1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Li H, Chen Y, Dai Y, Yang L, Zhang S. Genome-wide identification and expression analysis of histone deacetylase and histone acetyltransferase genes in response to drought in poplars. BMC Genomics 2024; 25:657. [PMID: 38956453 PMCID: PMC11218084 DOI: 10.1186/s12864-024-10570-1] [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: 12/04/2023] [Accepted: 06/26/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are involved in plant growth and development as well as in response to environmental changes, by dynamically regulating gene acetylation levels. Although there have been numerous reports on the identification and function of HDAC and HAT in herbaceous plants, there are fewer report related genes in woody plants under drought stress. RESULTS In this study, we performed a genome-wide analysis of the HDAC and HAT families in Populus trichocarpa, including phylogenetic analysis, gene structure, conserved domains, and expression analysis. A total of 16 PtrHDACs and 12 PtrHATs were identified in P. trichocarpa genome. Analysis of cis-elements in the promoters of PtrHDACs and PtrHATs revealed that both gene families could respond to a variety of environmental signals, including hormones and drought. Furthermore, real time quantitative PCR indicated that PtrHDA906 and PtrHAG3 were significantly responsive to drought. PtrHDA906, PtrHAC1, PtrHAC3, PtrHAG2, PtrHAG6 and PtrHAF1 consistently responded to abscisic acid, methyl jasmonate and salicylic acid under drought conditions. CONCLUSIONS Our study demonstrates that PtrHDACs and PtrHATs may respond to drought through hormone signaling pathways, which helps to reveal the hub of acetylation modification in hormone regulation of abiotic stress.
Collapse
Affiliation(s)
- Huanhuan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yao Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yujie Dai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Le Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Sheng Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
3
|
Sun Y, Xie Z, Jin L, Qin T, Zhan C, Huang J. Histone deacetylase OsHDA716 represses rice chilling tolerance by deacetylating OsbZIP46 to reduce its transactivation function and protein stability. THE PLANT CELL 2024; 36:1913-1936. [PMID: 38242836 PMCID: PMC11062455 DOI: 10.1093/plcell/koae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Low temperature is a major environmental factor limiting plant growth and crop production. Epigenetic regulation of gene expression is important for plant adaptation to environmental changes, whereas the epigenetic mechanism of cold signaling in rice (Oryza sativa) remains largely elusive. Here, we report that the histone deacetylase (HDAC) OsHDA716 represses rice cold tolerance by interacting with and deacetylating the transcription factor OsbZIP46. The loss-of-function mutants of OsHDA716 exhibit enhanced chilling tolerance, compared with the wild-type plants, while OsHDA716 overexpression plants show chilling hypersensitivity. On the contrary, OsbZIP46 confers chilling tolerance in rice through transcriptionally activating OsDREB1A and COLD1 to regulate cold-induced calcium influx and cytoplasmic calcium elevation. Mechanistic investigation showed that OsHDA716-mediated OsbZIP46 deacetylation in the DNA-binding domain reduces the DNA-binding ability and transcriptional activity as well as decreasing OsbZIP46 protein stability. Genetic evidence indicated that OsbZIP46 deacetylation mediated by OsHDA716 reduces rice chilling tolerance. Collectively, these findings reveal that the functional interplay between the chromatin regulator and transcription factor fine-tunes the cold response in plant and uncover a mechanism by which HDACs repress gene transcription through deacetylating nonhistone proteins and regulating their biochemical functions.
Collapse
Affiliation(s)
- Ying Sun
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Zizhao Xie
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Tian Qin
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Chenghang Zhan
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Junli Huang
- Key Laboratory of Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, China
| |
Collapse
|
4
|
Cai J, Hu F, Yang M, Wu R, Liu X. Genome-wide identification of HDAC members and function analysis of PnHDT1/2 in salt stress response in Phyla nodiflora (L.) Greene. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108442. [PMID: 38382345 DOI: 10.1016/j.plaphy.2024.108442] [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: 10/04/2023] [Revised: 01/28/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible histone acetylation and deacetylation play an essential role in regulating chromatin structure and gene expression. Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysine residues of core histones, resulting in closed chromatin structure and transcription repression. Although the HDCAs have been extensively studied in model plants, the HDAC members have not been identified in Phyla nodiflora (L.) Greene (P. nodiflora), a salt-tolerant plant species. Here, 17 PnHDAC genes were identified in the genome of P. nodiflora. Phylogenetic analysis displayed that the PnHDACs were classified into three groups, the RPD3/HDA1-group (11 members), the SIR2-group (2 members) and the plant-specific HD2-group (4 members). Transcription analysis displayed that the gene expression patterns of PnHDACs were affected by salt stress in P. nodiflora seedlings. PnHDT1 and PnHDT2, two HD2-type HDAC proteins were found to be subcellular localized in the nucleolus. Furthermore, overexpressing PnHDT1 and PnHDT2 in Arabidopsis decreased the sensitivity to plant hormone abscisic acid whereas reduced the tolerance to salt stress during seed germination and seedling stages. Overall, our work identified the PnHDAC gene family for the first time in P. nodiflora and revealed an involvement of PnHDT1 and PnHDT2 in salt stress tolerance, which may contribute to uncover the mechanism of P. nodiflora in adaption to salt environments.
Collapse
Affiliation(s)
- Jiajia Cai
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Feng Hu
- Department of Landscape and Tourism Planning and Design, Guangzhou Urban Planning and Design Survey Research Institute, Guangzhou, 510650, China
| | - Min Yang
- Department of Landscape and Tourism Planning and Design, Guangzhou Urban Planning and Design Survey Research Institute, Guangzhou, 510650, China
| | - Ronghua Wu
- Department of Landscape and Tourism Planning and Design, Guangzhou Urban Planning and Design Survey Research Institute, Guangzhou, 510650, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| |
Collapse
|
5
|
Rehman S, Ahmad Z, Ramakrishnan M, Kalendar R, Zhuge Q. Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture. Funct Integr Genomics 2023; 23:298. [PMID: 37700098 DOI: 10.1007/s10142-023-01219-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Abstract
Plants have evolved to adapt and grow in hot and cold climatic conditions. Some also adapt to daily and seasonal temperature changes. Epigenetic modifications play an important role in regulating plant tolerance under such conditions. DNA methylation and post-translational modifications of histone proteins influence gene expression during plant developmental stages and under stress conditions, including cold and heat stress. While short-term modifications are common, some modifications may persist and result in stress memory that can be inherited by subsequent generations. Understanding the mechanisms of epigenomes responding to stress and the factors that trigger stress memory is crucial for developing climate-resilient agriculture, but such an integrated view is currently limited. This review focuses on the plant epigenetic stress memory during cold and heat stress. It also discusses the potential of machine learning to modify stress memory through epigenetics to develop climate-resilient crops.
Collapse
Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014 University of Helsinki, Helsinki, Finland.
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China.
| |
Collapse
|
6
|
Liu K, Chen J, Sun S, Chen X, Zhao X, Hu Y, Qi G, Li X, Xu B, Miao J, Xue C, Zhou Y, Gong Z. Histone deacetylase OsHDA706 increases salt tolerance via H4K5/K8 deacetylation of OsPP2C49 in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36807738 DOI: 10.1111/jipb.13470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
High salt is a major environmental factor that threatens plant growth and development. Increasing evidence indicates that histone acetylation is involved in plant responses to various abiotic stress; however, the underlying epigenetic regulatory mechanisms remain poorly understood. In this study, we revealed that the histone deacetylase OsHDA706 epigenetically regulates the expression of salt stress response genes in rice (Oryza sativa L.). OsHDA706 localizes to the nucleus and cytoplasm and OsHDA706 expression is significantly induced under salt stress. Moreover, oshda706 mutants showed a higher sensitivity to salt stress than the wild-type. In vivo and in vitro enzymatic activity assays demonstrated that OsHDA706 specifically regulates the deacetylation of lysines 5 and 8 on histone H4 (H4K5 and H4K8). By combining chromatin immunoprecipitation and mRNA sequencing, we identified the clade A protein phosphatase 2 C gene, OsPP2C49, which is involved in the salt response as a direct target of H4K5 and H4K8 acetylation. We found that the expression of OsPP2C49 is induced in the oshda706 mutant under salt stress. Furthermore, the knockout of OsPP2C49 enhances plant tolerance to salt stress, while its overexpression has the opposite effect. Taken together, our results indicate that OsHDA706, a histone H4 deacetylase, participates in the salt stress response by regulating the expression of OsPP2C49 via H4K5 and H4K8 deacetylation.
Collapse
Affiliation(s)
- Kai Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Jijin Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Shang Sun
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xu Chen
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xinru Zhao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Guoxiao Qi
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Xiya Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
| | - Bo Xu
- Institute of Lianyungang Agricultural Science of Xuhuai Area, Lianyungang, 222006, China
| | - Jun Miao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Chao Xue
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zhiyun Gong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| |
Collapse
|
7
|
Bano N, Fakhrah S, Lone RA, Mohanty CS, Bag SK. Genome-wide identification and expression analysis of the HD2 protein family and its response to drought and salt stress in Gossypium species. FRONTIERS IN PLANT SCIENCE 2023; 14:1109031. [PMID: 36860898 PMCID: PMC9968887 DOI: 10.3389/fpls.2023.1109031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Histone deacetylase 2 (HD2) proteins play an important role in the regulation of gene expression. This helps with the growth and development of plants and also plays a crucial role in responses to biotic and abiotic stress es. HD2s comprise a C2H2-type Zn2+ finger at their C-terminal and an HD2 label, deacetylation and phosphorylation sites, and NLS motifs at their N-terminal. In this study, a total of 27 HD2 members were identified, using Hidden Markov model profiles, in two diploid cotton genomes (Gossypium raimondii and Gossypium arboretum) and two tetraploid cotton genomes (Gossypium hirsutum and Gossypium barbadense). These cotton HD2 members were classified into 10 major phylogenetic groups (I-X), of which group III was found to be the largest with 13 cotton HD2 members. An evolutionary investigation showed that the expansion of HD2 members primarily occurred as a result of segmental duplication in paralogous gene pairs. Further qRT-PCR validation of nine putative genes using RNA-Seq data suggested that GhHDT3D.2 exhibits significantly higher levels of expression at 12h, 24h, 48h, and 72h of exposure to both drought and salt stress conditions compared to a control measure at 0h. Furthermore, gene ontology, pathways, and co-expression network study of GhHDT3D.2 gene affirmed their significance in drought and salt stress responses.
Collapse
Affiliation(s)
- Nasreen Bano
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shafquat Fakhrah
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Department of Botany, University of Lucknow, Lucknow, India
| | - Rayees Ahmad Lone
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandra Sekhar Mohanty
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sumit Kumar Bag
- Council of Scientific & Industrial Research (CSIR)-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
8
|
Cadavid IC, Balbinott N, Margis R. Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress. Genet Mol Biol 2023; 46:e20220166. [PMID: 36706026 PMCID: PMC9881580 DOI: 10.1590/1678-4685-gmb-2022-0166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/18/2022] [Indexed: 01/28/2023] Open
Abstract
Abiotic stresses such as nutritional imbalance, salt, light intensity, and high and low temperatures negatively affect plant growth and development. Through the course of evolution, plants developed multiple mechanisms to cope with environmental variations, such as physiological, morphological, and molecular adaptations. Epigenetic regulation, transcription factor activity, and post-transcriptional regulation operated by RNA molecules are mechanisms associated with gene expression regulation under stress. Epigenetic regulation, including histone and DNA covalent modifications, triggers chromatin remodeling and changes the accessibility of transcription machinery leading to alterations in gene activity and plant homeostasis responses. Soybean is a legume widely produced and whose productivity is deeply affected by abiotic stresses. Many studies explored how soybean faces stress to identify key elements and improve productivity through breeding and genetic engineering. This review summarizes recent progress in soybean gene expression regulation through epigenetic modifications and circRNAs pathways, and points out the knowledge gaps that are important to study by the scientific community. It focuses on epigenetic factors participating in soybean abiotic stress responses, and chromatin modifications in response to stressful environments and draws attention to the regulatory potential of circular RNA in post-transcriptional processing.
Collapse
Affiliation(s)
- Isabel Cristina Cadavid
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Porto Alegre, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofisica, Porto Alegre, Brazil
| |
Collapse
|
9
|
Wu S, Yang Y, Chen J, Li J, Jian G, Yang J, Mao K, Zeng L, Gu D. Histone deacetylase CsHDA6 mediates the regulated formation of the anti-insect metabolite α-farnesene in tea (Camellia sinensis). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111501. [PMID: 36257410 DOI: 10.1016/j.plantsci.2022.111501] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/19/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
α-Farnesene accumulated in tea plants following infestations by most insects, and mechanical wounding is the common factor. However, the specific mechanism underlying the wounding-regulated accumulation of α-farnesene in tea plants remains unclear. In this study, we observed that histone deacetylase inhibitor treatment induced the accumulation of α-farnesene. The histone deacetylase CsHDA6 interacted directly with CsMYC2, which was an important transcription factor in the jasmonic acid (JA) pathway, and co-regulated the expression of the key α-farnesene synthesis gene CsAFS. Wounding caused by insect infestation affected CsHDA6 production at the transcript and protein levels, while also inhibited the binding of CsHDA6 to the CsAFS promoter. The resulting increased acetylation of histones H3/H4 in CsAFS enhanced the expression of CsAFS and the accumulation of α-farnesene. In conclusion, our study demonstrated the effect of histone acetylation on the production of tea plant HIPVs and revealed the importance of the CsHDA6-CsMYC2 transcriptional regulatory module.
Collapse
Affiliation(s)
- Shuhua Wu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Yuhua Yang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Jiaming Chen
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Jianlong Li
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, No. 6 Dafeng Road, Tianhe District, Guangzhou 510640, China
| | - Guotai Jian
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Jie Yang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Kaiquan Mao
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Lanting Zeng
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Dachuan Gu
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China; South China National Botanical Garden, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China.
| |
Collapse
|
10
|
Ramakrishnan M, Zhang Z, Mullasseri S, Kalendar R, Ahmad Z, Sharma A, Liu G, Zhou M, Wei Q. Epigenetic stress memory: A new approach to study cold and heat stress responses in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1075279. [PMID: 36570899 PMCID: PMC9772030 DOI: 10.3389/fpls.2022.1075279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
Understanding plant stress memory under extreme temperatures such as cold and heat could contribute to plant development. Plants employ different types of stress memories, such as somatic, intergenerational and transgenerational, regulated by epigenetic changes such as DNA and histone modifications and microRNAs (miRNA), playing a key role in gene regulation from early development to maturity. In most cases, cold and heat stresses result in short-term epigenetic modifications that can return to baseline modification levels after stress cessation. Nevertheless, some of the modifications may be stable and passed on as stress memory, potentially allowing them to be inherited across generations, whereas some of the modifications are reactivated during sexual reproduction or embryogenesis. Several stress-related genes are involved in stress memory inheritance by turning on and off transcription profiles and epigenetic changes. Vernalization is the best example of somatic stress memory. Changes in the chromatin structure of the Flowering Locus C (FLC) gene, a MADS-box transcription factor (TF), maintain cold stress memory during mitosis. FLC expression suppresses flowering at high levels during winter; and during vernalization, B3 TFs, cold memory cis-acting element and polycomb repressive complex 1 and 2 (PRC1 and 2) silence FLC activation. In contrast, the repression of SQUAMOSA promoter-binding protein-like (SPL) TF and the activation of Heat Shock TF (HSFA2) are required for heat stress memory. However, it is still unclear how stress memory is inherited by offspring, and the integrated view of the regulatory mechanisms of stress memory and mitotic and meiotic heritable changes in plants is still scarce. Thus, in this review, we focus on the epigenetic regulation of stress memory and discuss the application of new technologies in developing epigenetic modifications to improve stress memory.
Collapse
Affiliation(s)
- Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guohua Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| |
Collapse
|
11
|
Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
Collapse
Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
12
|
Gu D, Wu S, Yu Z, Zeng L, Qian J, Zhou X, Yang Z. Involvement of histone deacetylase CsHDA2 in regulating ( E)-nerolidol formation in tea ( Camellia sinensis) exposed to tea green leafhopper infestation. HORTICULTURE RESEARCH 2022; 9:uhac158. [PMID: 36324644 PMCID: PMC9613726 DOI: 10.1093/hr/uhac158] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Herbivore-induced plant volatiles (HIPVs) help the tea plant (Camellia sinensis) adapt to environmental stress, and they are also quality-related components of tea. However, the upstream mechanism regulating the herbivore-induced expression of volatile biosynthesis genes is unclear, especially at the level of epigenetic regulation. In this study, similar to the effects of a tea green leafhopper infestation, treatments with exogenous jasmonic acid (JA) and histone deacetylase inhibitors significantly increased the (E)-nerolidol content in tea and induced the expression of the associated biosynthesis gene CsNES. Furthermore, a key transcription factor related to JA signaling, myelocytomatosis 2 (CsMYC2), interacted with histone deacetylase 2 (CsHDA2) in vitro and in vivo. A tea green leafhopper infestation inhibited CsHDA2 expression and decreased CsHDA2 abundance. Moreover, the tea green leafhopper infestation increased H3 and H4 acetylation levels in the promoter region of CsNES, which in turn upregulated the expression of CsNES and increased the (E)-nerolidol content. In this study, we revealed the effects of histone acetylations on the accumulation of HIPVs, while also confirming that CsHDA2-CsMYC2 is an important transcriptional regulatory module for the accumulation of (E)-nerolidol induced by tea green leafhoppers. The results of this study may be useful for characterizing plant aromatic compounds and the main upstream stress-responsive signaling molecules. Furthermore, the study findings will assist researchers clarify the epigenetic regulation influencing plant secondary metabolism in response to external stress.
Collapse
Affiliation(s)
| | | | | | - Lanting Zeng
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Jiajia Qian
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiaochen Zhou
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | | |
Collapse
|
13
|
Comprehensive Genome-Wide Analysis of Histone Acetylation Genes in Roses and Expression Analyses in Response to Heat Stress. Genes (Basel) 2022; 13:genes13060980. [PMID: 35741743 PMCID: PMC9222719 DOI: 10.3390/genes13060980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Roses have high economic values as garden plants and for cut-flower and cosmetics industries. The growth and development of rose plants is affected by exposure to high temperature. Histone acetylation plays an important role in plant development and responses to various stresses. It is a dynamic and reversible process mediated by histone deacetylases (HDAC) and histone acetyltransferases (HAT). However, information on HDAC and HAT genes of roses is scarce. Here, 23 HDAC genes and 10 HAT genes were identified in the Rosa chinensis ‘Old Blush’ genome. Their gene structures, conserved motifs, physicochemical properties, phylogeny, and synteny were assessed. Analyses of the expression of HDAC and HAT genes using available RNAseq data showed that these genes exhibit different expression patterns in different organs of the three analyzed rose cultivars. After heat stress, while the expression of most HDAC genes tend to be down-regulated, that of HAT genes was up-regulated when rose plants were grown at high-temperature conditions. These data suggest that rose likely respond to high-temperature exposure via modification in histone acetylation, and, thus, paves the way to more studies in order to elucidate in roses the molecular mechanisms underlying rose plants development and flowering.
Collapse
|
14
|
HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume. Int J Mol Sci 2022; 23:ijms23115957. [PMID: 35682633 PMCID: PMC9180812 DOI: 10.3390/ijms23115957] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes—especially PmHDA1/6/14, PmHDT1, and PmSRT1/2—significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei.
Collapse
|
15
|
Lysine crotonylation: A challenging new player in the epigenetic regulation of plants. J Proteomics 2022; 255:104488. [DOI: 10.1016/j.jprot.2022.104488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/20/2022]
|
16
|
Yang L, Meng X, Chen S, Li J, Sun W, Chen W, Wang S, Wan H, Qian G, Yi X, Li J, Zheng Y, Luo M, Chen S, Liu X, Mi Y. Identification of the Histone Deacetylases Gene Family in Hemp Reveals Genes Regulating Cannabinoids Synthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:755494. [PMID: 34868143 PMCID: PMC8636033 DOI: 10.3389/fpls.2021.755494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Histone deacetylases (HDACs) play crucial roles nearly in all aspects of plant biology, including stress responses, development and growth, and regulation of secondary metabolite biosynthesis. The molecular functions of HDACs have been explored in depth in Arabidopsis thaliana, while little research has been reported in the medicinal plant Cannabis sativa L. Here, we excavated 14 CsHDAC genes of C. sativa L that were divided into three relatively conserved subfamilies, including RPD3/HDA1 (10 genes), SIR2 (2 genes), and HD2 (2 genes). Genes associated with the biosynthesis of bioactive constituents were identified by combining the distribution of cannabinoids with the expression pattern of HDAC genes in various organs. Using qRT-PCR and transcription group analysis, we verified the expression of candidate genes in different tissues. We found that the histone inhibitor Trichostatin A (TSA) affected the expression of key genes in the cannabinoid metabolism pathway and the accumulation of synthetic precursors, which indirectly indicates that histone inhibitor may regulate the synthesis of active substances in C. sativa L.
Collapse
Affiliation(s)
- Liu Yang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiangxiao Meng
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sifan Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guangtao Qian
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Xiaozhe Yi
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Juncan Li
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Yaqin Zheng
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Shanshan Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xia Liu
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, China
| | - Yaolei Mi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
17
|
Li W, Xiong Y, Lai LB, Zhang K, Li Z, Kang H, Dai L, Gopalan V, Wang G, Liu W. The rice RNase P protein subunit Rpp30 confers broad-spectrum resistance to fungal and bacterial pathogens. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1988-1999. [PMID: 33932077 PMCID: PMC8486239 DOI: 10.1111/pbi.13612] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/25/2021] [Accepted: 04/25/2021] [Indexed: 05/23/2023]
Abstract
RNase P functions either as a catalytic ribonucleoprotein (RNP) or as an RNA-free polypeptide to catalyse RNA processing, primarily tRNA 5' maturation. To the growing evidence of non-canonical roles for RNase P RNP subunits including regulation of chromatin structure and function, we add here a role for the rice RNase P Rpp30 in innate immunity. This protein (encoded by LOC_Os11g01074) was uncovered as the top hit in yeast two-hybrid assays performed with the rice histone deacetylase HDT701 as bait. We showed that HDT701 and OsRpp30 are localized to the rice nucleus, OsRpp30 expression increased post-infection by Pyricularia oryzae (syn. Magnaporthe oryzae), and OsRpp30 deacetylation coincided with HDT701 overexpression in vivo. Overexpression of OsRpp30 in transgenic rice increased expression of defence genes and generation of reactive oxygen species after pathogen-associated molecular pattern elicitor treatment, outcomes that culminated in resistance to a fungal (P. oryzae) and a bacterial (Xanthomonas oryzae pv. oryzae) pathogen. Knockout of OsRpp30 yielded the opposite phenotypes. Moreover, HA-tagged OsRpp30 co-purified with RNase P pre-tRNA cleavage activity. Interestingly, OsRpp30 is conserved in grass crops, including a near-identical C-terminal tail that is essential for HDT701 binding and defence regulation. Overall, our results suggest that OsRpp30 plays an important role in rice immune response to pathogens and provides a new approach to generate broad-spectrum disease-resistant rice cultivars.
Collapse
Affiliation(s)
- Wei Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant ProtectionHunan Agricultural UniversityChangshaHunanChina
- Department of Plant PathologyThe Ohio State UniversityColumbusOHUSA
| | - Yehui Xiong
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Lien B. Lai
- Department of Chemistry and BiochemistryCenter for RNA BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Kai Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests and College of Plant ProtectionHunan Agricultural UniversityChangshaHunanChina
| | - Venkat Gopalan
- Department of Chemistry and BiochemistryCenter for RNA BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Guo‐Liang Wang
- Department of Plant PathologyThe Ohio State UniversityColumbusOHUSA
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
18
|
Du Q, Qu Z, Wang L, Jiang J, Fu X, Fang Y, Li X, Xie X. Histone deacetylase SbHDT701 in Sorghum bicolor reveals functions in response to stress factors by enhancing acetylation. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 178:104908. [PMID: 34446212 DOI: 10.1016/j.pestbp.2021.104908] [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: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Histone acetylation plays important roles in eukaryotic chromatin modification and gene expression regulation. Acetylation levels are modulated by histone deacetylases (HDACs), which function as key epigenetic factors that regulate gene expression in response to various stresses. HDT701, a member of the HD2 subfamily of HDACs, plays crucial roles in plant responses to abiotic stress and pathogen infection. Here, we analysed the expression pattern of SbHDT701 in sorghum. Real-time fluorescence quantitative PCR (RT-qPCR) results showed that expression of SbHDT701 was tissue-specific, and up-regulated under drought (d-mannitol) and salt (NaCl) stresses. We also determined the optimal expression conditions for SbHDT701 protein accumulation, and successfully expressed and purified SbHDT701 protein. Besides, overexpression of SbHDT701 in could promote the growth of recombinant cells under abiotic stress. SbHDT701 expression in Escherichia coli also increased acetylation modification levels following treatment with 750 mM NaCl, and 100 mM or 300 mM d-mannitol. In summary, the sorghum HDAC SbHDT701 mediates stress responses by enhancing acetylation modification levels.
Collapse
Affiliation(s)
- Qiaoli Du
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Zhiguang Qu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Li Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Junmei Jiang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Xiaodong Fu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, PR China.
| |
Collapse
|
19
|
Zhao J, Zhang W, da Silva JAT, Liu X, Duan J. Rice histone deacetylase HDA704 positively regulates drought and salt tolerance by controlling stomatal aperture and density. PLANTA 2021; 254:79. [PMID: 34542712 DOI: 10.1007/s00425-021-03729-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/10/2021] [Indexed: 05/26/2023]
Abstract
HDA704 enhances drought and salt tolerance via stomata-regulated mechanism. HDA704 negatively regulates stomatal aperture and density, repressing the transcription of DST and ABIL2 by histone deacetylation modification. Drought and salinity can damage crop growth and reduce yield. Stomata play an important role in abiotic stress tolerance. In this study on rice, we identified the RPD3/HDA1-type histone deacetylase HDA704 as a positive regulatory factor in drought and salt tolerance. HDA704 was induced by drought and salt stresses. Overexpression of HDA704 in transgenic rice promoted stomatal closure, decreased the number of stomata and slowed down the rate of water loss, consequently resulting in increased drought and salt tolerance. By contrast, knockdown of HDA704 in transgenic rice decreased stomatal closure and accelerated the rate of water loss, leading to decrease drought and salt tolerance. We detected the transcript expression of DST (Drought and Salt Tolerance) and ABIL2 (Abscisic Acid-insensitive Like2), which positively regulate stomatal aperture and density in rice. Our results showed that HDA704 directly binds to DST and ABIL2, repressing their expression via histone deacetylation modification. Collectively, these findings reveal that HDA704 positively regulates drought and salt tolerance by repressing the expression of DST and ABIL2. Our findings provide a new insight into the molecular mechanisms of stomata-regulated abiotic stress tolerance of plants.
Collapse
Affiliation(s)
- Jinhui Zhao
- College of Life Sciences and Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Zhang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | | | - Xuncheng Liu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jun Duan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| |
Collapse
|
20
|
Li S, He X, Gao Y, Zhou C, Chiang VL, Li W. Histone Acetylation Changes in Plant Response to Drought Stress. Genes (Basel) 2021; 12:genes12091409. [PMID: 34573391 PMCID: PMC8468061 DOI: 10.3390/genes12091409] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Drought stress causes recurrent damage to a healthy ecosystem because it has major adverse effects on the growth and productivity of plants. However, plants have developed drought avoidance and resilience for survival through many strategies, such as increasing water absorption and conduction, reducing water loss and conversing growth stages. Understanding how plants respond and regulate drought stress would be important for creating and breeding better plants to help maintain a sound ecosystem. Epigenetic marks are a group of regulators affecting drought response and resilience in plants through modification of chromatin structure to control the transcription of pertinent genes. Histone acetylation is an ubiquitous epigenetic mark. The level of histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines whether the chromatin is open or closed, thereby controlling access of DNA-binding proteins for transcriptional activation. In this review, we summarize histone acetylation changes in plant response to drought stress, and review the functions of HATs and HDACs in drought response and resistance.
Collapse
Affiliation(s)
- Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
- Correspondence: ; Tel.: +86-15114585206
| | - Xu He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Yuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| |
Collapse
|
21
|
Tahir MS, Tian L. HD2-type histone deacetylases: unique regulators of plant development and stress responses. PLANT CELL REPORTS 2021; 40:1603-1615. [PMID: 34041586 DOI: 10.1007/s00299-021-02688-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate with each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.
Collapse
Affiliation(s)
- Muhammad Sufyan Tahir
- Department of Biology, University of Western Ontario, London, ON, Canada.
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| |
Collapse
|
22
|
Yruela I, Moreno-Yruela C, Olsen CA. Zn 2+-Dependent Histone Deacetylases in Plants: Structure and Evolution. TRENDS IN PLANT SCIENCE 2021; 26:741-757. [PMID: 33461867 DOI: 10.1016/j.tplants.2020.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Zn2+-dependent histone deacetylases are widely distributed in archaea, bacteria, and eukaryotes. Through deacetylation of histones and other biomolecules, these enzymes regulate mammalian gene expression, microtubule stability, and polyamine metabolism. In plants, they play essential roles in development and stress response, but little is known about their biochemistry. We provide here a holistic revision of plant histone deacetylase (HDA) phylogeny and translate recent lessons from other organisms. HDA evolution correlates with a gain of structural ductility/disorder, as observed for other proteins. We also highlight two recently identified Brassicaceae-specific HDAs, as well as unprecedented key mutations that would affect the catalytic activity of individual HDAs. This revised phylogeny will contextualize future studies and illuminate research on plant development and adaptation.
Collapse
Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Montañana 1005, 50059 Zaragoza, Spain; Group of Biochemistry, Biophysics, and Computational Biology (GBsC), Institute for Biocomputation and Physics of Complex Systems (BIFI) and Universidad de Zaragoza (UNIZAR) Joint Unit to CSIC, Zaragoza, Spain.
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| |
Collapse
|
23
|
Adhikari N, Jha T, Ghosh B. Dissecting Histone Deacetylase 3 in Multiple Disease Conditions: Selective Inhibition as a Promising Therapeutic Strategy. J Med Chem 2021; 64:8827-8869. [PMID: 34161101 DOI: 10.1021/acs.jmedchem.0c01676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The acetylation of histone and non-histone proteins has been implicated in several disease states. Modulation of such epigenetic modifications has therefore made histone deacetylases (HDACs) important drug targets. HDAC3, among various class I HDACs, has been signified as a potentially validated target in multiple diseases, namely, cancer, neurodegenerative diseases, diabetes, obesity, cardiovascular disorders, autoimmune diseases, inflammatory diseases, parasitic infections, and HIV. However, only a handful of HDAC3-selective inhibitors have been reported in spite of continuous efforts in design and development of HDAC3-selective inhibitors. In this Perspective, the roles of HDAC3 in various diseases as well as numerous potent and HDAC3-selective inhibitors have been discussed in detail. It will surely open up a new vista in the discovery of newer, more effective, and more selective HDAC3 inhibitors.
Collapse
Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata, 700032 West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata, 700032 West Bengal, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, BITS-Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| |
Collapse
|
24
|
Xu Q, Liu Q, Chen Z, Yue Y, Liu Y, Zhao Y, Zhou DX. Histone deacetylases control lysine acetylation of ribosomal proteins in rice. Nucleic Acids Res 2021; 49:4613-4628. [PMID: 33836077 PMCID: PMC8096213 DOI: 10.1093/nar/gkab244] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 01/04/2023] Open
Abstract
Lysine acetylation (Kac) is well known to occur in histones for chromatin function and epigenetic regulation. In addition to histones, Kac is also detected in a large number of proteins with diverse biological functions. However, Kac function and regulatory mechanism for most proteins are unclear. In this work, we studied mutation effects of rice genes encoding cytoplasm-localized histone deacetylases (HDAC) on protein acetylome and found that the HDAC protein HDA714 was a major deacetylase of the rice non-histone proteins including many ribosomal proteins (r-proteins) and translation factors that were extensively acetylated. HDA714 loss-of-function mutations increased Kac levels but reduced abundance of r-proteins. In vitro and in vivo experiments showed that HDA714 interacted with r-proteins and reduced their Kac. Substitutions of lysine by arginine (depleting Kac) in several r-proteins enhance, while mutations of lysine to glutamine (mimicking Kac) decrease their stability in transient expression system. Ribo-seq analysis revealed that the hda714 mutations resulted in increased ribosome stalling frequency. Collectively, the results uncover Kac as a functional posttranslational modification of r-proteins which is controlled by histone deacetylases, extending the role of Kac in gene expression to protein translational regulation.
Collapse
Affiliation(s)
- Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhengting Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yuan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.,Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, 91405 Orsay, France
| |
Collapse
|
25
|
Kumar V, Thakur JK, Prasad M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci 2021; 78:4467-4486. [PMID: 33638653 PMCID: PMC11072255 DOI: 10.1007/s00018-021-03794-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.
Collapse
Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- 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.
| |
Collapse
|
26
|
Hou J, Ren R, Xiao H, Chen Z, Yu J, Zhang H, Shi Q, Hou H, He S, Li L. Characteristic and evolution of HAT and HDAC genes in Gramineae genomes and their expression analysis under diverse stress in Oryza sativa. PLANTA 2021; 253:72. [PMID: 33606144 DOI: 10.1007/s00425-021-03589-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Comprehensive characterization of Gramineae HATs and HDACs reveals their conservation and variation. The recent WGD/SD gene pairs in the CBP and RPD/HDA1 gene family may confer specific adaptive evolutionary changes. Expression of OsHAT and OsHDAC genes provides a new vision in different aspects of development and response to diverse stress. The histone acetylase (HAT) and histone deacetylase (HDAC) have been proven to be tightly linked to play a crucial role in plant growth, development and response to abiotic stress by regulating histone acetylation levels. However, the evolutionary dynamics and functional differentiation of HATs and HDACs in Gramineae remain largely unclear. In the present study, we identified 37 HAT genes and 110 HDAC genes in seven Gramineae genomes by a detailed analysis. Phylogenetic trees of these HAT and HDAC proteins were constructed to illustrate evolutionary relationship in Gramineae. Gene structure, protein property and protein motif composition illustrated the conservation and variation of HATs and HDACs in Gramineae. Gene duplication analysis suggested that recent whole genome duplication (WGD)/segmental duplication (SD) events contributed to the diversification of the CBP and RPD3/HDA1 gene family in Gramineae. Furthermore, promoter cis-element prediction indicated that OsHATs and OsHDACs were likely functional proteins and involved in various signaling pathways. Expression analysis by RNA-seq data showed that all OsHAT and OsHDAC genes were expressed in different tissues or development stages, revealing that they were ubiquitously expressed. In addition, we found that their expression patterns were altered in response to cold, drought, salt, light, abscisic acid (ABA), and indole-3-acetic acid (IAA) treatments. These findings provide the basis for further identification of candidate OsHAT and OsHDAC genes that may be utilized in regulating growth and development and improving crop tolerance to abiotic stress.
Collapse
Affiliation(s)
- Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ruifei Ren
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Huangzhuo Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhenfei Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jinfu Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haorui Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qipeng Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
27
|
Zhang M, Teixeira da Silva JA, Yu Z, Wang H, Si C, Zhao C, He C, Duan J. Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments. PeerJ 2020; 8:e10482. [PMID: 33362966 PMCID: PMC7747690 DOI: 10.7717/peerj.10482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/12/2020] [Indexed: 11/20/2022] Open
Abstract
The deacetylation of core histones controlled by the action of histone deacetylases (HDACs) plays an important role in the epigenetic regulation of plant gene transcription. However, no systematic analysis of HDAC genes in Dendrobium officinale, a medicinal orchid, has been performed. In the current study, a total of 14 histone deacetylases in D. officinale were identified and characterized using bioinformatics-based methods. These genes were classified into RPD3/HDA1, SIR2, and HD2 subfamilies. Most DoHDAC genes in the same subfamily shared similar structures, and their encoded proteins contained similar motifs, suggesting that the HDAC family members are highly conserved and might have similar functions. Different cis-acting elements in promoters were related to abiotic stresses and exogenous plant hormones. A transient expression assay in onion epidermal cells by Agrobacterium-mediated transformation indicated that all of the detected histone deacetylases such as DoHDA7, DoHDA9, DoHDA10, DoHDT3, DoHDT4, DoSRT1 and DoSRT2, were localized in the nucleus. A tissue-specific analysis based on RNA-seq suggested that DoHDAC genes play a role in growth and development in D. officinale. The expression profiles of selected DoHDAC genes under abiotic stresses and plant hormone treatments were analyzed by qRT-PCR. DoHDA3, DoHDA8, DoHDA10 and DoHDT4 were modulated by multiple abiotic stresses and phytohormones, indicating that these genes were involved in abiotic stress response and phytohormone signaling pathways. These results provide valuable information for molecular studies to further elucidate the function of DoHDAC genes.
Collapse
Affiliation(s)
- Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Zhenming Yu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Haobin Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Conghui Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| |
Collapse
|
28
|
Wang R, Wang HL, Tang RP, Sun MY, Chen TM, Duan XC, Lu XF, Liu D, Shi XC, Laborda P, Wang SY. Pseudomonas putida Represses JA- and SA-Mediated Defense Pathways in Rice and Promotes an Alternative Defense Mechanism Possibly through ABA Signaling. PLANTS 2020; 9:plants9121641. [PMID: 33255501 PMCID: PMC7760693 DOI: 10.3390/plants9121641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 12/05/2022]
Abstract
The signaling pathways induced by Pseudomonas putida in rice plants at the early plant–rhizobacteria interaction stages, with and without inoculation of Xanthomonas oryzae pv. oryzae, were studied. In the absence of pathogen, P. putida reduced ethylene (ET) production, and promoted root and stem elongation. Interestingly, gene OsHDA702, which plays an important role in root formation, was found significantly up-regulated in the presence of the rhizobacterium. Although X. oryzae pv. oryzae inoculation enhanced ET production in rice plants, P. putida treatment repressed ET-, jasmonic acid (JA)- and salicylic acid (SA)-mediated defense pathways, and induced the biosynthesis of abscisic acid (ABA), and the overexpression of OsHDA705 and some pathogenesis-related proteins (PRs), which in turn increased the susceptibility of the rice plants against the pathogen. Collectively, this is the first work on the defense signaling induced by plant growth-promoting rhizobacteria in plants at the early interaction stages, and suggests that rhizobacteria stimulate an alternative defense mechanism in plants based on ABA accumulation and OsHDA705 signaling.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Xin-Chi Shi
- Correspondence: (X.-C.S.); (P.L.); (S.-Y.W.)
| | | | - Su-Yan Wang
- Correspondence: (X.-C.S.); (P.L.); (S.-Y.W.)
| |
Collapse
|
29
|
Yuan L, Dai H, Zheng S, Huang R, Tong H. Genome-wide identification of the HDAC family proteins and functional characterization of CsHD2C, a HD2-type histone deacetylase gene in tea plant (Camellia sinensis L. O. Kuntze). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:898-913. [PMID: 32916640 DOI: 10.1016/j.plaphy.2020.07.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
The histone deacetylases (HDACs) are involved in growth, development and stress responses in many plants. However, the functions of HDACs in tea plant (Camellia sinensis L. O. Kuntze) and other woody plants remain unclear. Here, 18 CsHDAC genes were identified by genome-wide analysis in tea plant. The phylogenetic analysis demonstrated that the CsHDAC proteins were divided into three subfamilies, namely, the RPD3/HDA1 subfamily (8 members), the SIR2 subfamily (4 members) and the plant specific HD2 subfamily (6 members). The expression patterns showed that most members of CsHDACs family were regulated by different abiotic stress. High correlation was found between the expression of the CsHDACs and the accumulation of theanine, catechin, EGCG and other metabolites in tea plant. Most of the CsHDAC proteins were negative regulators. We further studied a specific gene CsHD2C (NCBI-ID: KY364373) in tea plant, which is the homolog of AtHD2C, encoded a protein of 306 aa. CsHD2C was highly expressed in leaves, young buds and stems. The transcription of CsHD2C was inhibited by ABA, NaCl and low temperature. It was found localized in the nucleus when fused with a YFP reporter gene. Overexpression of CsHD2C can rescue the phenotype related to different abiotic stresses in the mutant of AtHD2C in Arabidopsis. The stress-responsive genes RD29A, RD29B, ABI1 and ABI2 were also investigated to understand the regulating role of CsHD2C under abiotic stresses. We also found that CsHD2C could renew the change of acetylation level for histone H4 and the RNAP-II occupancy accumulation in the promoter of abiotic stress responses gene in the hd2c Arabidopsis mutant. Together, our results suggested that CsHD2C may act as a positive regulator in abiotic stress responses in tea plant.
Collapse
Affiliation(s)
- Lianyu Yuan
- College of Food Science, Southwest University, Chongqing, 400715, China.
| | - Hongwei Dai
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Shuting Zheng
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Rui Huang
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - HuaRong Tong
- College of Food Science, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
30
|
Wang H, Jiao X, Kong X, Liu Y, Chen X, Fang R, Yan Y. The histone deacetylase HDA703 interacts with OsBZR1 to regulate rice brassinosteroid signaling, growth and heading date through repression of Ghd7 expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:447-459. [PMID: 33617099 DOI: 10.1111/tpj.14936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/08/2020] [Indexed: 06/12/2023]
Abstract
The plant steroid hormones brassinosteroids (BRs) play crucial roles in plant growth and development. The BR signal transduction pathway from perception to the key transcription factors has been well understood in Arabidopsis thaliana and in rice (Oryza sativa); however, the mechanisms conferring BR-mediated growth and flowering remain largely unknown, especially in rice. In this study, we show that HDA703 is a histone H4K8 and H4K12 deacetylase in rice. Hda703 mutants display a typical BR loss-of-function phenotype and reduced sensitivity to brassinolide, the most active BR. Rice plants overexpressing HDA703 exhibit some BR gain-of-function phenotypes dependent on BR biosynthesis and signaling. We also show that HDA703 is a direct target of BRASSINAZOLE-RESISTANT1 (OsBZR1), a primary regulator of rice BR signaling, and HDA703 interacts with OsBZR1 in rice. We further show that GRAIN NUMBER, PLANT HEIGHT, and HEADING DATE 7 (Ghd7), a central regulator of growth, development, and the stress response, is a direct target of OsBZR1. HDA703 directly targets Ghd7 and represses its expression through histone H4 deacetylation. HDA703-overexpressing rice plants phenocopy Ghd7-silencing rice plants in both growth and heading date. Together, our study suggests that HDA703, a histone H4 deacetylase, interacts with OsBZR1 to regulate rice BR signaling, growth, and heading date through epigenetic regulation of Ghd7.
Collapse
Affiliation(s)
- Huacai Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoming Jiao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoyu Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yawen Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoying Chen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- National Plant Gene Research Center, Beijing, 100101, China
| | - Yongsheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
31
|
Zhang J, Wu A, Wei H, Hao P, Zhang Q, Tian M, Yang X, Cheng S, Fu X, Ma L, Wang H, Yu S. Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton. BMC Genomics 2020; 21:643. [PMID: 32948145 PMCID: PMC7501681 DOI: 10.1186/s12864-020-07069-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/14/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. RESULTS In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. CONCLUSIONS Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.
Collapse
Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qi Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Miaomiao Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xu Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaokang Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| |
Collapse
|
32
|
Zhang H, Guo F, Qi P, Huang Y, Xie Y, Xu L, Han N, Xu L, Bian H. OsHDA710-Mediated Histone Deacetylation Regulates Callus Formation of Rice Mature Embryo. PLANT & CELL PHYSIOLOGY 2020; 61:1646-1660. [PMID: 32592489 DOI: 10.1093/pcp/pcaa086] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/17/2020] [Indexed: 05/18/2023]
Abstract
Histone deacetylases (HDACs) play important roles in the regulation of eukaryotic gene expression. The role of HDACs in specialized transcriptional regulation and biological processes is poorly understood. In this study, we evaluated the global expression patterns of genes related to epigenetic modifications during callus initiation in rice. We found that the repression of HDAC activity by trichostatin A (TSA) or by OsHDA710 mutation (hda710) results in impaired callus formation of rice mature embryo and increased global histone H3 acetylation levels. The HDAC inhibition decreased auxin response and cell proliferation in callus formation. Meanwhile, the transcriptional repressors OsARF18 and OsARF22 were upregulated in the callus of hda710. The chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) analysis demonstrated that the callus of hda710 exhibited enhanced histone H3 acetylation levels at the chromatin regions of OsARF18 and OsARF22. Furthermore, we found that OsARF18 and OsARF22 were regulated through OsHDA710 recruitment to their target loci. In addition, overexpression of OsARF18 decreased the transcription of downstream genes PLT1 and PLT2 and inhibited callus formation of the mature embryo. These results demonstrate that OsHDA710 regulates callus formation by suppressing repressive OsARFs via histone deacetylation during callus formation of rice mature embryo. This indicates that OsHDA710-mediated histone deacetylation is an epigenetic regulation pathway for maintaining auxin response during cell dedifferentiation.
Collapse
Affiliation(s)
- Haidao Zhang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fu Guo
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peipei Qi
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yizi Huang
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Lei Xu
- Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ning Han
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Hongwu Bian
- Institute of Genetic and Regenerative Biology, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
33
|
Wang L, Zhang F, Qiao H. Chromatin Regulation in the Response of Ethylene: Nuclear Events in Ethylene Signaling. SMALL METHODS 2020; 4:1900288. [PMID: 34189257 PMCID: PMC8238466 DOI: 10.1002/smtd.201900288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Indexed: 05/15/2023]
Abstract
Plant hormones, produced in response to environmental stimuli, regulate almost all aspects of plant growth and development. Ethylene is a gaseous plant hormone that plays pleotropic roles in plant growth, plant development, fruit ripening, stress responses, and pathogen defenses. After decades of research, the key components of ethylene signaling have been identified and characterized. Although the molecular mechanisms of the sensing of ethylene signal and the transduction of ethylene signaling have been studied extensively, how chromatin influences ethylene signaling and ethylene response is a new area of research. This review describes the current understanding of how chromatin modifications, specifically histone acetylation, regulate ethylene signaling and the ethylene response.
Collapse
Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fan Zhang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
34
|
Zhang K, Yu L, Pang X, Cao H, Si H, Zang J, Xing J, Dong J. In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses. PeerJ 2020; 8:e8539. [PMID: 32095360 PMCID: PMC7023831 DOI: 10.7717/peerj.8539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/09/2020] [Indexed: 01/20/2023] Open
Abstract
Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.
Collapse
Affiliation(s)
- Kang Zhang
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Lu Yu
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Xi Pang
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Hongzhe Cao
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Helong Si
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Jinping Zang
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Jihong Xing
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| | - Jingao Dong
- College of Life Science, Hebei Agricultrual University, Baoding, Hebei, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultrual University, Baoding, Hebei, China
| |
Collapse
|
35
|
Ma X, Liang X, Lv S, Guan T, Jiang T, Cheng Y. Histone deacetylase gene PtHDT902 modifies adventitious root formation and negatively regulates salt stress tolerance in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110301. [PMID: 31779889 DOI: 10.1016/j.plantsci.2019.110301] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 05/24/2023]
Abstract
Histone deacetylases (HDACs) regulate gene transcription, and play a critical role in plant growth, development and stress responses. HD2 proteins are plant specific histone deacetylases. In woody plants, functions of HD2s are not known. In this study, we cloned an HD2 gene PtHDT902 from Populus trichocarpa and investigated its sequence, expression, subcellular localization, and functions in root development and salt stress responses. Our findings indicated that PtHDT902 was a nuclear protein and its expression was regulated by abiotic stresses. The over-expression of PtHDT902 in both Arabidopsis and poplar increased the expression levels of gibberellin (GA) biosynthetic genes. The expression of PtHDT902 in Arabidopsis enhanced primary root growth, and its over-expression in poplar inhibited adventitious root formation. These phenotypes resulted from over-expression of PtHDT902 were consistent with the GA-overproduction phenotypes. In addition, the poplar plants over-expressing PtHDT902 exhibited lower tolerance to salt than non-transgenic plants. These findings indicated that PtHDT902 worked as an important regulator in adventitious root formation and salt stress tolerance in poplar.
Collapse
Affiliation(s)
- Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Xueying Liang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Shibo Lv
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Tao Guan
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| |
Collapse
|
36
|
Song J, Henry HAL, Tian L. Brachypodium histone deacetylase BdHD1 positively regulates ABA and drought stress responses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:355-365. [PMID: 31128706 DOI: 10.1016/j.plantsci.2019.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Despite recent evidence that HDACs are involved in the environmental stress responses of plants, their roles in the abiotic stress responses of monocot plants remain largely unexplored. We investigated a HDAC gene, Bradi3g08060 (BdHD1), in Brachypodium distachyon. The Brachypodium BdHD1-overexpression plants displayed a hypersensitive phenotype to ABA and exhibited better survival under drought conditions. On the other hand, the RNA-interference plants were insensitive to ABA and showed low survival under drought stress. At the genome-wide level, overexpression of BdHD1 led to lower H3K9 acetylation at the transcriptional start sites of 230 genes than in the wild type plants under the drought treatment. We validated our ChIP-Seq data on 10 selected transcription factor genes from the 230 drought-specific genes. These genes exhibited much lower expression in the BdHD1-overexpression plants compared to the wild type plants under drought stress. We further identified an ABA-inducible transcription factor gene BdWRKY24 that was repressed in BdHD1-OE plants, but highly expressed in RNA-interference plants under drought stress. These results indicate that BdHD1 plays a positive role in ABA sensitivity and drought stress tolerance and they provide a link between the role of BdHD1 and the drought stress response at a genome-wide level in Brachypodium.
Collapse
Affiliation(s)
- Jingpu Song
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada; London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Hugh A L Henry
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Lining Tian
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada; London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada.
| |
Collapse
|
37
|
Begcy K, Dresselhaus T. Epigenetic responses to abiotic stresses during reproductive development in cereals. PLANT REPRODUCTION 2018; 31:343-355. [PMID: 29943158 PMCID: PMC6244825 DOI: 10.1007/s00497-018-0343-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 06/22/2018] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Overview of current understanding of epigenetic alterations after abiotic stresses during reproductive development in cereals. Abiotic stresses, including heat, drought, cold, flooding, and salinity, negatively impact crop productivity. Various stages during reproductive development are especially sensitive to environmental stresses, which may lead to complete sterility and severe yield losses. Plants exhibit diverse responses to ameliorate stress damage. Changes in DNA methylation, histone modification as well as regulation of small RNA and long noncoding RNA pathways have been shown to represent key modulators in plant stress responses. During reproductive development in cereals, various protein complexes controlling histone and DNA methylation have been identified, revealing conserved and novel mechanisms regulating abiotic stress responses in cereals and other plant species. New findings highlight the role of transposable elements during stress periods. Here, we review our current understanding of epigenetic stress responses during male and female gametophyte formation (germline development), fertilization, early seed devolvement, and seed maturation in cereals. An integrative model of epigenetic responses during reproductive development in cereals is proposed, emphasizing the role of DNA methylation and histone modifications during abiotic stresses.
Collapse
Affiliation(s)
- Kevin Begcy
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053, Regensburg, Germany.
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053, Regensburg, Germany.
| |
Collapse
|
38
|
Yang C, Shen W, Chen H, Chu L, Xu Y, Zhou X, Liu C, Chen C, Zeng J, Liu J, Li Q, Gao C, Charron JB, Luo M. Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean. BMC PLANT BIOLOGY 2018; 18:226. [PMID: 30305032 PMCID: PMC6180487 DOI: 10.1186/s12870-018-1454-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 10/01/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Histone deacetylases (HDACs) function as key epigenetic factors in repressing the expression of genes in multiple aspects of plant growth, development and plant response to abiotic or biotic stresses. To date, the molecular function of HDACs is well described in Arabidopsis thaliana, but no systematic analysis of this gene family in soybean (Glycine max) has been reported. RESULTS In this study, 28 HDAC genes from soybean genome were identified, which were asymmetrically distributed on 12 chromosomes. Phylogenetic analysis demonstrated that GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2. Subcellular localization analysis revealed that YFP-tagged GmSRT4, GmHDT2 and GmHDT4 were predominantly localized in the nucleus, whereas GmHDA6, GmHDA13, GmHDA14 and GmHDA16 were found in both the cytoplasm and nucleus. Real-time quantitative PCR showed that GmHDA6, GmHDA13, GmHDA14, GmHDA16 and GmHDT4 were broadly expressed across plant tissues, while GmHDA8, GmSRT2, GmSRT4 and GmHDT2 showed differential expression across various tissues. Interestingly, we measured differential changes in GmHDACs transcripts accumulation in response to several abiotic cues, indicating that these epigenetic modifiers could potentially be part of a dynamic transcriptional response to stress in soybean. Finally, we show that the levels of histone marks previously reported to be associated with plant HDACs are modulated by cold and heat in this legume. CONCLUSION We have identified and classified 28 HDAC genes in soybean. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to environmental stress.
Collapse
Affiliation(s)
- Chao Yang
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Hongfeng Chen
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Liutian Chu
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yingchao Xu
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaochen Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chuanliang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Chunmiao Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Jiahui Zeng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Jin Liu
- Institute for Food and Bioresource Engineering, Department of Energy and Resources Engineering and BIC-ESAT, College of Engineering, Peking University, Beijing, 100871 China
| | - Qianfeng Li
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009 China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631 China
| | - Jean-Benoit Charron
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| |
Collapse
|
39
|
Tong B, Xia D, Lv S, Ma X. Cloning and expression analysis of PtHDT903, a HD2-type histone deacetylase gene in Populus trichocarpa. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1478749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Dean Xia
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Shibo Lv
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| |
Collapse
|
40
|
Adhikari N, Amin SA, Trivedi P, Jha T, Ghosh B. HDAC3 is a potential validated target for cancer: An overview on the benzamide-based selective HDAC3 inhibitors through comparative SAR/QSAR/QAAR approaches. Eur J Med Chem 2018; 157:1127-1142. [DOI: 10.1016/j.ejmech.2018.08.081] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/08/2018] [Accepted: 08/27/2018] [Indexed: 02/06/2023]
|
41
|
Cho LH, Yoon J, Wai AH, An G. Histone Deacetylase 701 (HDT701) Induces Flowering in Rice by Modulating Expression of OsIDS1. Mol Cells 2018; 41:665-675. [PMID: 29991671 PMCID: PMC6078857 DOI: 10.14348/molcells.2018.0148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/10/2018] [Accepted: 06/25/2018] [Indexed: 12/13/2022] Open
Abstract
Rice is a facultative short-day (SD) plant in which flowering is induced under SD conditions or by other environmental factors and internal genetic programs. Overexpression of Histone Deacetylase 701 (HDT701) accelerates flowering in hybrid rice. In this study, mutants defective in HDT701 flowered late under both SD and long-day conditions. Expression levels of florigens Heading date 3a (Hd3a) and Rice Flowering Locus T1 (RFT1), and their immediate upstream floral activator Early heading date 1 (Ehd1), were significantly decreased in the hdt701 mutants, indicating that HDT701 functions upstream of Ehd1 in controlling flowering time. Transcript levels of OsINDETERMINATE SPIKELET 1 (OsIDS1), an upstream repressor of Ehd1, were significantly increased in the mutants while those of OsGI and Hd1 were reduced. Chromatin-immunoprecipitation assays revealed that HDT701 directly binds to the promoter region of OsIDS1. These results suggest that HDT701 induces flowering by suppressing OsIDS1.
Collapse
Affiliation(s)
- Lae-Hyeon Cho
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Jinmi Yoon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Antt Htet Wai
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| | - Gynheung An
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104,
Korea
| |
Collapse
|
42
|
Lee K, Lee HY, Back K. Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes encode N-acetylserotonin deacetylase, which catalyzes conversion of N-acetylserotonin into serotonin, a reverse reaction for melatonin biosynthesis in plants. J Pineal Res 2018; 64. [PMID: 29247559 DOI: 10.1111/jpi.12460] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/05/2017] [Indexed: 12/16/2022]
Abstract
In plants, melatonin production is strictly regulated, unlike the production of its precursor, serotonin, which is highly inducible in response to stimuli, such as senescence and pathogen exposure. Exogenous serotonin treatment does not greatly induce the production of N-acetylserotonin (NAS) and melatonin in plants, which suggests the possible existence of one or more regulatory genes in the pathway for the biosynthesis of melatonin from serotonin. In this report, we found that NAS was rapidly and abundantly converted into serotonin in rice seedlings, indicating the presence of an N-acetylserotonin deacetylase (ASDAC). To clone the putative ASDAC gene, we screened 4 genes that were known as histone deacetylase (HDAC) genes, but encoded proteins targeted into chloroplasts or mitochondria rather than nuclei. Of 4 recombinant Escherichia coli strains expressing these genes, one E. coli strain expressing the rice HDAC10 gene was found to be capable of producing serotonin in response to treatment with NAS. The recombinant purified rice HDAC10 (OsHDAC10) protein exhibited ASDAC enzyme activity toward NAS, N-acetyltyramine (NAT), N-acetyltryptamine, and melatonin, with the highest ASDAC activity for NAT. In addition, its Arabidopsis ortholog, AtHDAC14, showed similar ASDAC activity to that of OsHDAC10. Both OsHDAC10 and AtHDAC14 were found to be expressed in chloroplasts. Phylogenetic analysis indicated that ASDAC homologs were present in archaea, but not in cyanobacteria, which differs from the distribution of serotonin N-acetyltransferase (SNAT). This suggests that SNAT and ASDAC may have evolved differently from ancestral eukaryotic cells.
Collapse
Affiliation(s)
- Kyungjin Lee
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
| | - Hyoung Yool Lee
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
| | - Kyoungwhan Back
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
| |
Collapse
|
43
|
Markus C, Pecinka A, Karan R, Barney JN, Merotto A. Epigenetic regulation - contribution to herbicide resistance in weeds? PEST MANAGEMENT SCIENCE 2018; 74:275-281. [PMID: 28888062 DOI: 10.1002/ps.4727] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 05/10/2023]
Abstract
Continuous use of herbicides has resulted in the evolution of resistance to all major herbicide modes of action worldwide. Besides the well-documented cases of newly acquired resistance through genetic changes, epigenetic regulation may also contribute to herbicide resistance in weeds. Epigenetics involves processes that modify the expression of specific genetic elements without changes in the DNA sequence, and play an important role in re-programming gene expression. Epigenetic modifications can be induced spontaneously, genetically or environmentally. Stress-induced epigenetic changes are normally reverted soon after stress exposure, although in specific cases they can also be carried over multiple generations, thereby having a selective benefit. Here, we provide an overview of the basis of epigenetic regulation in plants and discuss the possible effect of epigenetic changes on herbicide resistance. The understanding of these epigenetic changes would add a new perspective to our knowledge of environmental and management stresses and their effects on the evolution of herbicide resistance in weeds. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- Catarine Markus
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ratna Karan
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Jacob N Barney
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, USA
| | - Aldo Merotto
- Department of Crop Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| |
Collapse
|
44
|
Ma X, Zhang B, Liu C, Tong B, Guan T, Xia D. Expression of a populus histone deacetylase gene 84KHDA903 in tobacco enhances drought tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:1-11. [PMID: 29223330 DOI: 10.1016/j.plantsci.2017.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/21/2017] [Accepted: 09/12/2017] [Indexed: 05/07/2023]
Abstract
Histone deacetylases (HDACs) play a key role in regulating plant growth, development and stress responses. However, functions of HDACs in woody plants are largely unknown. In this study, a novel gene encoding a RPD3/HDA1-type histone deacetylase was cloned from 84K poplar (Populus alba×Populus glandulosa) and designated as 84KHDA903. The 84KHDA903 encodes a protein composed of 500 amino acid residues, which contains a conserved HDAC domain. Transient expression of 84KHDA903 in onion epidermal cells suggested that it was exclusively localized in nucleus. The 84KHDA903 exhibited different expression patterns under drought, salt and ABA treatments. The expression of 84KHDA903 was responsive to drought and ABA but not to salt. To understand the function of 84KHDA903 in stress responses, the 84KHDA903 gene was transformed into tobacco. The expression of 84KHDA903 in tobacco increased the tolerance of transgenic seeds to mannitol but not to salt. In adult stage, the 84KHDA903-expressing tobacco exhibited drought tolerance and showed strong capacity to recover after drought. During the recovery period, the stress-responsive genes including NtDREB4, NtDREB3 and NtLEA5 were induced to be highly expressed in the 84KHDA903 transgenic plants in contrast to wild-type plants. Taken together, for the first time, we reported a RPD3/HDA1-type histone deacetylase from poplar, 84KHDA903, which acted as a positive regulator in drought stress responses.
Collapse
Affiliation(s)
- Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin 150040, China.
| | - Bing Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin 150040, China
| | - Chunjuan Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin 150040, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin 150040, China
| | - Tao Guan
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin 150040, China
| | - Dean Xia
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin 150040, China.
| |
Collapse
|
45
|
Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
Collapse
Affiliation(s)
- Xian Deng
- 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
| | - Xianwei Song
- 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
| | - Liya Wei
- 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
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- 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
| | - Xiaofeng Cao
- 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
| |
Collapse
|
46
|
Abstract
Reversible histone acetylation and deacetylation at the N-terminus of histone tails play a crucial role in regulation of gene activity. Hyperacetylation of histones relaxes chromatin structure and is associated with transcriptional activation, whereas hypoacetylation of histones induces chromatin compaction and gene repression. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. Emerging evidences revealed that plant HATs and HDACs play essential roles in regulation of gene expression in plant development and plant responses to environmental stresses. Furthermore, HATs and HDACs were shown to interact with various chromatin-remodeling factors and transcription factors involved in transcriptional regulation of multiple developmental processes.
Collapse
Affiliation(s)
- X Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - S Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - C-W Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - C-Y Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - K Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
47
|
Identification of genes regulated by histone acetylation during root development in Populus trichocarpa. BMC Genomics 2016; 17:96. [PMID: 26847576 PMCID: PMC4743431 DOI: 10.1186/s12864-016-2407-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/20/2016] [Indexed: 11/10/2022] Open
Abstract
Background Histone deacetylases (HDACs) are key enzymes catalyzing the removal of acetyl groups from histones. HDACs act in concert with histone acetyltransferases (HATs) to regulate histone acetylation status, which modifies chromatin structure, affecting gene transcription and thus regulating multiple biological processes such as plant growth and development. Over a decade, certain HDACs in herbaceous plants have been deeply studied. However, functions of HDACs in woody plants are not well understood. Results Histone deacetylase specific inhibitor trichostatin A (TSA) was used to investigate the role of HDACs in organogenesis of roots and root development in Populus trochocarpa. The adventitious roots were regenerated and grown on medium supplemented with 0, 1, and 2.5 μM TSA. TSA treatment delayed root regeneration and inhibited primary root growth. To examine the genes modified by TSA in the regenerated roots, tag-based digital gene expression (DGE) analysis was performed using Illumina HiSeqTM 2000. Approximately 4.5 million total clean tags were mapped per library. The distinct clean tags for the three libraries corresponding to 0, 1 and 2.5 μM TSA treatment were 166167, 143103 and 153507, from which 38.45 %, 31.84 % and 38.88 % were mapped unambiguously to the unigene database, respectively. Most of the tags were expressed at similar levels, showing a < 5-fold difference after 1 μM and 2.5 μM TSA treatments and the maximum fold-change of the tag copy number was around 20. The expression levels of many genes in roots were significantly altered by TSA. A total of 36 genes were up-regulated and 1368 genes were down-regulated after 1 μM TSA treatment, while 166 genes were up-regulated and 397 genes were down-regulated after 2.5 μM TSA treatment. Gene ontology (GO) and pathway analyses indicated that the differentially expressed genes were related to many kinds of molecular functions and biological processes. The genes encoding key enzymes catalyzing gibberellin biosynthesis were significantly down-regulated in the roots exposed to 2.5 μM TSA and their expression changes were validated by using real-time PCR. Conclusions HDACs were required for de novo organogenesis and normal growth of populus roots. DGE data provides the gene profiles in roots probably regulated by histone acetylation during root growth and development, which will lead to a better understanding of the mechanism controlling root development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2407-x) contains supplementary material, which is available to authorized users.
Collapse
|
48
|
Zhao J, Li M, Gu D, Liu X, Zhang J, Wu K, Zhang X, Teixeira da Silva JA, Duan J. Involvement of rice histone deacetylase HDA705 in seed germination and in response to ABA and abiotic stresses. Biochem Biophys Res Commun 2016; 470:439-444. [PMID: 26772883 DOI: 10.1016/j.bbrc.2016.01.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
Histone acetylation and deacetylation play crucial roles in the modification of chromatin structure and regulation of gene expression in eukaryotes. Histone acetyltransferases (HATs) and histone deacetylases (HDACs) assist to maintain the balance of chromatin acetylation status. Previous studies showed that plant HDACs are key regulators involved in response to development and stresses. In this study, we examined the expression pattern and function of HDA705, a member of the RPD3/HDA1-type HDAC in rice. Overexpression of HDA705 in rice decreased ABA and salt stress resistance during seed germination. Delayed seed germination of HDA705 overexpression lines was associated with down-regulated expression of GA biosynthetic genes and up-regulation of ABA biosynthetic genes. Moreover, overexpression of HDA705 in rice enhanced osmotic stress resistance during the seedling stage. Our findings demonstrate that HDA705 may play a role in regulating seed germination and the response to abiotic stresses in rice.
Collapse
Affiliation(s)
- Jinhui Zhao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Dachuan Gu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianxia Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Kunlin Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xinhua Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| |
Collapse
|
49
|
Quantification and Gene Expression Analysis of Histone Deacetylases in Common Bean during Rust Fungal Inoculation. Int J Genomics 2015; 2015:153243. [PMID: 26824033 PMCID: PMC4707378 DOI: 10.1155/2015/153243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/27/2015] [Indexed: 11/17/2022] Open
Abstract
Histone deacetylases (HDACs) play an important role in plant growth, development, and defense processes and are one of the primary causes of epigenetic modifications in a genome. There was only one study reported on epigenetic modifications of the important legume crop, common bean, and its interaction with the fungal rust pathogen Uromyces appendiculatus prior to this project. We measured the total active HDACs levels in leaf tissues and observed expression patterns for the selected HDAC genes at 0, 12, and 84 hours after inoculation in mock inoculated and inoculated plants. Colorimetric analysis showed that the total amount of HDACs present in the leaf tissue decreased at 12 hours in inoculated plants compared to mock inoculated control plants. Gene expression analyses indicated that the expression pattern of gene PvSRT1 is similar to the trend of total active HDACs in this time course experiment. Gene PvHDA6 showed increased expression in the inoculated plants during the time points measured. This is one of the first attempts to study expression levels of HDACs in economically important legumes in the context of plant pathogen interactions. Findings from our study will be helpful to understand trends of total active HDACs and expression patterns of these genes under study during biotic stress.
Collapse
|
50
|
Wang Z, Cao H, Chen F, Liu Y. The roles of histone acetylation in seed performance and plant development. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:125-133. [PMID: 25270163 DOI: 10.1016/j.plaphy.2014.09.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/23/2014] [Indexed: 05/08/2023]
Abstract
Histone acetylation regulates gene transcription by chromatin modifications and plays a crucial role in the plant development and response to environment cues. The homeostasis of histone acetylation is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in different plant tissues and development stages. The vigorous knowledge of the function and co-factors about HATs (e.g. GCN5) and HDACs (e.g. HDA19, HDA6) has been obtained from model plant Arabidopsis. However, understanding individual role of other HATs and HDACs require more work, especially in the major food crops such as rice, maize and wheat. Many co-regulators have been recently identified to function as a component of HAT or HDAC complex in some specific developmental processes. The described findings show a distinctive and interesting epigenetic regulation network composed of HATs, HDACs and co-regulators playing crucial roles in the seed performance, flowering time, plant morphogenesis, plant response to stresses etc. In this review, we summarized the recent progresses and suggested the perspective of histone acetylation research, which might provide us a new window to understand the epigenetic code of plant development and to improve the crop production and quality.
Collapse
Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| |
Collapse
|