1
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Yuan P, Cai Q, Hu Z. Arabidopsis DEAD-box RNA helicase 12 is required for salt tolerance during seed germination. Biochem Biophys Res Commun 2024; 725:150228. [PMID: 38936167 DOI: 10.1016/j.bbrc.2024.150228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
The DEAD-box family is the largest family of RNA helicases (RHs), playing crucial roles in RNA metabolism and plant stress resistance. In this study, we report that an RNA helicase, RH12, positively regulates plant salt tolerance, as rh12 knockout mutants exhibit heightened sensitivity to salt stress. Further analysis indicates that RH12 is involved in the abscisic acid (ABA) response, as rh12 knockout mutants show increased sensitivity to ABA. Examination of reactive oxygen species (ROS) revealed that RH12 helps inhibit ROS accumulation under salt stress during seed germination. Additionally, RH12 accelerates the degradation of specific germination-related transcripts. In conclusion, our results demonstrate that RH12 plays multiple roles in the salt stress response in Arabidopsis.
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Affiliation(s)
- Penglai Yuan
- College of Life Sciences, Nanjing Agricultural University, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Qingsheng Cai
- College of Life Sciences, Nanjing Agricultural University, China.
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China.
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2
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Shilpa, Thakur R, Prasad P. Epigenetic regulation of abiotic stress responses in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130661. [PMID: 38885816 DOI: 10.1016/j.bbagen.2024.130661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/15/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Plants face a wide array of challenges in their environment, both from living organisms (biotic stresses) and non-living factors (abiotic stresses). Among the major abiotic stressors affecting crop plants, variations in temperature, water availability, salinity, and cold pose significant threats to crop yield and the quality of produce. Plants possess remarkable adaptability and resilience, and they employ a range of genetic and epigenetic mechanisms to respond and cope with abiotic stresses. A few crucial set of epigenetic mechanisms that support plants in their battle against these stresses includes DNA methylation and histone modifications. These mechanisms play a pivotal role in enabling plants to endure and thrive under challenging environmental conditions. The mechanisms of different epigenetic mechanisms in responding to the abiotic stresses vary. Each plant species and type of stress may trigger distinct epigenetic responses, highlighting the complexity of the plant's ability to adapt under stress conditions. This review focuses on the paramount importance of epigenetics in enhancing a plant's ability to survive and excel under various abiotic stresses. It highlights recent advancements in our understanding of the epigenetic mechanisms that contribute to abiotic stress tolerance in plants. This growing knowledge is pivotal for shaping future efforts aimed at mitigating the impact of abiotic stresses on diverse crop plants.
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Affiliation(s)
- Shilpa
- Department of Biotechnology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
| | - Rajnikant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India
| | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India.
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3
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Wang Z, Luo R, Wen Q, Liang X, Zhao H, Zhao Y, Yin M, Wen Y, Hu X, Huang F. Screening and functional verification of drought resistance-related genes in castor bean seeds. BMC PLANT BIOLOGY 2024; 24:493. [PMID: 38831288 PMCID: PMC11145773 DOI: 10.1186/s12870-024-04997-7] [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: 09/01/2023] [Accepted: 04/08/2024] [Indexed: 06/05/2024]
Abstract
Drought is one of the natural stresses that greatly impact plants. Castor bean (Ricinus communis L.) is an oil crop with high economic value. Drought is one of the factors limiting castor bean growth. The drought resistance mechanisms of castor bean have become a research focus. In this study, we used castor germinating embryos as experimental materials, and screened genes related to drought resistance through physiological measurements, proteomics and metabolomics joint analysis; castor drought-related genes were subjected to transient silencing expression analysis in castor leaves to validate their drought-resistant functions, and heterologous overexpression and backward complementary expression in Arabidopsis thaliana, and analysed the mechanism of the genes' response to the participation of Arabidopsis thaliana in drought-resistance.Three drought tolerance-related genes, RcECP 63, RcDDX 31 and RcA/HD1, were obtained by screening and analysis, and transient silencing of expression in castor leaves further verified that these three genes corresponded to drought stress, and heterologous overexpression and back-complementary expression of the three genes in Arabidopsis thaliana revealed that the function of these three genes in drought stress response.In this study, three drought tolerance related genes, RcECP 63, RcDDX 31 and RcA/HD1, were screened and analysed for gene function, which were found to be responsive to drought stress and to function in drought stress, laying the foundation for the study of drought tolerance mechanism in castor bean.
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Grants
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 2021BS03036 Analysis of the R2R3-MYB transcription factor gene family in castor bean and functional resolution of RcMYB61 in response to drought stress
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 31860071 National Natural Science Foundation of China
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2020114 Ministry of Education New Agricultural Research and Reform Practice Project
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2021MS03008 Upper Level Project of Inner Mongolia Natural Science Foundation
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 2022 Inner Mongolia Autonomous Region Grassland Talent Innovation Team - Rolling Support Programme for Castor Molecular Breeding Research Innovation Talent Team
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 21082 2021 Research Project on Higher Education Teaching Reform of the National People's Committee
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- 237 Inner Mongolia University for Nationalities 2022 Basic Research Operating Expenses of Colleges and Universities directly under the Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
- MDK2021011, MDK2022014 Project of the Open Fund of the Collaborative Innovation Centre for Castor Industry in Inner Mongolia Autonomous Region
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Affiliation(s)
- Zhiyan Wang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, Inner Mongolia, China
| | - Rui Luo
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, Inner Mongolia, China
| | - Qi Wen
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, Inner Mongolia, China
| | - Xiaotian Liang
- Agronomy College, Jilin Agricultural University, Changchun, 130118, China
- National Oat Improvement Center, Baicheng Academy of Agricultural Sciences, Baicheng, 137000, China
| | - Huibo Zhao
- China National Rice Research Institute, Hangzhou, 311400, China
| | - Yong Zhao
- School of Life Sciences, Laboratory of Genetics, Baicheng Normal University, Baicheng, 137000, China
| | - Mingda Yin
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, Inner Mongolia, China
| | - Yanpeng Wen
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, Inner Mongolia, China
| | - Xuemei Hu
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, 028000, Inner Mongolia, China
| | - Fenglan Huang
- Key Laboratory of Castor Breeding of the National Ethnic Affairs Commission of the People's Republic of China, Tongliao, 028000, Inner Mongolia, China.
- Inner Mongolia Key Laboratory of Castor Breeding and Comprehensive Utilization, Tongliao, 028000, Inner Mongolia, China.
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4
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Zheng M, Song Y, Wang L, Yang D, Yan J, Sun Y, Hsu YF. CaRH57, a RNA helicase, contributes pepper tolerance to heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108202. [PMID: 37995575 DOI: 10.1016/j.plaphy.2023.108202] [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: 08/01/2023] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
RNA helicases (RHs) are required for most aspects of RNA metabolism and play an important role in plant stress tolerance. Heat stress (HS) causes the deleterious effects on plant cells, such as membrane disruption and protein misfolding, which results in the inhibition of plant growth and development. In this study, CaRH57 was identified from pepper (Capsicum annuum) and encodes a DEAD-box RH. CaRH57 was induced by HS, and overexpression of CaRH57 in Atrh57-1 rescued the glucose-sensitive phenotype of Atrh57-1, suggesting the functional replacement of CaRH57 to AtRH57. The nucleolus-localized CaRH57 possessed a RH activity in vitro. CaRH57 knockdown impaired pepper heat tolerance, showing severe necrosis and enhanced ROS accumulation in the region of the shoot tip. Additionally, accumulation of aberrant-spliced CaHSFA1d and CaHSFA9d was enhanced, and the corresponding mature mRNA levels were reduced in the TRV2 (Tobacco rattle virus)-CaRH57-infected plants compared with the control plants under HS. Overall, these results suggested that CaRH57 acted as a RH to confer pepper heat tolerance and was required for the proper pre-mRNA splicing of some HS-related genes.
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Affiliation(s)
- Min Zheng
- School of Life Sciences, Southwest University, Chongqing, China.
| | - Yu Song
- School of Life Sciences, Southwest University, Chongqing, China
| | - Lingyu Wang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Dandan Yang
- School of Life Sciences, Southwest University, Chongqing, China
| | - Jiawen Yan
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yutao Sun
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yi-Feng Hsu
- School of Life Sciences, Southwest University, Chongqing, China.
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5
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Fernandes R, Ostendorp A, Ostendorp S, Mehrmann J, Falke S, Graewert MA, Weingartner M, Kehr J, Hoth S. Structural and functional analysis of a plant nucleolar RNA chaperone-like protein. Sci Rep 2023; 13:9656. [PMID: 37316549 DOI: 10.1038/s41598-023-36426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/03/2023] [Indexed: 06/16/2023] Open
Abstract
Ribosome biogenesis is a key process in all eukaryotic cells that requires hundreds of ribosome biogenesis factors (RBFs), which are essential to build the mature ribosomes consisting of proteins and rRNAs. The processing of the required rRNAs has been studied extensively in yeast and mammals, but in plants much is still unknown. In this study, we focused on a RBF from A. thaliana that we named NUCLEOLAR RNA CHAPERONE-LIKE 1 (NURC1). NURC1 was localized in the nucleolus of plant cell nuclei, and other plant RBF candidates shared the same localization. SEC-SAXS experiments revealed that NURC1 has an elongated and flexible structure. In addition, SEC-MALLS experiments confirmed that NURC1 was present in its monomeric form with a molecular weight of around 28 kDa. RNA binding was assessed by performing microscale thermophoresis with the Arabidopsis internal transcribed spacer 2 (ITS2) of the polycistronic pre-rRNA precursor, which contains the 5.8S, 18S, and 25S rRNA. NURC1 showed binding activity to the ITS2 with a dissociation constant of 228 nM and exhibited RNA chaperone-like activity. Our data suggested that NURC1 may have a function in pre-rRNA processing and thus ribosome biogenesis.
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Affiliation(s)
- Rita Fernandes
- Molecular Plant Physiology, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
- Molecular Plant Genetics, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Anna Ostendorp
- Molecular Plant Genetics, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Steffen Ostendorp
- Molecular Plant Genetics, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Judith Mehrmann
- Molecular Plant Physiology, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Sven Falke
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Magdalena Weingartner
- Molecular Plant Physiology, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Julia Kehr
- Molecular Plant Genetics, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany
| | - Stefan Hoth
- Molecular Plant Physiology, Institute of Plant Science and Microbiology, Department of Biology, Universität Hamburg, Hamburg, Germany.
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6
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Zhang L, Xu Y, Liu X, Qin M, Li S, Jiang T, Yang Y, Jiang CZ, Gao J, Hong B, Ma C. The chrysanthemum DEAD-box RNA helicase CmRH56 regulates rhizome outgrowth in response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5671-5681. [PMID: 35595538 DOI: 10.1093/jxb/erac213] [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: 10/17/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Plants have evolved complex mechanisms to reprogram growth in response to drought stress. In herbaceous perennial plant species, the rhizome, which is normally an organ for propagation and food storage, can also support plant growth in stressful environments, and allows the plant to perennate and survive stress damage. However, the mechanisms that regulate rhizome growth in perennial herbs during abiotic stresses are unknown. Here, we identified a chrysanthemum (Chrysanthemum morifolium) DEAD-box RNA helicase gene, CmRH56, that is specifically expressed in the rhizome shoot apex. Knock down of CmRH56 transcript levels decreased the number of rhizomes and enhanced drought stress tolerance. We determined that CmRH56 represses the expression of a putative gibberellin (GA) catabolic gene, GA2 oxidase6 (CmGA2ox6). Exogenous GA treatment and silencing of CmGA2ox6 resulted in more rhizomes. These results demonstrate that CmRH56 suppresses rhizome outgrowth under drought stress conditions by blocking GA biosynthesis.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yanjie Xu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Xuening Liu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Meizhu Qin
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Shenglan Li
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Tianhua Jiang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yingjie Yang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, USA
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Junping Gao
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Bo Hong
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Chao Ma
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
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7
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Yadav S, Yadava YK, Kohli D, Meena S, Kalwan G, Bharadwaj C, Gaikwad K, Arora A, Jain PK. Genome-wide identification, in silico characterization and expression analysis of the RNA helicase gene family in chickpea (C. arietinum L.). Sci Rep 2022; 12:9778. [PMID: 35697711 PMCID: PMC9192698 DOI: 10.1038/s41598-022-13823-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022] Open
Abstract
The RNA helicases are an important class of enzymes which are known to influence almost every aspect of RNA metabolism. The majority of RNA helicases belong to the SF2 (superfamily 2) superfamily, members of which are further categorized into three separate subfamilies i.e., the DEAD, DEAH and DExD/H-box subfamilies. In chickpea, these RNA helicases have not been characterized until now. A genome-wide analysis across the chickpea genome led to the identification of a total of 150 RNA helicase genes which included 50 DEAD, 33 DEAH and 67 DExD/H-box genes. These were distributed across all the eight chromosomes, with highest number on chromosome 4 (26) and least on chromosome 8 (8). Gene duplication analysis resulted in identification of 15 paralogous gene pairs with Ka/Ks values < 1, indicating towards the genes being under purifying selection during the course of evolution. The promoter regions of the RNA helicase genes were enriched in cis-acting elements like the light and ABA-responsive elements. The drought responsiveness of the genes was analysed by studying the expression profiles of few of these genes, in two different genotypes, the cultivated variety ICC 8261 (kabuli, C. arietinum) and the wild accession ILWC 292 (C. reticulatum), through qRT-PCR. These genotypes were selected based on their drought responsiveness in a field experiment, where it was observed that the percentage (%) reduction in relative water content (RWC) and membrane stability index (MSI) for the drought stressed plants after withholding water for 24 days, over the control or well-watered plants, was least for both the genotypes. The genes CaDEAD50 and CaDExD/H66 were identified as drought-responsive RNA helicase genes in chickpea. The protein encoded by the CaDExD/H66 gene shares a high degree of homology with one of the CLSY (CLASSY) proteins of A. thaliana. We hypothesize that this gene could possibly be involved in regulation of DNA methylation levels in chickpea by regulating siRNA production, in conjunction with other proteins like the Argonaute, RNA dependent RNA polymerases and Dicer-like proteins.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Deshika Kohli
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Shashi Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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8
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Ru JN, Hou ZH, Zheng L, Zhao Q, Wang FZ, Chen J, Zhou YB, Chen M, Ma YZ, Xi YJ, Xu ZS. Genome-Wide Analysis of DEAD-box RNA Helicase Family in Wheat ( Triticum aestivum) and Functional Identification of TaDEAD-box57 in Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:797276. [PMID: 34956297 PMCID: PMC8699334 DOI: 10.3389/fpls.2021.797276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/01/2021] [Indexed: 05/29/2023]
Abstract
DEAD-box RNA helicases constitute the largest subfamily of RNA helicase superfamily 2 (SF2), and play crucial roles in plant growth, development, and abiotic stress responses. Wheat is one of the most important cereal crops in worldwide, and abiotic stresses greatly restrict its production. So far, the DEAD-box RNA helicase family has yet to be characterized in wheat. Here, we performed a comprehensive genome-wide analysis of the DEAD-box RNA helicase family in wheat, including phylogenetic relationships, chromosomal distribution, duplication events, and protein motifs. A total of 141 TaDEAD-box genes were identified and found to be unevenly distributed across all 21 chromosomes. Whole genome/segmental duplication was identified as the likely main driving factor for expansion of the TaDEAD-box family. Expression patterns of the 141 TaDEAD-box genes were compared across different tissues and under abiotic stresses to identify genes to be important in growth or stress responses. TaDEAD-box57-3B was significantly up-regulated under multiple abiotic stresses, and was therefore selected for further analysis. TaDEAD-box57-3B was localized to the cytoplasm and plasma membrane. Ectopic expression of TaDEAD-box57-3B in Arabidopsis improved tolerance to drought and salt stress as measured by germination rates, root lengths, fresh weights, and survival rates. Transgenic lines also showed higher levels of proline and chlorophyll and lower levels of malonaldehyde (MDA) than WT plants in response to drought or salt stress. In response to cold stress, the transgenic lines showed significantly better growth and higher survival rates than WT plants. These results indicate that TaDEAD-box57-3B may increase tolerance to drought, salt, and cold stress in transgenic plants through regulating the degree of membrane lipid peroxidation. This study provides new insights for understanding evolution and function in the TaDEAD-box gene family.
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Affiliation(s)
- Jing-Na Ru
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ze-Hao Hou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Lei Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Qi Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Feng-Zhi Wang
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement/Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Jun Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Yong-Bin Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ming Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - You-Zhi Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
| | - Ya-Jun Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Zhao-Shi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, China
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9
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Yadav V, Arif N, Singh VP, Guerriero G, Berni R, Shinde S, Raturi G, Deshmukh R, Sandalio LM, Chauhan DK, Tripathi DK. Histochemical Techniques in Plant Science: More Than Meets the Eye. PLANT & CELL PHYSIOLOGY 2021; 62:1509-1527. [PMID: 33594421 DOI: 10.1093/pcp/pcab022] [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: 05/31/2020] [Accepted: 01/31/2021] [Indexed: 05/12/2023]
Abstract
Histochemistry is an essential analytical tool interfacing extensively with plant science. The literature is indeed constellated with examples showing its use to decipher specific physiological and developmental processes, as well as to study plant cell structures. Plant cell structures are translucent unless they are stained. Histochemistry allows the identification and localization, at the cellular level, of biomolecules and organelles in different types of cells and tissues, based on the use of specific staining reactions and imaging. Histochemical techniques are also widely used for the in vivo localization of promoters in specific tissues, as well as to identify specific cell wall components such as lignin and polysaccharides. Histochemistry also enables the study of plant reactions to environmental constraints, e.g. the production of reactive oxygen species (ROS) can be traced by applying histochemical staining techniques. The possibility of detecting ROS and localizing them at the cellular level is vital in establishing the mechanisms involved in the sensitivity and tolerance to different stress conditions in plants. This review comprehensively highlights the additional value of histochemistry as a complementary technique to high-throughput approaches for the study of the plant response to environmental constraints. Moreover, here we have provided an extensive survey of the available plant histochemical staining methods used for the localization of metals, minerals, secondary metabolites, cell wall components, and the detection of ROS production in plant cells. The use of recent technological advances like CRISPR/Cas9-based genome-editing for histological application is also addressed. This review also surveys the available literature data on histochemical techniques used to study the response of plants to abiotic stresses and to identify the effects at the tissue and cell levels.
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Affiliation(s)
- Vaishali Yadav
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Namira Arif
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj 211002, India
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, Hautcharage, Luxembourg
| | - Roberto Berni
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
| | - Suhas Shinde
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112, USA
| | - Gaurav Raturi
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rupesh Deshmukh
- Department of Agri-Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Luisa M Sandalio
- Department of Biochemistry, Cellular and Molecular Biology of Plants, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, Granada 18008, Spain
| | - Devendra Kumar Chauhan
- D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, Prayagraj 211002, India
| | - Durgesh Kumar Tripathi
- Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, I 2 Block, 5th Floor, AUUP Campus Sector-125, Noida 201313, India
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10
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Li L, Luo H, Lim DH, Han L, Li Y, Fu XD, Qi Y. Global profiling of RNA-chromatin interactions reveals co-regulatory gene expression networks in Arabidopsis. NATURE PLANTS 2021; 7:1364-1378. [PMID: 34650265 DOI: 10.1038/s41477-021-01004-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
It is increasingly evident that various RNAs can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA-chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than 10,000 RNA-chromatin interactions mediated by protein-coding RNAs and non-coding RNAs. Cis and intra-chromosomal interactions are mainly mediated by protein-coding RNAs, whereas inter-chromosomal interactions are primarily mediated by non-coding RNAs. Many RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting their mutual influence and reinforcement. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses and that altered RNA-chromatin interactions form co-regulatory networks. Our study provides a global view on RNA-chromatin interactions in Arabidopsis and a rich resource for future investigations of regulatory roles of RNAs in gene expression and genome organization.
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Affiliation(s)
- Lanxia Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Haofei Luo
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Do-Hwan Lim
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lu Han
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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11
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Cheng J, Zhou S, Yang K, Yu H, Chen R, Zeng L, Li H, Wang Y, Song J. Identification of RNA helicases in Medicago truncatula and their expression patterns under abiotic stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2283-2296. [PMID: 34744366 PMCID: PMC8526662 DOI: 10.1007/s12298-021-01087-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 05/29/2023]
Abstract
UNLABELLED RNA helicase catalyzes the denaturation of DNA or the unwinding of double-stranded RNA. It is vital to RNA splicing, transport, editing, degradation and the initiation of protein translation. However, the function of RNA helicase in Medicago truncatula has rarely been reported. In this study, 170 putative RNA helicase genes were identified in the M. truncatula genome, and classified into three subfamilies based on the presence of either a DEAD-box (52 genes), DEAH-box (38 genes), or DExD/H-box (80 genes) in their coding regions. Additionally, conserved helicase_C domains and other functional domains (e.g., the HA2, DUF, and ZnF domains) were also present in these genes. Chromosomal mapping and synteny analyses showed that there were tandem and segment duplications of RNA helicase genes. Furthermore, transcriptome and real-time PCR analysis showed that the expression of 35 RNA helicase genes was affected by abiotic stress. To be specific, 17, 12 and 19 genes were regulated by salt, drought and cold stress, respectively. It is worth noting that MtDEAD8, MtDEAH3, MtDExD/H18 and MtDExD/H23 responded to all three types of stress. These results provide valuable information for understanding the RNA helicase genes in M. truncatula and their abiotic stress-related functions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01087-y.
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Affiliation(s)
- Jie Cheng
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Songsong Zhou
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
- Camphor Engineering Technology Research Center for State Forestry Administration, Jiangxi Academy of Forestry, Nanchang, 330032 People’s Republic of China
| | - Kun Yang
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Hongyang Yu
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Rongrong Chen
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Liming Zeng
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Hua Li
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002 People’s Republic of China
| | - Yihua Wang
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
- College of Science, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
| | - Jianbo Song
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, 330045 People’s Republic of China
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12
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Böwer F, Schnittger A. How to Switch from Mitosis to Meiosis: Regulation of Germline Entry in Plants. Annu Rev Genet 2021; 55:427-452. [PMID: 34530640 DOI: 10.1146/annurev-genet-112618-043553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
One of the major cell fate transitions in eukaryotes is entry into meiosis. While in single-celled yeast this decision is triggered by nutrient starvation, in multicellular eukaryotes, such as plants, it is under developmental control. In contrast to animals, plants have only a short germline and instruct cells to become meiocytes in reproductive organs late in development. This situation argues for a fundamentally different mechanism of how plants recruit meiocytes, and consistently, none of the regulators known to control meiotic entry in yeast and animals are present in plants. In recent years, several factors involved in meiotic entry have been identified, especially in the model plant Arabidopsis, and pieces of a regulatory network of germline control in plants are emerging. However, the corresponding studies also show that the mechanisms of meiotic entry control are diversified in flowering plants, calling for further analyses in different plant species. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Franziska Böwer
- Department of Developmental Biology, Institute for Plant Sciences and Microbiology, University of Hamburg, D-22609 Hamburg, Germany;
| | - Arp Schnittger
- Department of Developmental Biology, Institute for Plant Sciences and Microbiology, University of Hamburg, D-22609 Hamburg, Germany;
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13
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Yue M, Gautam M, Chen Z, Hou J, Zheng X, Hou H, Li L. Histone acetylation of 45S rDNA correlates with disrupted nucleolar organization during heat stress response in Zea mays L. PHYSIOLOGIA PLANTARUM 2021; 172:2079-2089. [PMID: 33887068 DOI: 10.1111/ppl.13438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
The role of the nucleolus in plant response to heat stress remains largely obscure. Our current efforts focused on exploring the underlying mechanism by which nucleolar disorganization is regulated in heat stressed-maize lines. Here, two maize lines, a heat-sensitive line, ZD958, and a heat-tolerant line, ZDH, were submitted to heat stress for investigating their association with the nucleolar disruption. Immunofluorescence staining showed that nucleolar disruption increased with prolonged treatment time. After heat treatment, a significant change in nucleolus organization was observed in the ZD958 line, but the ZDH line showed mild alteration. Moreover, actinomycin D (ActD)-induced nucleolus fission led to inhibition of maize growth under the normal condition. The ZD958 line exhibited a significant increase in the level of H3K9ac and H4K5ac of the 45S rDNA accompanied by a higher transcription of the 5'-external transcribed spacer (ETS) region, while the line ZDH showed a slight increase in histone acetylation levels and the transcriptional initiation at this site after heat treatment. To our knowledge, this is the first report providing a comparative insight between heat stress, rDNA histone modifications, and nucleolus disintegration in a heat-tolerant ZDH compared with a heat-sensitive line ZD958. Our investigation might assist maize breeders in obtaining heat-tolerant lines by targeting nucleoli using epigenetics.
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Affiliation(s)
- Mengxia Yue
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mayank Gautam
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhenfei Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xueke Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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14
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Plants' Epigenetic Mechanisms and Abiotic Stress. Genes (Basel) 2021; 12:genes12081106. [PMID: 34440280 PMCID: PMC8394019 DOI: 10.3390/genes12081106] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are sessile organisms that need to adapt to constantly changing environmental conditions. Unpredictable climate change places plants under a variety of abiotic stresses. Studying the regulation of stress-responsive genes can help to understand plants’ ability to adapt to fluctuating environmental conditions. Changes in epigenetic marks such as histone modifications and DNA methylation are known to regulate gene expression by their dynamic variation in response to stimuli. This can then affect their phenotypic plasticity, which helps with the adaptation of plants to adverse conditions. Epigenetic marks may also provide a mechanistic basis for stress memory, which enables plants to respond more effectively and efficiently to recurring stress and prepare offspring for potential future stresses. Studying epigenetic changes in addition to genetic factors is important to better understand the molecular mechanisms underlying plant stress responses. This review summarizes the epigenetic mechanisms behind plant responses to some main abiotic stresses.
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15
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Plant RNA Binding Proteins as Critical Modulators in Drought, High Salinity, Heat, and Cold Stress Responses: An Updated Overview. Int J Mol Sci 2021; 22:ijms22136731. [PMID: 34201749 PMCID: PMC8269355 DOI: 10.3390/ijms22136731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Plant abiotic stress responses are tightly regulated by different players at multiple levels. At transcriptional or post-transcriptional levels, several RNA binding proteins (RBPs) regulate stress response genes through RNA metabolism. They are increasingly recognized as critical modulators of a myriad of biological processes, including stress responses. Plant RBPs are heterogeneous with one or more conservative RNA motifs that constitute canonical/novel RNA binding domains (RBDs), which can bind to target RNAs to determine their regulation as per the plant requirements at given environmental conditions. Given its biological significance and possible consideration as a potential tool in genetic manipulation programs to improve key agronomic traits amidst frequent episodes of climate anomalies, studies concerning the identification and functional characterization of RBP candidate genes are steadily mounting. This paper presents a comprehensive overview of canonical and novel RBPs and their functions in major abiotic stresses including drought, heat, salt, and cold stress conditions. To some extent, we also briefly describe the basic motif structure of RBPs that would be useful in forthcoming studies. Additionally, we also collected RBP genes that were modulated by stress, but that lacked functional characterization, providing an impetus to conduct further research.
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16
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Hou XL, Chen WQ, Hou Y, Gong HQ, Sun J, Wang Z, Zhao H, Cao X, Song XF, Liu CM. DEAD-BOX RNA HELICASE 27 regulates microRNA biogenesis, zygote division, and stem cell homeostasis. THE PLANT CELL 2021; 33:66-84. [PMID: 33751089 PMCID: PMC8136522 DOI: 10.1093/plcell/koaa001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 10/14/2020] [Indexed: 05/18/2023]
Abstract
After double fertilization, zygotic embryogenesis initiates a new life cycle, and stem cell homeostasis in the shoot apical meristem (SAM) and root apical meristem (RAM) allows plants to produce new tissues and organs continuously. Here, we report that mutations in DEAD-BOX RNA HELICASE 27 (RH27) affect zygote division and stem cell homeostasis in Arabidopsis (Arabidopsis thaliana). The strong mutant allele rh27-1 caused a zygote-lethal phenotype, while the weak mutant allele rh27-2 led to minor defects in embryogenesis and severely compromised stem cell homeostasis in the SAM and RAM. RH27 is expressed in embryos from the zygote stage, and in both the SAM and RAM, and RH27 is a nucleus-localized protein. The expression levels of genes related to stem cell homeostasis were elevated in rh27-2 plants, alongside down-regulation of their regulatory microRNAs (miRNAs). Further analyses of rh27-2 plants revealed reduced levels of a large subset of miRNAs and their pri-miRNAs in shoot apices and root tips. In addition, biochemical studies showed that RH27 associates with pri-miRNAs and interacts with miRNA-biogenesis components, including DAWDLE, HYPONASTIC LEAVES 1, and SERRATE. Therefore, we propose that RH27 is a component of the microprocessor complex and is critical for zygote division and stem cell homeostasis.
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Affiliation(s)
- Xiu-Li Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Qiang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifeng Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua-Qin Gong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Heng Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaofeng Cao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiu-Fen Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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17
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Yang W, Wang D, Li Y, Zhang Z, Tong S, Li M, Zhang X, Zhang L, Ren L, Ma X, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, Liu J, DiFazio SP, Olson M, Ma T. A General Model to Explain Repeated Turnovers of Sex Determination in the Salicaceae. Mol Biol Evol 2021; 38:968-980. [PMID: 33027519 PMCID: PMC7947767 DOI: 10.1093/molbev/msaa261] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms by which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex-determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosomes in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.
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Affiliation(s)
- Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deyan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiyang Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Liwen Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin—Madison, Madison, WI
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, China
| | | | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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18
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Xu X, Chen X, Shen X, Chen R, Zhu C, Zhang Z, Chen Y, Lin W, Xu X, Lin Y, Lai Z. Genome-wide identification and characterization of DEAD-box helicase family associated with early somatic embryogenesis in Dimocarpus longan Lour. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153364. [PMID: 33465637 DOI: 10.1016/j.jplph.2021.153364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 06/12/2023]
Abstract
DEAD-box (DDX) proteins belong to the largest subfamily of RNA helicase SF2, which contributes to all biological processes of RNA metabolism in the plant kingdom. Till now, no significant data are available regarding studies on DDX in Somatic Embryogenesis (SE) of woody plants. It is important to investigate the biological function of the DlDDX family in longan SE. Thus, a comprehensive analysis of 58 longan DEAD-box (DlDDX) genes characterization was performed by genome-wide identification and transcript abundance validation analysis. Homologous evolution has revealed that some DlDDXs in longan had high sequence similarity with Mus musculus, Citrus and Saccharomyces cerevisiae, indicating that DlDDXs were highly conservative in the animal, plant, and microorganism. Remarkably, gene duplication, purifying selection, and alternative splicing events, and new auxiliary domains have likely contributed to the functional evolution of DlDDX, indicating that DlDDX appeared neofunctionalization in longan. Besides, DlDDX3, 15, 28, 36 might interact with protein complex (MAC3A, MAC3B, CDC5, CBP20) of miRNA biosynthesis. Notably, DlDDX28 contained a novel auxiliary domain (CAF-1 p150), which might contribute to DNA demethylation in longan early SE. 4 DlDDX genes significantly expressed not only in early SE and zygotic embryogenesis (ZE) but also up-regulated at high levels in 'Honghezi' and 'Quanlongbaihe' with abortive seeds, which are of great significance. Moreover, some DlDDXs presented abiotic stress-response dynamic expression patterns by ABA, SA, JA, and NaCl treatments during early SE. Hence, DEAD-box is essential to SE development and seed abortive in longan.
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Affiliation(s)
- Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Shen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rongzhu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenzhong Lin
- Quanzhou Agricultural Science Research Institute, Quanzhou, 362212, China
| | - Xuhan Xu
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300, Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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19
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Bhadouriya SL, Mehrotra S, Basantani MK, Loake GJ, Mehrotra R. Role of Chromatin Architecture in Plant Stress Responses: An Update. FRONTIERS IN PLANT SCIENCE 2021; 11:603380. [PMID: 33510748 PMCID: PMC7835326 DOI: 10.3389/fpls.2020.603380] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 05/08/2023]
Abstract
Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression. DNA methylation and histone modification are crucial for genome reprogramming for tissue-specific gene expression and global gene silencing. Different classes of chromatin remodelers including SWI/SNF, ISWI, INO80, and CHD are reported to act upon chromatin in different organisms, under diverse stresses, to convert chromatin from a transcriptionally inactive to a transcriptionally active state. The architecture of chromatin at a given promoter is crucial for determining the transcriptional readout. Further, the connection between somatic memory and chromatin modifications may suggest a mechanistic basis for a stress memory. Studies have suggested that there is a functional connection between changes in nuclear organization and stress conditions. In this review, we discuss the role of chromatin architecture in different stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Sneha Lata Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Mahesh K. Basantani
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow, India
| | - Gary J. Loake
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburg, Edinburg, United Kingdom
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
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20
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Zhou Y, Wei X, Li Y, Liu Z, Duan Y, Zou H. ' Candidatus Liberibacter Asiaticus' SDE1 Effector Induces Huanglongbing Chlorosis by Downregulating Host DDX3 Gene. Int J Mol Sci 2020; 21:E7996. [PMID: 33121168 PMCID: PMC7662370 DOI: 10.3390/ijms21217996] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 10/25/2020] [Indexed: 11/21/2022] Open
Abstract
'Candidatus Liberibacter asiaticus' (CLas) is the pathogenic bacterium that causes the disease Huanglongbing (HLB) in citrus and some model plants, such as Nicotiana benthamiana. After infection, CLas releases a set of effectors to modulate host responses. One of these critical effectors is Sec-delivered effector 1 (SDE1), which induces chlorosis and cell death in N. benthamiana. In this study, we revealed the DEAD-box RNA helicase (DDX3) interacts with SDE1. Gene silencing study revealed that knockdown of the NbDDX3 gene triggers leaf chlorosis, mimicking the primary symptom of CLas infection in N. benthamiana. The interactions between SDE1 and NbDDX3 were localized in the cell membrane. Overexpression of SDE1 resulted in suppression of NbDDX3 gene expression in N. benthamiana, which suggests a critical role of SDE1 in modulating NbDDX3 expression. Furthermore, we verified the interaction of SDE1 with citrus DDX3 (CsDDX3), and demonstrated that the expression of the CsDDX3 gene was significantly reduced in HLB-affected yellowing and mottled leaves of citrus. Thus, we provide molecular evidence that the downregulation of the host DDX3 gene is a crucial mechanism of leaf chlorosis in HLB-affected plants. The identification of CsDDX3 as a critical target of SDE1 and its association with HLB symptom development indicates that the DDX3 gene is an important target for gene editing, to interrupt the interaction between DDX3 and SDE1, and therefore interfere host susceptibility.
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Affiliation(s)
- Yinghui Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.L.); (Z.L.)
| | - Xiangying Wei
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China;
- U.S. Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Fort Pierce, FL 34945, USA;
| | - Yanjiao Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.L.); (Z.L.)
| | - Zhiqin Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.L.); (Z.L.)
| | - Yongping Duan
- U.S. Horticultural Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Fort Pierce, FL 34945, USA;
| | - Huasong Zou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (Y.L.); (Z.L.)
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21
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Pandey S, Prasad A, Sharma N, Prasad M. Linking the plant stress responses with RNA helicases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110607. [PMID: 32900445 DOI: 10.1016/j.plantsci.2020.110607] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 05/21/2023]
Abstract
RNA helicases are omnipresent plant proteins across all kingdoms and have been demonstrated to play an essential role in all cellular processes involving nucleic acids. Currently, these proteins emerged as a new tool for plant molecular biologists to modulate plant stress responses. Here, we review the crucial role of RNA helicases triggered by biotic, abiotic, and multiple stress conditions. In this review, the emphasis has been given on the role of these proteins upon viral stress. Further, we have explored RNA helicase mediated regulation of RNA metabolism, starting from ribosome biogenesis to its decay upon stress induction. We also highlighted the cross-talk between RNA helicase, phytohormones, and ROS. Different overexpression and transgenic studies have been provided in the text to indicate the stress tolerance abilities of these proteins.
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Affiliation(s)
- Saurabh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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22
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Santos AP, Gaudin V, Mozgová I, Pontvianne F, Schubert D, Tek AL, Dvořáčková M, Liu C, Fransz P, Rosa S, Farrona S. Tidying-up the plant nuclear space: domains, functions, and dynamics. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5160-5178. [PMID: 32556244 PMCID: PMC8604271 DOI: 10.1093/jxb/eraa282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/12/2020] [Indexed: 05/07/2023]
Abstract
Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.
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Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova
de Lisboa, Oeiras, Portugal
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université
Paris-Saclay, Versailles, France
| | - Iva Mozgová
- Biology Centre of the Czech Academy of Sciences, České
Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České
Budějovice, Czech Republic
| | - Frédéric Pontvianne
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), Université de
Perpignan Via Domitia, Perpignan, France
| | - Daniel Schubert
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Ahmet L Tek
- Agricultural Genetic Engineering Department, Niğde Ömer Halisdemir
University, Niğde, Turkey
| | | | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of
Tübingen, Tübingen, Germany
- Institute of Biology, University of Hohenheim, Stuttgart,
Germany
| | - Paul Fransz
- University of Amsterdam, Amsterdam, The
Netherlands
| | - Stefanie Rosa
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, NUI Galway,
Galway, Ireland
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23
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Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG. Epigenetic regulation in plant abiotic stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:563-580. [PMID: 31872527 DOI: 10.1111/jipb.12901] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/20/2020] [Indexed: 05/18/2023]
Abstract
In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress-responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross-talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.
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Affiliation(s)
- Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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24
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Perrone A, Martinelli F. Plant stress biology in epigenomic era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110376. [PMID: 32234231 DOI: 10.1016/j.plantsci.2019.110376] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/07/2019] [Accepted: 12/10/2019] [Indexed: 05/24/2023]
Abstract
Recent progress in "omics" methodologies allow us to gain insight into the complex molecular regulatory networks underlying plant responses to environmental stresses. Among the different genome-wide analysis, epigenomics is the most under-investigated "omic" approach requiring more critical and speculative discussion about approaches, methods and experimental designs. Epigenomics allows us to gain insight into the molecular adaptation of plants in response to environmental stresses. The identification of epigenetic marks transmitted during filial generations enables new theories to be developed on the evolution of living organisms in relation to environmental changes. The molecular mechanisms driving the capacity of plants to memorize a stress and to generate stress-resistant progenies are still unclear and scarcely investigated. The elucidation of these cryptic molecular switches will assist breeders in designing crops characterized by minimally compromised productivity in relation to stresses caused by climate change. The aim of this review is to briefly describe the most uptodate epigenomic approaches, update recent progresses in crop epigenomics in plant stress biology, and to stimulate the discussion of new epigenomic methods and approaches in the new era of "omic" sciences.
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Affiliation(s)
- Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo, 90128, Italy.
| | - Federico Martinelli
- Department of Biology, University of Firenze, Sesto Fiorentino, Florence, 50019, Italy.
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25
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Seok HY, Nguyen LV, Nguyen DV, Lee SY, Moon YH. Investigation of a Novel Salt Stress-Responsive Pathway Mediated by Arabidopsis DEAD-Box RNA Helicase Gene AtRH17 Using RNA-Seq Analysis. Int J Mol Sci 2020; 21:ijms21051595. [PMID: 32111079 PMCID: PMC7084250 DOI: 10.3390/ijms21051595] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
Previously, we reported that overexpression of AtRH17, an Arabidopsis DEAD-box RNA helicase gene, confers salt stress-tolerance via a pathway other than the well-known salt stress-responsive pathways. To decipher the salt stress-responsive pathway in AtRH17-overexpressing transgenic plants (OXs), we performed RNA-Sequencing and identified 397 differentially expressed genes between wild type (WT) and AtRH17 OXs. Among them, 286 genes were upregulated and 111 genes were downregulated in AtRH17 OXs relative to WT. Gene ontology annotation enrichment and KEGG pathway analysis showed that the 397 upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4-5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4-5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition. Taken together, our results suggest that a high AtRH17 expression confers salt stress-tolerance through a novel salt stress-responsive pathway involving nine genes, other than the well-known ABA-dependent and ABA-independent pathways.
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Affiliation(s)
- Hye-Yeon Seok
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea;
| | - Linh Vu Nguyen
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea (D.V.N.)
| | - Doai Van Nguyen
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea (D.V.N.)
| | - Sun-Young Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Yong-Hwan Moon
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea;
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea (D.V.N.)
- Department of Molecular Biology, Pusan National University, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2592
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26
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Ganguly DR, Stone BAB, Bowerman AF, Eichten SR, Pogson BJ. Excess Light Priming in Arabidopsis thaliana Genotypes with Altered DNA Methylomes. G3 (BETHESDA, MD.) 2019; 9:3611-3621. [PMID: 31484672 PMCID: PMC6829136 DOI: 10.1534/g3.119.400659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/31/2019] [Indexed: 01/17/2023]
Abstract
Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant's ability to respond to future events. A clear example of priming is provided by the model plant Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes toward stress priming and, consequently, the potential contribution from DNA methylation - a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess-light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance, or removal of DNA methylation. Importantly, no differences in development or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional 'dampening' in response to an additional EL exposure, likely a consequence of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Bethany A B Stone
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Andrew F Bowerman
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University Canberra, Acton, ACT, 2601, Australia
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27
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Zhang Y, Deng G, Fan W, Yuan L, Wang H, Zhang P. NHX1 and eIF4A1-stacked transgenic sweetpotato shows enhanced tolerance to drought stress. PLANT CELL REPORTS 2019; 38:1427-1438. [PMID: 31396684 DOI: 10.1007/s00299-019-02454-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Co-expression of Na+/H+ antiporter NHX1 and DEAD-box RNA helicase eIF4A1 from Arabidopsis positively regulates drought stress tolerance by improving ROS scavenging capacity and maintaining membrane integrity in sweetpotato. Plants evolve multiple strategies for stress adaptation in nature. To improve sweetpotato resistance to drought stress, transgenic sweetpotato plants overexpressing the Arabidopsis Na+/H+ antiporter, NHX1, and the translation initiation factor elF4A1 were characterized for phenotypic traits and physiological performance. Without drought treatment, the NHX1-elF4A1 stacked lines (NE lines) showed normal, vigorous growth comparable to the WT plants. The NE plants showed dense green foliage with delayed leaf senescence and developed more roots than WT plants under drought treatment for 18 days. Compared to WT plants, higher level of reactive oxygen scavenging capacity was detected in NE lines as indicated by reduced H2O2 accumulation as well as increased superoxide dismutase activity and proline content. The relative ion leakage and malondialdehyde content were reduced in NE plants, indicating improved maintenance of intact membranes system. Both NE plants and NHX1-overexpressing plants (N lines) showed larger aerial parts and well-developed root system compared to WT plants under the drought stress conditions, likely due to the improved antioxidant capacity. The NE plants showed better ROS scavenging than N-line plants. All N- and NE-line plants produced normal storage roots with similar yields as WT in the field under normal growth conditions. These results demonstrated the potential to enhance sweetpotato productivity through stacking genes that are involved in ion compartmentalization and translation initiation.
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Affiliation(s)
- Yandi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gaifang Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Science, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China.
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Nidumukkala S, Tayi L, Chittela RK, Vudem DR, Khareedu VR. DEAD box helicases as promising molecular tools for engineering abiotic stress tolerance in plants. Crit Rev Biotechnol 2019; 39:395-407. [DOI: 10.1080/07388551.2019.1566204] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Lavanya Tayi
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, India
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29
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Erbasol Serbes I, Palovaara J, Groß-Hardt R. Development and function of the flowering plant female gametophyte. Curr Top Dev Biol 2019; 131:401-434. [DOI: 10.1016/bs.ctdb.2018.11.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Nguyen LV, Seok HY, Woo DH, Lee SY, Moon YH. Overexpression of the DEAD-Box RNA Helicase Gene AtRH17 Confers Tolerance to Salt Stress in Arabidopsis. Int J Mol Sci 2018; 19:ijms19123777. [PMID: 30486488 PMCID: PMC6321491 DOI: 10.3390/ijms19123777] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 01/13/2023] Open
Abstract
Plants adapt to abiotic stresses by complex mechanisms involving various stress-responsive genes. Here, we identified a DEAD-box RNA helicase (RH) gene, AtRH17, in Arabidopsis, involved in salt-stress responses using activation tagging, a useful technique for isolating novel stress-responsive genes. AT895, an activation tagging line, was more tolerant than wild type (WT) under NaCl treatment during germination and seedling development, and AtRH17 was activated in AT895. AtRH17 possesses nine well-conserved motifs of DEAD-box RHs, consisting of motifs Q, I, Ia, Ib, and II-VI. Although at least 12 orthologs of AtRH17 have been found in various plant species, no paralog occurs in Arabidopsis. AtRH17 protein is subcellularily localized in the nucleus. AtRH17-overexpressing transgenic plants (OXs) were more tolerant to high concentrations of NaCl and LiCl compared with WT, but no differences from WT were detected among seedlings exposed to mannitol and freezing treatments. Moreover, in the mature plant stage, AtRH17 OXs were also more tolerant to NaCl than WT, but not to drought, suggesting that AtRH17 is involved specifically in the salt-stress response. Notably, transcriptions of well-known abscisic acid (ABA)-dependent and ABA-independent stress-response genes were similar or lower in AtRH17 OXs than WT under salt-stress treatments. Taken together, our findings suggest that AtRH17, a nuclear DEAD-box RH protein, is involved in salt-stress tolerance, and that its overexpression confers salt-stress tolerance via a pathway other than the well-known ABA-dependent and ABA-independent pathways.
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Affiliation(s)
- Linh Vu Nguyen
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Hye-Yeon Seok
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Dong-Hyuk Woo
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Sun-Young Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
| | - Yong-Hwan Moon
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Korea.
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Meier SK, Adams N, Wolf M, Balkwill K, Muasya AM, Gehring CA, Bishop JM, Ingle RA. Comparative RNA-seq analysis of nickel hyperaccumulating and non-accumulating populations of Senecio coronatus (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1023-1038. [PMID: 29952120 DOI: 10.1111/tpj.14008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
Most metal hyperaccumulating plants accumulate nickel, yet the molecular basis of Ni hyperaccumulation is not well understood. We chose Senecio coronatus to investigate this phenomenon as this species displays marked variation in shoot Ni content across ultramafic outcrops in the Barberton Greenstone Belt (South Africa), thus allowing an intraspecific comparative approach to be employed. No correlation between soil and shoot Ni contents was observed, suggesting that this variation has a genetic rather than environmental basis. This was confirmed by our observation that the accumulation phenotype of plants from two hyperaccumulator and two non-accumulator populations was maintained when the plants were grown on a soil mix from these four sites for 12 months. We analysed the genetic variation among 12 serpentine populations of S. coronatus, and used RNA-seq for de novo transcriptome assembly and analysis of gene expression in hyperaccumulator versus non-accumulator populations. Genetic analysis revealed the presence of hyperaccumulators in two well supported evolutionary lineages, indicating that Ni hyperaccumulation may have evolved more than once in this species. RNA-Seq analysis indicated that putative homologues of transporters associated with root iron uptake in plants are expressed at elevated levels in roots and shoots of hyperaccumulating populations of S. coronatus from both evolutionary lineages. We hypothesise that Ni hyperaccumulation in S. coronatus may have evolved through recruitment of these transporters, which play a role in the iron-deficiency response in other plant species.
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Affiliation(s)
- Stuart K Meier
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Nicolette Adams
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
| | - Michael Wolf
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
| | - Kevin Balkwill
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Abraham Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7700, South Africa
| | - Christoph A Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jacqueline M Bishop
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7700, South Africa
| | - Robert A Ingle
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
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Baek W, Lim CW, Lee SC. A DEAD-box RNA helicase, RH8, is critical for regulation of ABA signalling and the drought stress response via inhibition of PP2CA activity. PLANT, CELL & ENVIRONMENT 2018; 41:1593-1604. [PMID: 29574779 DOI: 10.1111/pce.13200] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/07/2018] [Accepted: 03/19/2018] [Indexed: 05/21/2023]
Abstract
Abscisic acid (ABA) is major plant hormone involved in regulating abiotic stress responses. Several studies have established that an ABA-signalling transduction pathway-from ABA perception to response-functions in plant cells. The group A PP2Cs constitute core components of ABA signalling, and they negatively regulate ABA signalling and stress responses. Recent studies have identified and functionally analysed regulators of PP2C activity; however, the precise regulatory mechanisms remain unclear. In the present study, we used a yeast 2-hybrid (Y2H) screening analysis to identify the DEAD-box RNA helicase RH8, which interacted with PP2CA in the nucleus. rh8 knockout mutants exhibited ABA hyposensitivity and drought-susceptible phenotypes characterized by high levels of transpirational water loss via reduced stomatal closure and decreased leaf temperatures. However, rh8/pp2ca double mutants showed ABA hypersensitivity and drought-tolerant phenotypes, indicating that RH8 and PP2CA function in the same ABA-signalling pathway in the drought stress response; moreover, RH8 functions upstream of PP2CA. In vitro phosphatase and kinase assays revealed that RH8 inhibits PP2CA phosphatase activity. Our data indicate that RH8 and its interacting partner PP2CA modulate the drought stress response via ABA-dependent signalling.
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Affiliation(s)
- Woonhee Baek
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, 06974, South Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, 06974, South Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, 06974, South Korea
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Liu Y, Imai R. Function of Plant DExD/H-Box RNA Helicases Associated with Ribosomal RNA Biogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:125. [PMID: 29472942 PMCID: PMC5809497 DOI: 10.3389/fpls.2018.00125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
Ribosome biogenesis is a highly complex process that requires several cofactors, including DExD/H-box RNA helicases (RHs). RHs are a family of ATPases that rearrange the secondary structures of RNA and thus remodel ribonucleoprotein complexes. DExD/H-box RHs are found in most organisms and play critical roles in a variety of RNA-involved cellular events. In human and yeast cells, many DExD/H box RHs participate in multiple steps of ribosome biogenesis and regulate cellular proliferation and stress responses. In plants, several DExD/H-box RHs have been demonstrated to be associated with plant development and abiotic stress tolerance through their functions in modulating pre-rRNA processing. In this review, we summarize the pleiotropic roles of DExD/H-box RHs in rRNA biogenesis and other biological functions. We also describe the overall function of the DExD/H-box RH family in ribosome biogenesis based on data from human and yeast.
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Kalinina NO, Makarova S, Makhotenko A, Love AJ, Taliansky M. The Multiple Functions of the Nucleolus in Plant Development, Disease and Stress Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:132. [PMID: 29479362 PMCID: PMC5811523 DOI: 10.3389/fpls.2018.00132] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2018] [Indexed: 05/18/2023]
Abstract
The nucleolus is the most conspicuous domain in the eukaryotic cell nucleus, whose main function is ribosomal RNA (rRNA) synthesis and ribosome biogenesis. However, there is growing evidence that the nucleolus is also implicated in many other aspects of cell biology, such as regulation of cell cycle, growth and development, senescence, telomerase activity, gene silencing, responses to biotic and abiotic stresses. In the first part of the review, we briefly assess the traditional roles of the plant nucleolus in rRNA synthesis and ribosome biogenesis as well as possible functions in other RNA regulatory pathways such as splicing, nonsense-mediated mRNA decay and RNA silencing. In the second part of the review we summarize recent progress and discuss already known and new hypothetical roles of the nucleolus in plant growth and development. In addition, this part will highlight studies showing new nucleolar functions involved in responses to pathogen attack and abiotic stress. Cross-talk between the nucleolus and Cajal bodies is also discussed in the context of their association with poly(ADP ribose)polymerase (PARP), which is known to play a crucial role in various physiological processes including growth, development and responses to biotic and abiotic stresses.
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Affiliation(s)
- Natalia O. Kalinina
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Natalia O. Kalinina
| | - Svetlana Makarova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Antonida Makhotenko
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Taliansky
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Michael Taliansky
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Khandal H, Parween S, Roy R, Meena MK, Chattopadhyay D. MicroRNA profiling provides insights into post-transcriptional regulation of gene expression in chickpea root apex under salinity and water deficiency. Sci Rep 2017; 7:4632. [PMID: 28680071 PMCID: PMC5498500 DOI: 10.1038/s41598-017-04906-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/05/2017] [Indexed: 11/08/2022] Open
Abstract
Activity of root apical meristem (RAM) at the root apex is critical for stress-mediated modulation of root-architecture. Chickpea, like other legumes, possesses a basic open root meristem. Deep sequencing was used to perform microRNA expression profiling in root apex of chickpea (Cicer arietinum L.) in order to investigate post-transcriptional regulation of gene expression in this tissue in response to salinity and water deficit. Five small RNA libraries prepared from chickpea root apices at different stages of stress treatments were sequenced to obtain 284 unique miRNA sequences including 60 novel miRNAs belonging to total 255 families. Two hundred and fiftynine miRNAs were differentially expressed in stress. Six hundred and nine mRNA targets involved in diverse cellular processes were predicted for 244 miRNAs. Stress-responsive expression patterns of selected miRNAs, inverse expression patterns of their target genes and the target-cleavage sites were validated. Three candidate miRNA-target gene relationships were validated in transient expression system in chickpea. The miRNA expression profiling under salinity and water deficiency in a legume root apex and the reported function of their target genes suggested important roles of miRNA-mediated post-transcriptional regulation of gene expression involved in re-patterning of root hair cells, lateral root formation and high-affinity K+-uptake under these stresses.
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Affiliation(s)
- Hitaishi Khandal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sabiha Parween
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Riti Roy
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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36
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Makhathini KB, Abboussi O, Stein DJ, Mabandla MV, Daniels WM. Repetitive stress leads to impaired cognitive function that is associated with DNA hypomethylation, reduced BDNF and a dysregulated HPA axis. Int J Dev Neurosci 2017; 60:63-69. [DOI: 10.1016/j.ijdevneu.2017.04.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 03/13/2017] [Accepted: 04/11/2017] [Indexed: 11/28/2022] Open
Affiliation(s)
- Khayelihle B. Makhathini
- Department of Human PhysiologyCollege of Health Sciences, University of KwaZulu‐ NatalDurbanSouth Africa
| | - Oualid Abboussi
- Department of Human PhysiologyCollege of Health Sciences, University of KwaZulu‐ NatalDurbanSouth Africa
| | - Dan J. Stein
- Department of PsychiatryUniversity of Cape TownCape TownSouth Africa
| | - Musa V. Mabandla
- Department of Human PhysiologyCollege of Health Sciences, University of KwaZulu‐ NatalDurbanSouth Africa
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Fortes AM, Gallusci P. Plant Stress Responses and Phenotypic Plasticity in the Epigenomics Era: Perspectives on the Grapevine Scenario, a Model for Perennial Crop Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:82. [PMID: 28220131 PMCID: PMC5292615 DOI: 10.3389/fpls.2017.00082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants. In this perspective, we discuss the contribution of epigenetic mechanisms to our understanding of plant responses to biotic and abiotic stresses. This regulation of gene expression in response to environment raises important biological questions for perennial species such as grapevine which is asexually propagated and grown worldwide in contrasting terroirs and environmental conditions. However, most species used for epigenomic studies are annual herbaceous plants, and epigenome dynamics has been poorly investigated in perennial woody plants, including grapevine. In this context, we propose grape as an essential model for epigenetic and epigenomic studies in perennial woody plants of agricultural importance.
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Affiliation(s)
- Ana M. Fortes
- Faculdade de Ciências, Instituto de Biossistemas e Ciências Integrativas, Universidade de LisboaLisboa, Portugal
| | - Philippe Gallusci
- UMR EGFV, Université de Bordeaux, Institut national de la recherche agronomique, Institut des Sciences de la Vigne et du VinVillenave-d’Ornon, France
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38
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Zadražnik T, Egge-Jacobsen W, Meglič V, Šuštar-Vozlič J. Proteomic analysis of common bean stem under drought stress using in-gel stable isotope labeling. JOURNAL OF PLANT PHYSIOLOGY 2017; 209:42-50. [PMID: 28013170 DOI: 10.1016/j.jplph.2016.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/26/2016] [Accepted: 10/30/2016] [Indexed: 05/10/2023]
Abstract
Drought is an abiotic stress that strongly influences plant growth, development and productivity. Proteome changes in the stem of the drought-tolerant common bean (Phaseolus vulgaris L.) cultivar Tiber have were when the plants were exposed to drought. Five-week-old plants were subjected to water deficit by withholding irrigation for 7, 12 and 17days, whereas control plants were regularly irrigated. Relative water content (RWC) of leaves, as an indicator of the degree of cell and tissue hydration, showed the highest statistically significant differences between control and drought-stressed plants after 17days of treatment, where RWC remained at 90% for control and declined to 45% for stressed plants. Plants exposed to drought for 17days and control plants at the same developmental stage were included in quantitative proteomic analysis using in-gel stable isotope labeling of proteins in combination with mass spectrometry. The quantified proteins were grouped into several functional groups, mainly into energy metabolism, photosynthesis, proteolysis, protein synthesis and proteins related to defense and stress. 70kDa heat shock protein showed the greatest increase in abundance under drought of all the proteins, suggesting its role in protecting plants against stress by re-establishing normal protein conformations and thus cellular homeostasis. The abundance of proteins involved in protein synthesis also increased under drought stress, important for recovery of damaged proteins involved in the plant cell's metabolic activities. Other important proteins in this study were related to proteolysis and folding, which are necessary for maintaining proper cellular protein homeostasis. Taken together, these results reveal the complexity of pathways involved in the drought stress response in common bean stems and enable comparison with the results of proteomic analysis of leaves, thus providing important information to further understand the biochemical and molecular mechanisms of drought response in this important legume.
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Affiliation(s)
- Tanja Zadražnik
- Agricultural Institute of Slovenia, 1000, Ljubljana, Slovenia.
| | | | - Vladimir Meglič
- Agricultural Institute of Slovenia, 1000, Ljubljana, Slovenia
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A Cold-Inducible DEAD-Box RNA Helicase from Arabidopsis thaliana Regulates Plant Growth and Development under Low Temperature. PLoS One 2016; 11:e0154040. [PMID: 27116354 PMCID: PMC4846089 DOI: 10.1371/journal.pone.0154040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 01/29/2023] Open
Abstract
DEAD-box RNA helicases comprise a large family and are involved in a range of RNA processing events. Here, we identified one of the Arabidopsis thaliana DEAD-box RNA helicases, AtRH7, as an interactor of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 (AtCSP3), which is an RNA chaperone involved in cold adaptation. Promoter:GUS transgenic plants revealed that AtRH7 is expressed ubiquitously and that its levels of the expression are higher in rapidly growing tissues. Knockout mutant lines displayed several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis. In addition, aberrant floral development was also observed in rh7 mutants. When the mutants were germinated at low temperature (12°C), both radicle and first leaf emergence were severely delayed; after exposure of seedlings to a long period of cold, the mutants developed aberrant, fewer, and smaller leaves. RNA blots and circular RT-PCR revealed that 35S and 18S rRNA precursors accumulated to higher levels in the mutants than in WT under both normal and cold conditions, suggesting the mutants are partially impaired in pre-rRNA processing. Taken together, the results suggest that AtRH7 affects rRNA biogenesis and plays an important role in plant growth under cold.
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40
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Palm D, Simm S, Darm K, Weis BL, Ruprecht M, Schleiff E, Scharf C. Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana. RNA Biol 2016; 13:441-54. [PMID: 26980300 DOI: 10.1080/15476286.2016.1154252] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for Saccharomyces cerevisiae. Plant ortholog assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analyzed the proteome of the nucleus and nucleolus of Arabidopsis thaliana and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.
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Affiliation(s)
| | - Stefan Simm
- a Institute for Molecular Biosciences.,b Cluster of Excellence Macromolecular Complexes
| | - Katrin Darm
- d Department of Otorhinolaryngology , Head and Neck Surgery
| | | | | | - Enrico Schleiff
- a Institute for Molecular Biosciences.,b Cluster of Excellence Macromolecular Complexes.,c Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt , Max von Laue Str. Nine, Frankfurt , Germany
| | - Christian Scharf
- d Department of Otorhinolaryngology , Head and Neck Surgery.,e Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald , Ferdinand-Sauerbruch-Straße DZ7 J.05.06, Greifswald , Germany
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41
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Huang CK, Shen YL, Huang LF, Wu SJ, Yeh CH, Lu CA. The DEAD-Box RNA Helicase AtRH7/PRH75 Participates in Pre-rRNA Processing, Plant Development and Cold Tolerance in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:174-91. [PMID: 26637537 DOI: 10.1093/pcp/pcv188] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/18/2015] [Indexed: 05/18/2023]
Abstract
DEAD-box RNA helicases belong to an RNA helicase family that plays specific roles in various RNA metabolism processes, including ribosome biogenesis, mRNA splicing, RNA export, mRNA translation and RNA decay. This study investigated a DEAD-box RNA helicase, AtRH7/PRH75, in Arabidopsis. Expression of AtRH7/PRH75 was ubiquitous; however, the levels of mRNA accumulation were increased in cell division regions and were induced by cold stress. The phenotypes of two allelic AtRH7/PRH75-knockout mutants, atrh7-2 and atrh7-3, resembled auxin-related developmental defects that were exhibited in several ribosomal protein mutants, and were more severe under cold stress. Northern blot and circular reverse transcription-PCR (RT-PCR) analyses indicated that unprocessed 18S pre-rRNAs accumulated in the atrh7 mutants. The atrh7 mutants were hyposensitive to the antibiotic streptomycin, which targets ribosomal small subunits, suggesting that AtRH7 was also involved in ribosome assembly. In addition, the atrh7-2 and atrh7-3 mutants displayed cold hypersensitivity and decreased expression of CBF1, CBF2 and CBF3, which might be responsible for the cold intolerance. The present study indicated that AtRH7 participates in rRNA biogenesis and is also involved in plant development and cold tolerance in Arabidopsis.
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Affiliation(s)
- Chun-Kai Huang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC These authors contributed equally to this work
| | - Yu-Lien Shen
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC These authors contributed equally to this work
| | - Li-Fen Huang
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Shaw-Jye Wu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chin-Hui Yeh
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
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42
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Probst AV, Mittelsten Scheid O. Stress-induced structural changes in plant chromatin. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:8-16. [PMID: 26042538 DOI: 10.1016/j.pbi.2015.05.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 05/20/2023]
Abstract
Stress defense in plants is elaborated at the level of protection and adaptation. Dynamic changes in sophisticated chromatin substructures and concomitant transcriptional changes play an important role in response to stress, as illustrated by the transient rearrangement of compact heterochromatin structures or the modulation of chromatin composition and modification upon stress exposure. To connect cytological, developmental, and molecular data around stress and chromatin is currently an interesting, multifaceted, and sometimes controversial field of research. This review highlights some of the most recent findings on nuclear reorganization, histone variants, histone chaperones, DNA- and histone modifications, and somatic and meiotic heritability in connection with stress.
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Affiliation(s)
- Aline V Probst
- CNRS UMR6293 - INSERM U1103 - Clermont University, GReD, Campus Universitaire des Cézeaux, 10 Avenue Blaise Pascal, TSA 60026, CS 60026, 63178 Aubière Cedex, France
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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43
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Pan IC, Tsai HH, Cheng YT, Wen TN, Buckhout TJ, Schmidt W. Post-Transcriptional Coordination of the Arabidopsis Iron Deficiency Response is Partially Dependent on the E3 Ligases RING DOMAIN LIGASE1 (RGLG1) and RING DOMAIN LIGASE2 (RGLG2). Mol Cell Proteomics 2015; 14:2733-52. [PMID: 26253232 DOI: 10.1074/mcp.m115.048520] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 11/06/2022] Open
Abstract
Acclimation to changing environmental conditions is mediated by proteins, the abundance of which is carefully tuned by an elaborate interplay of DNA-templated and post-transcriptional processes. To dissect the mechanisms that control and mediate cellular iron homeostasis, we conducted quantitative high-resolution iTRAQ proteomics and microarray-based transcriptomic profiling of iron-deficient Arabidopsis thaliana plants. A total of 13,706 and 12,124 proteins was identified with a quadrupole-Orbitrap hybrid mass spectrometer in roots and leaves, respectively. This deep proteomic coverage allowed accurate estimates of post-transcriptional regulation in response to iron deficiency. Similarly regulated transcripts were detected in only 13% (roots) and 11% (leaves) of the 886 proteins that differentially accumulated between iron-sufficient and iron-deficient plants, indicating that the majority of the iron-responsive proteins was post-transcriptionally regulated. Mutants harboring defects in the RING DOMAIN LIGASE1 (RGLG1)(1) and RING DOMAIN LIGASE2 (RGLG2) showed a pleiotropic phenotype that resembled iron-deficient plants with reduced trichome density and the formation of branched root hairs. Proteomic and transcriptomic profiling of rglg1 rglg2 double mutants revealed that the functional RGLG protein is required for the regulation of a large set of iron-responsive proteins including the coordinated expression of ribosomal proteins. This integrative analysis provides a detailed catalog of post-transcriptionally regulated proteins and allows the concept of a chiefly transcriptionally regulated iron deficiency response to be revisited. Protein data are available via ProteomeXchange with identifier PXD002126.
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Affiliation(s)
- I-Chun Pan
- From the ‡Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Huei-Hsuan Tsai
- From the ‡Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ya-Tan Cheng
- From the ‡Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Tuan-Nan Wen
- From the ‡Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | - Wolfgang Schmidt
- From the ‡Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; ¶Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan; ‖Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
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Omidvar V, Fellner M. DNA methylation and transcriptomic changes in response to different lights and stresses in 7B-1 male-sterile tomato. PLoS One 2015; 10:e0121864. [PMID: 25849771 PMCID: PMC4388563 DOI: 10.1371/journal.pone.0121864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/16/2015] [Indexed: 01/18/2023] Open
Abstract
We reported earlier that 7B-1 mutant in tomato (Solanum lycopersicum L., cv. Rutgers), an ABA overproducer, is defective in blue light (B) signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP) assay, a number of genes were identified, which were differentially methylated between 7B-1 and its wild type (WT) seedlings in white (W), blue (B), red (R) lights and dark (D) or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between 7B-1 and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between 7B-1 and WT by B or D or in response to stresses. Blue light receptors cryptochrome 1 and 2 (CRY1 and CRY2) and phototropin 1 and 2 (PHOT1 and PHOT2) were not affected by the 7B-1 mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC) induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in 7B-1. In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated 7B-1 seedlings via the regulation of auxin-response factor (ARF) transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in 7B-1 and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between 7B-1 and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of ARFs expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.
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Affiliation(s)
- Vahid Omidvar
- Group of Molecular Physiology, Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany ASCR, Olomouc, Czech Republic
- * E-mail: (VO); (MF)
| | - Martin Fellner
- Group of Molecular Physiology, Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany ASCR, Olomouc, Czech Republic
- * E-mail: (VO); (MF)
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Ha CV, Watanabe Y, Tran UT, Le DT, Tanaka M, Nguyen KH, Seki M, Nguyen DV, Tran LSP. Comparative analysis of root transcriptomes from two contrasting drought-responsive Williams 82 and DT2008 soybean cultivars under normal and dehydration conditions. FRONTIERS IN PLANT SCIENCE 2015; 6:551. [PMID: 26300889 PMCID: PMC4528160 DOI: 10.3389/fpls.2015.00551] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/06/2015] [Indexed: 05/04/2023]
Abstract
The economically important DT2008 and the model Williams 82 (W82) soybean cultivars were reported to have differential drought-tolerant degree to dehydration and drought, which was associated with root trait. Here, we used 66K Affymetrix Soybean Array GeneChip to compare the root transcriptomes of DT2008 and W82 seedlings under normal, as well as mild (2 h treatment) and severe (10 h treatment) dehydration conditions. Out of the 38172 soybean genes annotated with high confidence, 822 (2.15%) and 632 (1.66%) genes showed altered expression by dehydration in W82 and DT2008 roots, respectively, suggesting that a larger machinery is required to be activated in the drought-sensitive W82 cultivar to cope with the stress. We also observed that long-term dehydration period induced expression change of more genes in soybean roots than the short-term one, independently of the genotypes. Furthermore, our data suggest that the higher drought tolerability of DT2008 might be attributed to the higher number of genes induced in DT2008 roots than in W82 roots by early dehydration, and to the expression changes of more genes triggered by short-term dehydration than those by prolonged dehydration in DT2008 roots vs. W82 roots. Differentially expressed genes (DEGs) that could be predicted to have a known function were further analyzed to gain a basic understanding on how soybean plants respond to dehydration for their survival. The higher drought tolerability of DT2008 vs. W82 might be attributed to differential expression in genes encoding osmoprotectant biosynthesis-, detoxification- or cell wall-related proteins, kinases, transcription factors and phosphatase 2C proteins. This research allowed us to identify genetic components that contribute to the improved drought tolerance of DT2008, as well as provide a useful genetic resource for in-depth functional analyses that ultimately leads to development of soybean cultivars with improved tolerance to drought.
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Affiliation(s)
- Chien Van Ha
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Yasuko Watanabe
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Uyen Thi Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Dung Tien Le
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Kien Huu Nguyen
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- CREST, Japan Science and Technology AgencyKawaguchi, Japan
| | - Dong Van Nguyen
- National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Vietnamese Academy of Agricultural ScienceHanoi, Vietnam
| | - Lam-Son Phan Tran
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- *Correspondence: Lam-Son Phan Tran, Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Stress induces cell dedifferentiation in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:378-84. [PMID: 25086338 DOI: 10.1016/j.bbagrm.2014.07.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022]
Abstract
Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress, dedifferentiation and a switch in cell fate. We emphasize the epigenetic modifications associated with stress-induced global changes in chromatin structure and conclude with the implications for genetic variation and for induced pluripotent stem cells in animals. It appears that stress is perceived as a signal that directs plant cells to undergo reprogramming (dedifferentiation) as a means for adaptation and in preparation for a stimulus-based acquisition of a new cell fate. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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Barak S, Singh Yadav N, Khan A. DEAD-box RNA helicases and epigenetic control of abiotic stress-responsive gene expression. PLANT SIGNALING & BEHAVIOR 2014; 9:e977729. [PMID: 25517295 PMCID: PMC4622835 DOI: 10.4161/15592324.2014.977729] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Plant responses to abiotic stresses are controlled by a complex tier of epigenetic, transcriptional and post-transcriptional regulation. We have provided evidence that the DEAD-box RNA helicases, STRESS RESPONSE SUPPRESSOR (STRS) 1 and STRS2 are negative regulators of Arabidopsis thaliana stress-responsive transcription factors. Using GFP-STRS fusion proteins, we have demonstrated that the STRSs are localized to the nucleolus and chromocenters, and are rapidly removed to the nucleoplasm upon application of various abiotic stresses. The STRSs appear to act via RNA-directed DNA methylation to suppress Arabidopsis stress responses; this repressive epigenetic mechanism is abrogated by abiotic stress eventually leading to an open chromatin structure allowing expression of stress-responsive genes.
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Affiliation(s)
- Simon Barak
- French Associates Institute for Agriculture and Biotechnology of Drylands; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion, Israel
- Correspondence to: Simon Barak;
| | - Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion, Israel
| | - Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands; Jacob Blaustein Institutes for Desert Research; Ben-Gurion University of the Negev; Midreshet Ben-Gurion, Israel
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