Singh G, Batzenschlager M, Tomkova D, Herzog E, Hoffmann E, Houlné G, Schmit AC, Berr A, Chabouté ME. GIP1 and GIP2 Contribute to the Maintenance of Genome Stability at the Nuclear Periphery. FRONTIERS IN PLANT SCIENCE 2022; 12:804928. [PMID: 35154196 PMCID: PMC8830487 DOI: 10.3389/fpls.2021.804928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 06/02/2023]
Abstract
The maintenance of genetic information is important in eukaryotes notably through mechanisms occurring at the nuclear periphery where inner nuclear membrane proteins and nuclear pore-associated components are key factors regulating the DNA damage response (DDR). However, this aspect of DDR regulation is still poorly documented in plants. We addressed here how genomic stability is impaired in the gamma-tubulin complex component 3-interacting protein (gip1gip2) double mutants showing defective nuclear shaping. Using neutral comet assays for DNA double-strand breaks (DSBs) detection, we showed that GIP1 and GIP2 act redundantly to maintain genome stability. At the cellular level, γ-H2AX foci in gip1gip2 were more abundant and heterogeneous in their size compared to wild-type (WT) in root meristematic nuclei, indicative of constitutive DNA damage. This was linked to a constitutive activation of the DDR in the gip1gip2 mutant, with more emphasis on the homologous recombination (HR) repair pathway. In addition, we noticed the presence of numerous RAD51 foci which did not colocalize with γ-H2AX foci. The expression of GIP1-GFP in the double mutant rescued the cellular response to DNA damage, leading to the systematic colocalization of RAD51 and γ-H2AX foci. Interestingly, a significant proportion of RAD51 foci colocalized with GIP1-GFP at the nuclear periphery. Altogether, our data suggest that GIPs may partly contribute to the spatio-temporal recruitment of RAD51 at the nuclear periphery.
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Affiliation(s)
- Gaurav Singh
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | | | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Etienne Herzog
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Elise Hoffmann
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Guy Houlné
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Anne-Catherine Schmit
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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13
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Pan Y, Wen B, Zhang H, Zhang S. Comparison of 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA) and perfluorooctane sulfonate (PFOS) accumulation and toxicity in mung bean. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117332. [PMID: 33993016 DOI: 10.1016/j.envpol.2021.117332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/17/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
With the regulation of perfluorooctanesulfonate (PFOS), 6:2 chlorinated polyfluoroalkyl ether sulfonate (6:2 Cl-PFESA) has been used as a potential PFOS alternative in electroplating. In this study, the uptake, translocation and phytotoxicity of PFOS and 6:2 Cl-PFESA in mung bean (Vigna radiata (Linn.) Wilczek.) were investigated. The uptake kinetics of PFOS and 6:2 Cl-PFESA fit the Michaelis-Menten equation well, suggesting that the uptake is a carrier-mediated process. The root concentration factor (RCF) of 6:2 Cl-PFESA (34.55 mL g-1 dw) was 1.27 times that of PFOS (27.11 mL g-1 dw), and the translocation factor (TF) of 6:2 Cl-PFESA (0.177) was 1.07 times that of PFOS (0.165). Exposure to 6:2 Cl-PFESA and PFOS both resulted in the inhibition of mung bean seedling development. Treatment with 6:2 Cl-PFESA and PFOS led to the concentration-dependent elevation of malondialdehyde (MDA), carbonyl groups, and phosphorylated histone H2AX (γ-H2AX) levels in mung bean roots. The MDA and carbonyl group contents induced by 6:2 Cl-PFESA were 1.10-1.35 and 1.03-1.14 times, respectively, those of PFOS. The hydroxyl free radical (·OH) levels in mung bean roots after exposure to PFOS and 6:2 Cl-PFESA were elevated significantly, and the ·OH levels induced by 6:2 Cl-PFESA were higher than those induced by PFOS. Hydroxyl free radical levels were positively correlated with the MDA and carbonyl group contents in mung bean roots (p < 0.05). The dynamic changes in some antioxidative enzyme activities in mung bean seedlings were determined, including peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT). The results demonstrated the phytotoxicities of 6:2 Cl-PFESA and PFOS to mung bean in the early developmental stage. 6:2 Cl-PFESA is more harmful to mung beans than PFOS. The production of hydroxyl radical is the mechanism that causes the toxicity of PFOS and 6:2 Cl-PFESA toward plants.
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Affiliation(s)
- Ying Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bei Wen
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongna Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Mahapatra K, Roy S. SOG1 transcription factor promotes the onset of endoreduplication under salinity stress in Arabidopsis. Sci Rep 2021; 11:11659. [PMID: 34079040 PMCID: PMC8172935 DOI: 10.1038/s41598-021-91293-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/20/2021] [Indexed: 01/24/2023] Open
Abstract
As like in mammalian system, the DNA damage responsive cell cycle checkpoint functions play crucial role for maintenance of genome stability in plants through repairing of damages in DNA and induction of programmed cell death or endoreduplication by extensive regulation of progression of cell cycle. ATM and ATR (ATAXIA-TELANGIECTASIA-MUTATED and -RAD3-RELATED) function as sensor kinases and play key role in the transmission of DNA damage signals to the downstream components of cell cycle regulatory network. The plant-specific NAC domain family transcription factor SOG1 (SUPPRESSOR OF GAMMA RESPONSE 1) plays crucial role in transducing signals from both ATM and ATR in presence of double strand breaks (DSBs) in the genome and found to play crucial role in the regulation of key genes involved in cell cycle progression, DNA damage repair, endoreduplication and programmed cell death. Here we report that Arabidopsis exposed to high salinity shows generation of oxidative stress induced DSBs along with the concomitant induction of endoreduplication, displaying increased cell size and DNA ploidy level without any change in chromosome number. These responses were significantly prominent in SOG1 overexpression line than wild-type Arabidopsis, while sog1 mutant lines showed much compromised induction of endoreduplication under salinity stress. We have found that both ATM-SOG1 and ATR-SOG1 pathways are involved in the salinity mediated induction of endoreduplication. SOG1was found to promote G2-M phase arrest in Arabidopsis under salinity stress by downregulating the expression of the key cell cycle regulators, including CDKB1;1, CDKB2;1, and CYCB1;1, while upregulating the expression of WEE1 kinase, CCS52A and E2Fa, which act as important regulators for induction of endoreduplication. Our results suggest that Arabidopsis undergoes endoreduplicative cycle in response to salinity induced DSBs, showcasing an adaptive response in plants under salinity stress.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, West Bengal, 713 104, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, West Bengal, 713 104, India.
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15
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Direct Regulation of DNA Repair by E2F and RB in Mammals and Plants: Core Function or Convergent Evolution? Cancers (Basel) 2021; 13:cancers13050934. [PMID: 33668093 PMCID: PMC7956360 DOI: 10.3390/cancers13050934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Retinoblastoma (RB) proteins and E2F transcription factors partner together to regulate the cell cycle in many eukaryotic organisms. In organisms that lack one or both of these proteins, other proteins have taken on the essential function of cell cycle regulation. RB and E2F also have important functions outside of the cell cycle, including DNA repair. This review summarizes the non-canonical functions of RB and E2F in maintaining genome integrity and raises the question of whether such functions have always been present or have evolved more recently. Abstract Members of the E2F transcription factor family regulate the expression of genes important for DNA replication and mitotic cell division in most eukaryotes. Homologs of the retinoblastoma (RB) tumor suppressor inhibit the activity of E2F factors, thus controlling cell cycle progression. Organisms such as budding and fission yeast have lost genes encoding E2F and RB, but have gained genes encoding other proteins that take on E2F and RB cell cycle-related functions. In addition to regulating cell proliferation, E2F and RB homologs have non-canonical functions outside the mitotic cell cycle in a variety of eukaryotes. For example, in both mammals and plants, E2F and RB homologs localize to DNA double-strand breaks (DSBs) and directly promote repair by homologous recombination (HR). Here, we discuss the parallels between mammalian E2F1 and RB and their Arabidopsis homologs, E2FA and RB-related (RBR), with respect to their recruitment to sites of DNA damage and how they help recruit repair factors important for DNA end resection. We also explore the question of whether this role in DNA repair is a conserved ancient function of the E2F and RB homologs in the last eukaryotic common ancestor or whether this function evolved independently in mammals and plants.
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16
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Desvoyes B, Gutierrez C. Roles of plant retinoblastoma protein: cell cycle and beyond. EMBO J 2020; 39:e105802. [PMID: 32865261 PMCID: PMC7527812 DOI: 10.15252/embj.2020105802] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
The human retinoblastoma (RB1) protein is a tumor suppressor that negatively regulates cell cycle progression through its interaction with members of the E2F/DP family of transcription factors. However, RB-related (RBR) proteins are an early acquisition during eukaryote evolution present in plant lineages, including unicellular algae, ancient plants (ferns, lycophytes, liverworts, mosses), gymnosperms, and angiosperms. The main RBR protein domains and interactions with E2Fs are conserved in all eukaryotes and not only regulate the G1/S transition but also the G2/M transition, as part of DREAM complexes. RBR proteins are also important for asymmetric cell division, stem cell maintenance, and the DNA damage response (DDR). RBR proteins play crucial roles at every developmental phase transition, in association with chromatin factors, as well as during the reproductive phase during female and male gametes production and embryo development. Here, we review the processes where plant RBR proteins play a role and discuss possible avenues of research to obtain a full picture of the multifunctional roles of RBR for plant life.
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17
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Bäurle I, Trindade I. Chromatin regulation of somatic abiotic stress memory. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5269-5279. [PMID: 32076719 DOI: 10.1093/jxb/eraa098] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory.
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Affiliation(s)
- Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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18
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Mahapatra K, Ghosh AK, De S, Ghosh N, Sadhukhan P, Chatterjee S, Ghosh R, Sil PC, Roy S. Assessment of cytotoxic and genotoxic potentials of a mononuclear Fe(II) Schiff base complex with photocatalytic activity in Trigonella. Biochim Biophys Acta Gen Subj 2019; 1864:129503. [PMID: 31816347 DOI: 10.1016/j.bbagen.2019.129503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND In recent times, coordination complexes of iron in various oxidation states along with variety of ligand systems have been designed and developed for effective treatment of cancer cells without adversely affecting the normal cell and tissues of various organs. METHODS In this study, we have evaluated the mechanism of action of a Fe(II) Schiff base complex in the crop plant Trigonella foenum-graecum L. (Fenugreek) as the screening system by using morphological, cytological, biochemical and molecular approaches. Further functional characterization was performed using MCF-7 cell line and solid tumour model for the assessment of anti-tumour activity of the complex. RESULTS Our results indicate efficiency of the Fe(II) Schiff base complex in the induction of double strand breaks in DNA. Complex treatment clearly induced cytotoxic and genotoxic damage in Trigonella seedlings. The Fe-complex treatment caused cell cycle arrest via the activation of ATM-ATR kinase mediated DNA damage response pathway with the compromised expression of CDK1, CDK2 and CyclinB1 protein in Trigonella seedlings. In cultured MCF-7 cells, the complex induces cytotoxicity and DNA fragmentation through intracellular ROS generation. Fe-complex treatment inhibited tumour growth in solid tumour model with no additional side effects. CONCLUSION The growth inhibitory and cytotoxic effects of the complex result from activation of DNA damage response along with oxidative stress and cell cycle arrest. GENERAL SIGNIFICANCE Overall, our results have provided comprehensive information on the mechanism of action and efficacy of a Fe(II) Schiff base complex in higher eukaryotic genomes and indicated its future implications as potential therapeutic agent.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan 713104, West Bengal, India
| | - Ayon Kanti Ghosh
- Department of Chemistry, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan 713104, West Bengal, India
| | - Sayanti De
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan 713104, West Bengal, India
| | - Noyel Ghosh
- Division of Molecular Medicine, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Pritam Sadhukhan
- Division of Molecular Medicine, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Sharmistha Chatterjee
- Division of Molecular Medicine, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Rajarshi Ghosh
- Department of Chemistry, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan 713104, West Bengal, India
| | - Parames C Sil
- Division of Molecular Medicine, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Sujit Roy
- Department of Botany, UGC Centre for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan 713104, West Bengal, India.
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19
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Waterworth WM, Wilson M, Wang D, Nuhse T, Warward S, Selley J, West CE. Phosphoproteomic analysis reveals plant DNA damage signalling pathways with a functional role for histone H2AX phosphorylation in plant growth under genotoxic stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1007-1021. [PMID: 31410901 PMCID: PMC6900162 DOI: 10.1111/tpj.14495] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 05/23/2023]
Abstract
DNA damage responses are crucial for plant growth under genotoxic stress. Accumulating evidence indicates that DNA damage responses differ between plant cell types. Here, quantitative shotgun phosphoproteomics provided high-throughput analysis of the DNA damage response network in callus cells. MS analysis revealed a wide network of highly dynamic changes in the phosphoprotein profile of genotoxin-treated cells, largely mediated by the ATAXIA TELANGIECTASIA MUTATED (ATM) protein kinase, representing candidate factors that modulate plant growth, development and DNA repair. A C-terminal dual serine target motif unique to H2AX in the plant lineage showed 171-fold phosphorylation that was absent in atm mutant lines. The physiological significance of post-translational DNA damage signalling to plant growth and survival was demonstrated using reverse genetics and complementation studies of h2ax mutants, establishing the functional role of ATM-mediated histone modification in plant growth under genotoxic stress. Our findings demonstrate the complexity and functional significance of post-translational DNA damage signalling responses in plants and establish the requirement of H2AX phosphorylation for plant survival under genotoxic stress.
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Affiliation(s)
| | - Michael Wilson
- Centre for Plant SciencesUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Dapeng Wang
- Leeds OmicsUniversity of LeedsLeedsLS2 9JTUK
| | - Thomas Nuhse
- Faculty of Life SciencesUniversity of ManchesterOxford RoadManchesterM13 9PTUK
| | - Stacey Warward
- Faculty of Life SciencesUniversity of ManchesterOxford RoadManchesterM13 9PTUK
| | - Julian Selley
- Faculty of Life SciencesUniversity of ManchesterOxford RoadManchesterM13 9PTUK
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20
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Camborde L, Raynaud C, Dumas B, Gaulin E. DNA-Damaging Effectors: New Players in the Effector Arena. TRENDS IN PLANT SCIENCE 2019; 24:1094-1101. [PMID: 31699522 DOI: 10.1016/j.tplants.2019.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/24/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is activated to ensure lesion repair. Accumulation of DNA breaks is also detected in plants during microbial infection. In this opinion article we propose that phytopathogens can produce DNA-damaging effectors. The recent identification of a functional genotoxin in devastating eukaryotic plant pathogens, such as oomycetes, supports the concept that DNA-damaging effectors may contribute to pathogenicity. Additionally, this raises the question of how plants can perceive these damages and whether this perception can be connected to the plant immune system.
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Affiliation(s)
- Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Évry, Université Paris-Saclay, 91405, Orsay, Paris, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, France.
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21
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Xie E, Li Y, Tang D, Lv Y, Shen Y, Cheng Z. A strategy for generating rice apomixis by gene editing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:911-916. [PMID: 30697955 DOI: 10.1111/jipb.12785] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Apomixis is an asexual reproduction way of plants that can produce clonal offspring through seeds. In this study, we introduced apomixis into rice (Oryza sativa) by mutating OsSPO11-1, OsREC8, OsOSD1, and OsMATL through a CRISPR/Cas9 system. The quadruple mutant showed a transformation from meiosis to mitosis and produced clonal diploid gametes. With mutated Osmatl, which gives rise to haploid induction in plants, the quadruple mutant is expected to be able to be produced apomictic diploid offspring. We named this quadruple mutant as AOP (Apomictic Offspring Producer) for its ability to produce apomictic offspring.
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Affiliation(s)
- En Xie
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
| | - Yanli Lv
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Shen
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
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22
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Jia W, Wang C, Ma C, Wang J, Sun H, Xing B. Mineral elements uptake and physiological response of Amaranthus mangostanus (L.) as affected by biochar. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 175:58-65. [PMID: 30889400 DOI: 10.1016/j.ecoenv.2019.03.039] [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: 12/17/2018] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
Amaranthus mangostanus L. (amaranth) was hydroponically grown in different concentrations of biochar amended nutrient solution to investigate the mineral elements migration and physiological response of amaranth as affected by biochar. Our results showed that exposure to 26.6 g/L of biochar greatly increased the root and shoot K, Na and Al content, while 2.6 g/L of biochar greatly increased the root Ca and Mg content. The uptake of K and Al notably altered other elements' accumulation in shoots and roots upon the biochar exposure. The ratio of Ca: K in shoots and Mg: K in roots were negatively correlated to the biochar concentrations, while the ratio of Al: Ca and Al: Mg in roots were positively related to the biochar concentrations. The Al: Fe ratio was also polynomial correlated to the concentrations of biochar. The addition of biochar beyond 2.6 g/L resulted in the cell membrane and DNA damages in roots. The activity of SOD and CAT in 6.7 g/L biochar treated roots was significantly elevated as compared to the ones in other biochar treatments and was almost 2-fold of the control. The photosynthetic Fv/Fm intensity and subcellular structure in leaves were also compromised upon exposure to 26.6 g/L biochar. Taken together, biochar could significantly alter the mineral migration in amaranth and physiologically damage in the plants. It is essential to study the effect of biochar within appropriate concentrations on plants prior to wide application in agriculture.
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Affiliation(s)
- Weili Jia
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering/Sino-Canada R&D Centre on Water and Environmental Safety, Nankai University, Tianjin 300071, China
| | - Cuiping Wang
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering/Sino-Canada R&D Centre on Water and Environmental Safety, Nankai University, Tianjin 300071, China.
| | - Chuanxin Ma
- Department of Analytical Chemistry, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, United States.
| | - Jicheng Wang
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering/Sino-Canada R&D Centre on Water and Environmental Safety, Nankai University, Tianjin 300071, China
| | - Hongwen Sun
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering/Sino-Canada R&D Centre on Water and Environmental Safety, Nankai University, Tianjin 300071, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
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23
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Mahapatra K, De S, Banerjee S, Roy S. Pesticide mediated oxidative stress induces genotoxicity and disrupts chromatin structure in fenugreek (Trigonella foenum - graecum L.) seedlings. JOURNAL OF HAZARDOUS MATERIALS 2019; 369:362-374. [PMID: 30784966 DOI: 10.1016/j.jhazmat.2019.02.056] [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: 10/13/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Here we report cytototoxic and genotoxic potentials of four commonly used pesticides, including, tricyclazole, thiabendazole (fungicides), plethora and slash-360 (insecticides) in the non-target tropical crop plant Trigonella foenum - graecum L. (fenugreek). Three different concentrations of the selected pesticides were used. For fungicides, 0.05% and for insecticides, 0.1% concentration represents recommended doses, while, 2X and 4X concentrations of the recommended dose were used to test their phytotoxic effects. Inhibition of germination and seedling growth were clearly observed at 4X concentration of the pesticides. Tricyclazole and plethora showed more pronounced effects than the other two agrochemicals. The pesticides, particularly at 4X concentrations clearly induced oxidative stress and cytotoxic effects in Trigonella seedlings with appreciable reduction in mitotic index, induction of chromosomal abnormalities in root meristematic cell and decreased level of accumulation of some key cell cycle regulators, including CDK1, CDK2 and Cyclin B1.Detection of accumulation of DNA double strand breaks and histone H2AX phosphorylation in pesticide treated seedlings have revealed direct genotoxic effects of the selected pesticides. Overall, our results provide insights into the mechanism of pesticide induced cytotoxic and genotoxic effects in plant genome with future implications for designing pesticides to minimize their deleterious effects on non-target crop plants.
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Affiliation(s)
- Kalyan Mahapatra
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Sayanti De
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Samrat Banerjee
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Center for Advanced Studies, The University of Burdwan, Golapbag Campus, Burdwan, 713 104, West Bengal, India.
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24
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Nisa MU, Huang Y, Benhamed M, Raynaud C. The Plant DNA Damage Response: Signaling Pathways Leading to Growth Inhibition and Putative Role in Response to Stress Conditions. FRONTIERS IN PLANT SCIENCE 2019; 10:653. [PMID: 31164899 PMCID: PMC6534066 DOI: 10.3389/fpls.2019.00653] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/30/2019] [Indexed: 05/02/2023]
Abstract
Maintenance of genome integrity is a key issue for all living organisms. Cells are constantly exposed to DNA damage due to replication or transcription, cellular metabolic activities leading to the production of Reactive Oxygen Species (ROS) or even exposure to DNA damaging agents such as UV light. However, genomes remain extremely stable, thanks to the permanent repair of DNA lesions. One key mechanism contributing to genome stability is the DNA Damage Response (DDR) that activates DNA repair pathways, and in the case of proliferating cells, stops cell division until DNA repair is complete. The signaling mechanisms of the DDR are quite well conserved between organisms including in plants where they have been investigated into detail over the past 20 years. In this review we summarize the acquired knowledge and recent advances regarding the DDR control of cell cycle progression. Studying the plant DDR is particularly interesting because of their mode of development and lifestyle. Indeed, plants develop largely post-embryonically, and form new organs through the activity of meristems in which cells retain the ability to proliferate. In addition, they are sessile organisms that are permanently exposed to adverse conditions that could potentially induce DNA damage in all cell types including meristems. In the second part of the review we discuss the recent findings connecting the plant DDR to responses to biotic and abiotic stresses.
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25
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Hirakawa T, Matsunaga S. Characterization of DNA Repair Foci in Root Cells of Arabidopsis in Response to DNA Damage. FRONTIERS IN PLANT SCIENCE 2019; 10:990. [PMID: 31417598 PMCID: PMC6682680 DOI: 10.3389/fpls.2019.00990] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/15/2019] [Indexed: 05/20/2023]
Abstract
As a sessile organism, plants are constantly challenged by diverse environmental stresses that threaten genome integrity by way of induction of DNA damage. In plants, each tissue is composed of differentiated cell types, and the response to DNA damage differs among each cell type. However, limited information is available on the subnuclear dynamics of different cell types in response to DNA damage in plants. A chromatin remodeling factor RAD54, which plays an important role in the exchange reaction and alteration of chromatin structure during homologous recombination, specifically accumulates at damaged sites, forming DNA repair foci (termed RAD54 foci) in nuclei after γ-irradiation. In this study, we performed a time-course analysis of the appearance of RAD54 foci in root cells of Arabidopsis after γ-irradiation to characterize the subnuclear dynamics in each cell type. A short time after γ-irradiation, no significant difference in detection frequency of RAD54 foci was observed among epidermal, cortical, and endodermal cells in the meristematic zone of roots. Interestingly, cells showing RAD54 foci persisted in roots at long time after γ-irradiation, and RAD54 foci in these cells localized to nuclear periphery with high frequency. These observations suggest that the nuclear envelope plays a role in the maintenance of genome stability in response to DNA damage in Arabidopsis roots.
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26
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Rodriguez E, Chevalier J, El Ghoul H, Voldum-Clausen K, Mundy J, Petersen M. DNA damage as a consequence of NLR activation. PLoS Genet 2018; 14:e1007235. [PMID: 29462140 PMCID: PMC5834200 DOI: 10.1371/journal.pgen.1007235] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 03/02/2018] [Accepted: 01/31/2018] [Indexed: 01/20/2023] Open
Abstract
DNA damage observed during plant immune responses is reported to be an intrinsic component of plant immunity. However, other immune responses may suppress DNA damage to maintain host genome integrity. Here, we show that immunity-related DNA damage can be abrogated by preventing cell death triggered by Nucleotide-binding, Leucine-rich-repeat immune Receptors (NLRs). SNI1 (suppressor of npr1-1, inducible 1), a subunit of the structural maintenance of chromosome (SMC) 5/6 complex, was reported to be a negative regulator of systemic acquired resistance (SAR) and to be necessary for controlling DNA damage. We find that cell death and DNA damage in sni1 loss-of-function mutants are prevented by mutations in the NLR signaling component EDS1. Similar to sni1, elevated DNA damage is seen in other autoimmune mutants with cell death lesions, including camta3, pub13 and vad1, but not in dnd1, an autoimmune mutant with no visible cell death. We find that as in sni1, DNA damage in camta3 is EDS1-dependent, but that it is also NLR-dependent. Using the NLR RPM1 as a model, we also show that extensive DNA damage is observed when an NLR is directly triggered by effectors. We also find that the expression of DNA damage repair (DDR) genes in mutants with cell death lesions is down regulated, suggesting that degraded DNA that accumulates during cell death is a result of cellular dismantling and is not sensed as damaged DNA that calls for repair. Our observations also indicate that SNI1 is not directly involved in SAR or DNA damage accumulation.
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Affiliation(s)
- Eleazar Rodriguez
- Department of Biology, University of Copenhagen. Copenhagen, Denmark
| | | | - Hassan El Ghoul
- Department of Biology, University of Copenhagen. Copenhagen, Denmark
| | | | - John Mundy
- Department of Biology, University of Copenhagen. Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, University of Copenhagen. Copenhagen, Denmark
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27
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Pan X, Fang Y, Yang X, Zheng D, Chen L, Wang L, Xiao J, Wang XE, Wang K, Cheng Z, Yu H, Zhang W. Chromatin states responsible for the regulation of differentially expressed genes under 60Co~γ ray radiation in rice. BMC Genomics 2017; 18:778. [PMID: 29025389 PMCID: PMC5639768 DOI: 10.1186/s12864-017-4172-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/05/2017] [Indexed: 11/24/2022] Open
Abstract
Background The role of histone modifications in the DNA damage response has been extensively studied in non-plant systems, including mammals and yeast. However, there is a lack of detailed evidence showing how chromatin dynamics, either an individual mark or combined chromatin states, participate in regulating differentially expressed genes in the plant DNA damage response. Results In this study, we used RNA-seq and ChIP-seq to show that differentially expressed genes (DEGs), in response to ionizing radiation (IR), might be involved in different pathways responsible for the DNA damage response. Moreover, chromatin structures associated with promoters, exons and intergenic regions are significantly affected by IR. Most importantly, either an individual mark or a certain chromatin state was found to be highly correlated with the expression of up-regulated genes. In contrast, only the chromatin states, as opposed to any individual marks tested, are related to the expression of the down-regulated genes. Conclusions Our findings demonstrate that IR-related DEGs are modulated by distinct epigenetic mechanisms. Either chromatin states or distinct histone dynamics may act sequentially or in combination in regulating up-regulated genes, but the complex chromatin structure is mainly responsible for the expression of down-regulated genes. Thus, this study provides new insights into how up- and down-regulated genes are epigenetically regulated at the chromatin levels, thereby helping us to understand distinct epigenetic mechanisms that function in the plant DNA damage response. Electronic supplementary material The online version of this article (10.1186/s12864-017-4172-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiucai Pan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Yuan Fang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Xueming Yang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Dongyang Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Lifen Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Lei Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Jin Xiao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Xiu-E Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Kai Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, Fujian, 35002, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hengxiu Yu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China. .,JiangSu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP), Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China.
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28
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González-Arzola K, Díaz-Quintana A, Rivero-Rodríguez F, Velázquez-Campoy A, De la Rosa MA, Díaz-Moreno I. Histone chaperone activity of Arabidopsis thaliana NRP1 is blocked by cytochrome c. Nucleic Acids Res 2017; 45:2150-2165. [PMID: 27924001 PMCID: PMC5389710 DOI: 10.1093/nar/gkw1215] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022] Open
Abstract
Higher-order plants and mammals use similar mechanisms to repair and tolerate oxidative DNA damage. Most studies on the DNA repair process have focused on yeast and mammals, in which histone chaperone-mediated nucleosome disassembly/reassembly is essential for DNA to be accessible to repair machinery. However, little is known about the specific role and modulation of histone chaperones in the context of DNA damage in plants. Here, the histone chaperone NRP1, which is closely related to human SET/TAF-Iβ, was found to exhibit nucleosome assembly activity in vitro and to accumulate in the chromatin of Arabidopsis thaliana after DNA breaks. In addition, this work establishes that NRP1 binds to cytochrome c, thereby preventing the former from binding to histones. Since NRP1 interacts with cytochrome c at its earmuff domain, that is, its histone-binding domain, cytochrome c thus competes with core histones and hampers the activity of NRP1 as a histone chaperone. Altogether, the results obtained indicate that the underlying molecular mechanisms in nucleosome disassembly/reassembly are highly conserved throughout evolution, as inferred from the similar inhibition of plant NRP1 and human SET/TAF-Iβ by cytochrome c during DNA damage response.
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Affiliation(s)
- Katiuska González-Arzola
- Institute for Chemical Research (IIQ), Isla de la Cartuja Scientific Research Centre (cicCartuja), University of Seville-Spanish National Research Council (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Antonio Díaz-Quintana
- Institute for Chemical Research (IIQ), Isla de la Cartuja Scientific Research Centre (cicCartuja), University of Seville-Spanish National Research Council (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Francisco Rivero-Rodríguez
- Institute for Chemical Research (IIQ), Isla de la Cartuja Scientific Research Centre (cicCartuja), University of Seville-Spanish National Research Council (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit Institute of Physical Chemistry Rocasolano (IQFR)-BIFI-Spanish National Research Council (CSIC), University of Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain.,Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza (Spain); and Aragon Agency for Research and Development (ARAID), Regional Government of Aragon, Maria de Luna 11, 50018 Zaragoza, Spain
| | - Miguel A De la Rosa
- Institute for Chemical Research (IIQ), Isla de la Cartuja Scientific Research Centre (cicCartuja), University of Seville-Spanish National Research Council (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Isla de la Cartuja Scientific Research Centre (cicCartuja), University of Seville-Spanish National Research Council (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain
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29
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Horvath BM, Kourova H, Nagy S, Nemeth E, Magyar Z, Papdi C, Ahmad Z, Sanchez-Perez GF, Perilli S, Blilou I, Pettkó-Szandtner A, Darula Z, Meszaros T, Binarova P, Bogre L, Scheres B. Arabidopsis RETINOBLASTOMA RELATED directly regulates DNA damage responses through functions beyond cell cycle control. EMBO J 2017; 36:1261-1278. [PMID: 28320736 PMCID: PMC5412863 DOI: 10.15252/embj.201694561] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 12/26/2022] Open
Abstract
The rapidly proliferating cells in plant meristems must be protected from genome damage. Here, we show that the regulatory role of the Arabidopsis RETINOBLASTOMA RELATED (RBR) in cell proliferation can be separated from a novel function in safeguarding genome integrity. Upon DNA damage, RBR and its binding partner E2FA are recruited to heterochromatic γH2AX-labelled DNA damage foci in an ATM- and ATR-dependent manner. These γH2AX-labelled DNA lesions are more dispersedly occupied by the conserved repair protein, AtBRCA1, which can also co-localise with RBR foci. RBR and AtBRCA1 physically interact in vitro and in planta Genetic interaction between the RBR-silenced amiRBR and Atbrca1 mutants suggests that RBR and AtBRCA1 may function together in maintaining genome integrity. Together with E2FA, RBR is directly involved in the transcriptional DNA damage response as well as in the cell death pathway that is independent of SOG1, the plant functional analogue of p53. Thus, plant homologs and analogues of major mammalian tumour suppressor proteins form a regulatory network that coordinates cell proliferation with cell and genome integrity.
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Affiliation(s)
- Beatrix M Horvath
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
| | - Hana Kourova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Szilvia Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Edit Nemeth
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zoltan Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Csaba Papdi
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Zaki Ahmad
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Gabino F Sanchez-Perez
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Serena Perilli
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | - Ikram Blilou
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
| | | | - Zsuzsanna Darula
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary
| | - Tamas Meszaros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
- Technical Analytical Research Group of HAS, Budapest, Hungary
| | - Pavla Binarova
- Institute of Microbiology CAS, v.v.i., Laboratory of Cell Reproduction, Prague 4, Czech Republic
| | - Laszlo Bogre
- School of Biological Sciences, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham, UK
| | - Ben Scheres
- Department of Molecular Genetics, Utrecht University, Utrecht, The Netherlands
- Department of Plant Sciences, Wageningen University Research Centre, Wageningen, The Netherlands
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30
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Lorković ZJ, Park C, Goiser M, Jiang D, Kurzbauer MT, Schlögelhofer P, Berger F. Compartmentalization of DNA Damage Response between Heterochromatin and Euchromatin Is Mediated by Distinct H2A Histone Variants. Curr Biol 2017; 27:1192-1199. [PMID: 28392109 DOI: 10.1016/j.cub.2017.03.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/31/2022]
Abstract
DNA double-strand break (DSB) repair depends on the ataxia telangiectasia mutated (ATM) kinase that phosphorylates the conserved C-terminal SQ motif present in the histone variant H2A.X [1-7]. In constitutive heterochromatin of mammals, DSB repair is delayed and relies on phosphorylation of the proteins HP1 and KAP1 by ATM [2, 8-14]. However, KAP1 is not conserved in plants and the HP1-related protein Like-HP1 (LHP1) is not localized at constitutive heterochromatin [15], suggesting that in plants, alternative mechanisms could be responsible for repair of DSBs in heterochromatin. In Arabidopsis, constitutive heterochromatin is marked by H3K9 methylation and the plant-specific histone variants H2A.W, which are distinguished by their C-terminal motif KSPKK and required for heterochromatin compaction [16-18]. We report that the Arabidopsis histone variant H2A.W.7 is confined to heterochromatin and carries a SQ motif that is phosphorylated by ATM. In response to DNA damage, phosphorylation of H2A.W.7 takes place in heterochromatin, while H2A.X phosphorylation takes place primarily in euchromatin. We propose that H2A.W.7 evolved in addition to H2A.X to facilitate DNA damage response in highly condensed heterochromatin, thus playing a role similar to KAP1 and HP1 phosphorylation in mammals. These data support the idea of the functional diversification of histone variants and their role in spatial compartmentalization of chromatin-related functions in eukaryotes.
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Affiliation(s)
- Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chulmin Park
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Malgorzata Goiser
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Danhua Jiang
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Marie-Therese Kurzbauer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Hirakawa T, Hasegawa J, White CI, Matsunaga S. RAD54 forms DNA repair foci in response to DNA damage in living plant cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:372-382. [PMID: 28155243 DOI: 10.1111/tpj.13499] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
Plants have various defense mechanisms against environmental stresses that induce DNA damage. Genetic and biochemical analyses have revealed the sensing and signaling of DNA damage, but little is known about subnuclear dynamics in response to DNA damage in living plant cells. Here, we observed that the chromatin remodeling factor RAD54, which is involved in DNA repair via the homologous recombination pathway, formed subnuclear foci (termed RAD54 foci) in Arabidopsis thaliana after induction of DNA double-strand breaks. The appearance of RAD54 foci was dependent on the ATAXIA-TELANGIECTASIA MUTATED-SUPPRESSOR OF GAMMA RESPONSE 1 pathway, and RAD54 foci were co-localized with γH2AX signals. Laser irradiation of a subnuclear area demonstrated that in living cells RAD54 was specifically accumulated at the damaged site. In addition, the formation of RAD54 foci showed specificity for cell type and region. We conclude that RAD54 foci correspond to DNA repair foci in A. thaliana.
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Affiliation(s)
- Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Junko Hasegawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Charles I White
- Génétique, Reproduction et Développement, UMR CNRS 6293, Clermont Université, INSERM U1103, Université Blaise Pascal, Clermont-Ferrand, France
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
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Biedermann S, Harashima H, Chen P, Heese M, Bouyer D, Sofroni K, Schnittger A. The retinoblastoma homolog RBR1 mediates localization of the repair protein RAD51 to DNA lesions in Arabidopsis. EMBO J 2017; 36:1279-1297. [PMID: 28320735 PMCID: PMC5412766 DOI: 10.15252/embj.201694571] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 11/13/2022] Open
Abstract
The retinoblastoma protein (Rb), which typically functions as a transcriptional repressor of E2F‐regulated genes, represents a major control hub of the cell cycle. Here, we show that loss of the Arabidopsis Rb homolog RETINOBLASTOMA‐RELATED 1 (RBR1) leads to cell death, especially upon exposure to genotoxic drugs such as the environmental toxin aluminum. While cell death can be suppressed by reduced cell‐proliferation rates, rbr1 mutant cells exhibit elevated levels of DNA lesions, indicating a direct role of RBR1 in the DNA‐damage response (DDR). Consistent with its role as a transcriptional repressor, we find that RBR1 directly binds to and represses key DDR genes such as RADIATION SENSITIVE 51 (RAD51), leaving it unclear why rbr1 mutants are hypersensitive to DNA damage. However, we find that RBR1 is also required for RAD51 localization to DNA lesions. We further show that RBR1 is itself targeted to DNA break sites in a CDKB1 activity‐dependent manner and partially co‐localizes with RAD51 at damage sites. Taken together, these results implicate RBR1 in the assembly of DNA‐bound repair complexes, in addition to its canonical function as a transcriptional regulator.
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Affiliation(s)
- Sascha Biedermann
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France.,Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | | | - Poyu Chen
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Maren Heese
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Daniel Bouyer
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR 8197-INSERM U 1024, Paris, France
| | - Kostika Sofroni
- Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
| | - Arp Schnittger
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France .,Department of Developmental Biology, Biozentrum Klein Flottbek University of Hamburg, Hamburg, Germany
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Roy S, Das KP. Homologous Recombination Defective Arabidopsis Mutants Exhibit Enhanced Sensitivity to Abscisic Acid. PLoS One 2017; 12:e0169294. [PMID: 28046013 PMCID: PMC5207409 DOI: 10.1371/journal.pone.0169294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/14/2016] [Indexed: 12/27/2022] Open
Abstract
Abscisic acid (ABA) acts as an important plant hormone in regulating various aspects of plant growth and developmental processes particularly under abiotic stress conditions. An increased ABA level in plant cells inhibits DNA replication and cell division, causing plant growth retardation. In this study, we have investigated the effects of ABA on the growth responses of some major loss-of-function mutants of DNA double-stand break (DSB) repair genes in Arabidopsis during seed germination and early stages of seedling growth for understanding the role of ABA in the induction of genome instability in plants. A comparative analysis of ABA sensitivity of wild-type Arabidopsis and the knockout mutant lines related to DSB sensors, including atatm, atatr, the non-homologous end joining (NHEJ) pathway genes, and mutants related to homologous recombination (HR) pathway genes showed relatively enhanced sensitivity of atatr and HR-related mutants to ABA treatment. The expression levels of HR-related genes were increased in wild-type Arabidopsis (Col-0) during seed germination and early stages of seedling growth. Immunoblotting experiments detected phosphorylation of histone H2AX in wild-type (Col-0) and DSB repair gene mutants after ABA treatment, indicating the activation of DNA damage response due to ABA treatment. Analyses of DSB repair kinetics using comet assay under neutral condition have revealed comparatively slower DSB repair activity in HR mutants. Overall, our results have provided comprehensive information on the possible effect of ABA on DNA repair machinery in plants and also indicated potential functional involvement of HR pathway in repairing ABA induced DNA damage in Arabidopsis.
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Affiliation(s)
- Sujit Roy
- Protein Chemistry laboratory, Department of Chemistry, Bose Institute, Kolkata, India
| | - Kali Pada Das
- Protein Chemistry laboratory, Department of Chemistry, Bose Institute, Kolkata, India
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Xue Z, Li Y, Zhang L, Shi W, Zhang C, Feng M, Zhang F, Tang D, Yu H, Gu M, Cheng Z. OsMTOPVIB Promotes Meiotic DNA Double-Strand Break Formation in Rice. MOLECULAR PLANT 2016; 9:1535-1538. [PMID: 27456761 DOI: 10.1016/j.molp.2016.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/13/2016] [Accepted: 07/15/2016] [Indexed: 05/25/2023]
Affiliation(s)
- Zhihui Xue
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Zhang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqing Shi
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Zhang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengshi Feng
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Fanfan Zhang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hengxiu Yu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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35
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Wu T, Huang H, Zhang S. Accumulation and phytotoxicity of technical hexabromocyclododecane in maize. J Environ Sci (China) 2016; 42:97-104. [PMID: 27090699 DOI: 10.1016/j.jes.2015.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 06/05/2023]
Abstract
To investigate the accumulation and phytotoxicity of technical hexabromocyclododecane (HBCD) in maize, young seedlings were exposed to solutions of technical HBCD at different concentrations. The uptake kinetics showed that the HBCD concentration reached an apparent equilibrium within 96hr, and the accumulation was much higher in roots than in shoots. HBCD accumulation in maize had a positive linear correlation with the exposure concentration. The accumulation of different diastereoisomers followed the order γ-HBCD>β-HBCD>α-HBCD. Compared with their proportions in the technical HBCD exposure solution, the diastereoisomer contribution increased for β-HBCD and decreased for γ-HBCD in both maize roots and shoots with exposure time, whereas the contribution of α-HBCD increased in roots and decreased in shoots throughout the experimental period. These results suggest the diastereomer-specific accumulation and translocation of HBCD in maize. Inhibitory effects of HBCD on the early development of maize followed the order of germination rate>root biomass≥root elongation>shoot biomass≥shoot elongation. Hydroxyl radical (OH) and histone H2AX phosphorylation (γ-H2AX) were induced in maize by HBCD exposure, indicative of the generation of oxidative stress and DNA double-strand breaks in maize. An OH scavenger inhibited the expression of γ-H2AX foci in both maize roots and shoots, which suggests the involvement of OH generation in the HBCD-induced DNA damage. The results of this study will offer useful information for a more comprehensive assessment of the environmental behavior and toxicity of technical HBCD.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environmental Science and Engineering, Hebei University of Science and Technology, Hebei 050018, China.
| | - Honglin Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuzhen Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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36
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Abstract
Eyes absent (Eya), a protein conserved from plants to humans and best characterized as a transcriptional coactivator, is also the prototype for a novel class of eukaryotic aspartyl protein tyrosine phosphatases. This minireview discusses recent breakthroughs in elucidating the substrates and cellular events regulated by Eya's tyrosine phosphatase function and highlights some of the complexities, new questions, and surprises that have emerged from efforts to understand how Eya's unusual multifunctionality influences developmental regulation and signaling.
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37
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Histone H2AX and the small RNA pathway modulate both non-homologous end-joining and homologous recombination in plants. Mutat Res 2015; 783:9-14. [PMID: 26687994 DOI: 10.1016/j.mrfmmm.2015.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/05/2015] [Accepted: 12/01/2015] [Indexed: 11/21/2022]
Abstract
Using a zinc finger nuclease (ZFN) that creates a site-specific DNA double-strand break (DSB) at the endogenous ADH1 locus, we provide genetic evidence that histone H2AX and DSB-induced small RNAs modulate DNA repair by both non-homologous end-joining (NHEJ) and homologous recombination (HR) in the model plant Arabidopsis thaliana.
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38
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Zhang B, Wang M, Tang D, Li Y, Xu M, Gu M, Cheng Z, Yu H. XRCC3 is essential for proper double-strand break repair and homologous recombination in rice meiosis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5713-25. [PMID: 26034131 DOI: 10.1093/jxb/erv253] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
RAD51 paralogues play important roles in the assembly and stabilization of RAD51 nucleoprotein filaments, which promote homologous pairing and strand exchange reactions in organisms ranging from yeast to vertebrates. XRCC3, a RAD51 paralogue, has been characterized in budding yeast, mouse, and Arabidopsis. In the present study, XRCC3 in rice was identified and characterized. The rice xrcc3 mutant exhibited normal vegetative growth but complete male and female sterility. Cytological investigations revealed that homologous pairing and synapsis were severely disrupted in the mutant. Meiotic chromosomes were frequently entangled from diplotene to metaphase I, resulting in chromosome fragmentation at anaphase I. The immunostaining signals from γH2AX were regular, implying that double-strand break (DSB) formation was normal in xrcc3 meiocytes. However, COM1 was not detected on early prophase I chromosomes, suggesting that the DSB end-processing system was destroyed in the mutant. Moreover, abnormal chromosome localization of RAD51C, DMC1, ZEP1, ZIP4, and MER3 was observed in xrcc3. Taken together, the results suggest that XRCC3 plays critical roles in both DSB repair and homologous chromosome recombination during rice meiosis.
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Affiliation(s)
- Bingwei Zhang
- Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/ Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Mo Wang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Xu
- Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/ Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/ Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/ Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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39
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Zhou W, Zhu Y, Dong A, Shen WH. Histone H2A/H2B chaperones: from molecules to chromatin-based functions in plant growth and development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:78-95. [PMID: 25781491 DOI: 10.1111/tpj.12830] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 05/06/2023]
Abstract
Nucleosomal core histones (H2A, H2B, H3 and H4) must be assembled, replaced or exchanged to preserve or modify chromatin organization and function according to cellular needs. Histone chaperones escort histones, and play key functions during nucleosome assembly/disassembly and in nucleosome structure configuration. Because of their location at the periphery of nucleosome, histone H2A-H2B dimers are remarkably dynamic. Here we focus on plant histone H2A/H2B chaperones, particularly members of the NUCLEOSOME ASSEMBLY PROTEIN-1 (NAP1) and FACILITATES CHROMATIN TRANSCRIPTION (FACT) families, discussing their molecular features, properties, regulation and function. Covalent histone modifications (e.g. ubiquitination, phosphorylation, methylation, acetylation) and H2A variants (H2A.Z, H2A.X and H2A.W) are also discussed in view of their crucial importance in modulating nucleosome organization and function. We further discuss roles of NAP1 and FACT in chromatin-based processes, such as transcription, DNA replication and repair. Specific functions of NAP1 and FACT are evident when their roles are considered with respect to regulation of plant growth and development and in plant responses to environmental stresses. Future major challenges remain in order to define in more detail the overlapping and specific roles of various members of the NAP1 family as well as differences and similarities between NAP1 and FACT family members, and to identify and characterize their partners as well as new families of chaperones to understand histone variant incorporation and chromatin target specificity.
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Affiliation(s)
- Wangbin Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 20043, China
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, France
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40
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Kawashima T, Lorković ZJ, Nishihama R, Ishizaki K, Axelsson E, Yelagandula R, Kohchi T, Berger F. Diversification of histone H2A variants during plant evolution. TRENDS IN PLANT SCIENCE 2015; 20:419-25. [PMID: 25983206 DOI: 10.1016/j.tplants.2015.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 05/19/2023]
Abstract
Among eukaryotes, the four core histones show an extremely high conservation of their structure and form nucleosomes that compact, protect, and regulate access to genetic information. Nevertheless, in multicellular eukaryotes the two families, histone H2A and histone H3, have diversified significantly in key residues. We present a phylogenetic analysis across the green plant lineage that reveals an early diversification of the H2A family in unicellular green algae and remarkable expansions of H2A variants in flowering plants. We define motifs and domains that differentiate plant H2A proteins into distinct variant classes. In non-flowering land plants, we identify a new class of H2A variants and propose their possible role in the emergence of the H2A.W variant class in flowering plants.
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Affiliation(s)
- Tomokazu Kawashima
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Frederic Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria.
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41
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Xu X, Huang H, Wen B, Wang S, Zhang S. Phytotoxicity of Brominated Diphenyl Ether-47 (BDE-47) and Its Hydroxylated and Methoxylated Analogues (6-OH-BDE-47 and 6-MeO-BDE-47) to Maize (Zea mays L.). Chem Res Toxicol 2015; 28:510-7. [DOI: 10.1021/tx500484m] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Xuehui Xu
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Honglin Huang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Bei Wen
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
| | - Sen Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
- Department
of Environmental Sciences, College of Urban and Environmental Sciences, Northwest University, Xi’an 710027, China
| | - Shuzhen Zhang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P.O. Box 2871, Beijing 100085, China
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42
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Sidler C, Li D, Kovalchuk O, Kovalchuk I. Development-Dependent Expression of DNA Repair Genes and Epigenetic Regulators in Arabidopsis Plants Exposed to Ionizing Radiation. Radiat Res 2015; 183:219-32. [DOI: 10.1667/rr13840.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Corinne Sidler
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Dongping Li
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
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43
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Zhou S, Sun H, Zheng B, Li R, Zhang W. Cell cycle transcription factor E2F2 mediates non-stress temperature response of AtHSP70-4 in Arabidopsis. Biochem Biophys Res Commun 2014; 455:139-46. [DOI: 10.1016/j.bbrc.2014.10.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 01/24/2023]
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44
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Pecinka A, Liu CH. Drugs for Plant Chromosome and Chromatin Research. Cytogenet Genome Res 2014; 143:51-9. [DOI: 10.1159/000360774] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Amiard S, Gallego ME, White CI. Signaling of double strand breaks and deprotected telomeres in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2013; 4:405. [PMID: 24137170 PMCID: PMC3797388 DOI: 10.3389/fpls.2013.00405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/24/2013] [Indexed: 05/17/2023]
Abstract
Failure to repair DNA double strand breaks (DSB) can lead to chromosomal rearrangements and eventually to cancer or cell death. Radiation and environmental pollutants induce DSB and this is of particular relevance to plants due to their sessile life style. DSB also occur naturally in cells during DNA replication and programmed induction of DSB initiates the meiotic recombination essential for gametogenesis in most eukaryotes. The linear nature of most eukaryotic chromosomes means that each chromosome has two "broken" ends. Chromosome ends, or telomeres, are protected by nucleoprotein caps which avoid their recognition as DSB by the cellular DNA repair machinery. Deprotected telomeres are recognized as DSB and become substrates for recombination leading to chromosome fusions, the "bridge-breakage-fusion" cycle, genome rearrangements and cell death. The importance of repair of DSB and the severity of the consequences of their misrepair have led to the presence of multiple, robust mechanisms for their detection and repair. After a brief overview of DSB repair pathways to set the context, we present here an update of current understanding of the detection and signaling of DSB in the plant, Arabidopsis thaliana.
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Affiliation(s)
| | | | - Charles I. White
- Génétique, Reproduction et Développement, UMR CNRS 6293/U1103 INSERM/Clermont Université, Université Blaise PascalAubiére cedex, France
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Siddiqui MS, Filomeni E, Francois M, Collins SR, Cooper T, Glatz RV, Taylor PW, Fenech M, Leifert WR. Exposure of insect cells to ionising radiation in vivo induces persistent phosphorylation of a H2AX homologue (H2AvB). Mutagenesis 2013; 28:531-41. [DOI: 10.1093/mutage/get030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Gutzat R, Mittelsten Scheid O. Epigenetic responses to stress: triple defense? CURRENT OPINION IN PLANT BIOLOGY 2012; 15:568-73. [PMID: 22960026 PMCID: PMC3508409 DOI: 10.1016/j.pbi.2012.08.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/16/2012] [Indexed: 05/19/2023]
Abstract
Stressful conditions for plants can originate from numerous physical, chemical and biological factors, and plants have developed a plethora of survival strategies including developmental and morphological adaptations, specific signaling and defense pathways as well as innate and acquired immunity. While it has become clear in recent years that many stress responses involve epigenetic components, we are far from understanding the mechanisms and molecular interactions. Extending our knowledge is fundamental, not least for plant breeding and conservation biology. This review will highlight recent insights into epigenetic stress responses at the level of signaling, chromatin modification, and potentially heritable consequences.
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Wu T, Wang S, Huang H, Zhang S. Diastereomer-specific uptake, translocation, and toxicity of hexabromocyclododecane diastereoisomers to maize. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:8528-8534. [PMID: 22881704 DOI: 10.1021/jf302682p] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Hexabromocyclododecane (HBCD), a brominated flame retardant, has become a ubiquitous contaminant due to its wide application, persistence, and toxicity. HBCD diastereoisomers have different physical and chemical properties and may differ in their bioaccumulation and toxicity in plants. Accumulation and toxicity of α-, β-, and γ-HBCDs in maize were investigated in the present study. The accumulation was in the order β-HBCD > α-HBCD > γ-HBCD in roots and β-HBCD > γ-HBCD > α-HBCD in shoots. Both the inhibitory effect of the diastereoisomers on the early development of maize and the intensities of hydroxyl radical and histone H2AX phosphorylation in maize exposed to 2 μg L(-1) HBCD followed the order α-HBCD > β-HBCD > γ-HBCD, indicating the diastereomer-specific oxidative stress and DNA damage in maize. It was further confirmed that the generation of reactive oxygen species was one, but not the only, mechanism for DNA damage in maize exposed to HBCDs.
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Affiliation(s)
- Tong Wu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
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