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Ruan M, Zhao H, Wen Y, Chen H, He F, Hou X, Song X, Jiang H, Ruan YL, Wu L. The complex transcriptional regulation of heat stress response in maize. STRESS BIOLOGY 2024; 4:24. [PMID: 38668992 PMCID: PMC11052759 DOI: 10.1007/s44154-024-00165-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/01/2024] [Indexed: 04/29/2024]
Abstract
As one of the most important food and feed crops worldwide, maize suffers much more tremendous damages under heat stress compared to other plants, which seriously inhibits plant growth and reduces productivity. To mitigate the heat-induced damages and adapt to high temperature environment, plants have evolved a series of molecular mechanisms to sense, respond and adapt high temperatures and heat stress. In this review, we summarized recent advances in molecular regulations underlying high temperature sensing, heat stress response and memory in maize, especially focusing on several important pathways and signals in high temperature sensing, and the complex transcriptional regulation of ZmHSFs (Heat Shock Factors) in heat stress response. In addition, we highlighted interactions between ZmHSFs and several epigenetic regulation factors in coordinately regulating heat stress response and memory. Finally, we laid out strategies to systematically elucidate the regulatory network of maize heat stress response, and discussed approaches for breeding future heat-tolerance maize.
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Affiliation(s)
- Mingxiu Ruan
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Heng Zhao
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yujing Wen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hao Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Feng He
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xingbo Hou
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaoqin Song
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Haiyang Jiang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yong-Ling Ruan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Horticulture, Northwest A&F University, Yangling, 712100, China.
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Leiming Wu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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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.
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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.
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Sharma M, Sidhu AK, Samota MK, Gupta M, Koli P, Choudhary M. Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants. Proteomes 2023; 11:38. [PMID: 38133152 PMCID: PMC10747722 DOI: 10.3390/proteomes11040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Abiotic stresses profoundly alter plant growth and development, resulting in yield losses. Plants have evolved adaptive mechanisms to combat these challenges, triggering intricate molecular responses to maintain tissue hydration and temperature stability during stress. A pivotal player in this defense is histone modification, governing gene expression in response to diverse environmental cues. Post-translational modifications (PTMs) of histone tails, including acetylation, phosphorylation, methylation, ubiquitination, and sumoylation, regulate transcription, DNA processes, and stress-related traits. This review comprehensively explores the world of PTMs of histones in plants and their vital role in imparting various abiotic stress tolerance in plants. Techniques, like chromatin immune precipitation (ChIP), ChIP-qPCR, mass spectrometry, and Cleavage Under Targets and Tag mentation, have unveiled the dynamic histone modification landscape within plant cells. The significance of PTMs in enhancing the plants' ability to cope with abiotic stresses has also been discussed. Recent advances in PTM research shed light on the molecular basis of stress tolerance in plants. Understanding the intricate proteome complexity due to various proteoforms/protein variants is a challenging task, but emerging single-cell resolution techniques may help to address such challenges. The review provides the future prospects aimed at harnessing the full potential of PTMs for improved plant responses under changing climate change.
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Affiliation(s)
- Madhvi Sharma
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Amanpreet K. Sidhu
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Mahesh Kumar Samota
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Regional Station, Abohar 152116, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
| | - Pushpendra Koli
- Plant Animal Relationship Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi 284003, India;
- Post-Harvest Biosecurity, Murdoch University, Perth, WA 6150, Australia
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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Cui X, Dard A, Reichheld JP, Zhou DX. Multifaceted functions of histone deacetylases in stress response. TRENDS IN PLANT SCIENCE 2023; 28:1245-1256. [PMID: 37394308 DOI: 10.1016/j.tplants.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023]
Abstract
Histone deacetylases (HDACs) are important chromatin regulators essential for plant tolerance to adverse environments. In addition to histone deacetylation and epigenetic regulation, HDACs deacetylate non-histone proteins and thereby regulate multiple pathways. Like other post-translational modifications (PTMs), acetylation/deacetylation is a reversible switch regulating different cellular processes in plants. Here, by focusing on results obtained in arabidopsis (Arabidopsis thaliana) and rice plants, we analyze the different aspects of HDAC functions and the underlying regulatory mechanisms in modulating plant responses to stress. We hypothesize that, in addition to epigenetic regulation of gene expression, HDACs can also control plant tolerance to stress by regulating transcription, translation, and metabolic activities and possibly assembly-disassembly of stress granules (SGs) through lysine deacetylation of non-histone proteins.
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Affiliation(s)
- Xiaoyun Cui
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Saclay, 91405 Orsay, France
| | - Avilien Dard
- Laboratoire Génome et Développement des Plantes, CNRS, Université Perpignan Via Domitia, 66860 Perpignan, France; VIB-UGent Center for Plant Systems Biology, Ghent University, Technologiepark-Zwijnaarde 71, - 9052 Ghent, Belgium
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes, CNRS, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Saclay, 91405 Orsay, France; National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China.
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Kan Y, Mu XR, Gao J, Lin HX, Lin Y. The molecular basis of heat stress responses in plants. MOLECULAR PLANT 2023; 16:1612-1634. [PMID: 37740489 DOI: 10.1016/j.molp.2023.09.013] [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: 03/31/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Global warming impacts crop production and threatens food security. Elevated temperatures are sensed by different cell components. Temperature increases are classified as either mild warm temperatures or excessively hot temperatures, which are perceived by distinct signaling pathways in plants. Warm temperatures induce thermomorphogenesis, while high-temperature stress triggers heat acclimation and has destructive effects on plant growth and development. In this review, we systematically summarize the heat-responsive genetic networks in Arabidopsis and crop plants based on recent studies. In addition, we highlight the strategies used to improve grain yield under heat stress from a source-sink perspective. We also discuss the remaining issues regarding the characteristics of thermosensors and the urgency required to explore the basis of acclimation under multifactorial stress combination.
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Affiliation(s)
- Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiao-Rui Mu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Youshun Lin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Zhu J, Cao X, Deng X. Epigenetic and transcription factors synergistically promote the high temperature response in plants. Trends Biochem Sci 2023; 48:788-800. [PMID: 37393166 DOI: 10.1016/j.tibs.2023.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/03/2023]
Abstract
Temperature is one of the main environmental cues affecting plant growth and development, and plants have evolved multiple mechanisms to sense and acclimate to high temperature. Emerging research has shown that transcription factors, epigenetic factors, and their coordination are essential for plant temperature responses and the resulting phenological adaptation. Here, we summarize recent advances in molecular and cellular mechanisms to understand how plants acclimate to high temperature and describe how plant meristems sense and integrate environmental signals. Furthermore, we lay out future directions for new technologies to reveal heterogeneous responses in different cell types thus improving plant environmental plasticity.
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Affiliation(s)
- Jiaping Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
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Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
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Han Y, Haouel A, Georgii E, Priego-Cubero S, Wurm CJ, Hemmler D, Schmitt-Kopplin P, Becker C, Durner J, Lindermayr C. Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression. Genes (Basel) 2023; 14:1199. [PMID: 37372378 DOI: 10.3390/genes14061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Histone deacetylation catalyzed by histone deacetylase plays a critical role in gene silencing and subsequently controls many important biological processes. It was reported that the expression of the plant-specific histone deacetylase subfamily HD2s is repressed by ABA in Arabidopsis. However, little is known about the molecular relationship between HD2A/HD2B and ABA during the vegetative phase. Here, we describe that the hd2ahd2b mutant shows hypersensitivity to exogenous ABA during the germination and post-germination period. Additionally, transcriptome analyses revealed that the transcription of ABA-responsive genes was reprogrammed and the global H4K5ac level is specifically up-regulated in hd2ahd2b plants. ChIP-Seq and ChIP-qPCR results further verified that both HD2A and HD2B could directly and specifically bind to certain ABA-responsive genes. As a consequence, Arabidopsis hd2ahd2b plants displayed enhanced drought resistance in comparison to WT, which is consistent with increased ROS content, reduced stomatal aperture, and up-regulated drought-resistance-related genes. Moreover, HD2A and HD2B repressed ABA biosynthesis via the deacetylation of H4K5ac at NCED9. Taken together, our results indicate that HD2A and HD2B partly function through ABA signaling and act as negative regulators during the drought resistance response via the regulation of ABA biosynthesis and response genes.
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Affiliation(s)
- Yongtao Han
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | - Amira Haouel
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | - Elisabeth Georgii
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | | | - Christoph J Wurm
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | - Daniel Hemmler
- Research Unit Analytical Biogeochemistry, Helmholtz Munich, 85764 Oberschleißheim, Germany
| | | | - Claude Becker
- Genetics, LMU Biocenter, Ludwig-Maximilians-Universität München, 80539 München, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, 85354 Freising, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Munich, 85764 Oberschleißheim, Germany
- Institute of Lung Health and Immunity, Comprehensive Pneumology Center, Helmholtz Munich, 85764 Oberschleißheim, Germany
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Khan AH, Min L, Ma Y, Zeeshan M, Jin S, Zhang X. High-temperature stress in crops: male sterility, yield loss and potential remedy approaches. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:680-697. [PMID: 36221230 PMCID: PMC10037161 DOI: 10.1111/pbi.13946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 05/16/2023]
Abstract
Global food security is one of the utmost essential challenges in the 21st century in providing enough food for the growing population while coping with the already stressed environment. High temperature (HT) is one of the main factors affecting plant growth, development and reproduction and causes male sterility in plants. In male reproductive tissues, metabolic changes induced by HT involve carbohydrates, lipids, hormones, epigenetics and reactive oxygen species, leading to male sterility and ultimately reducing yield. Understanding the mechanism and genes involved in these pathways during the HT stress response will provide a new path to improve crops by using molecular breeding and biotechnological approaches. Moreover, this review provides insight into male sterility and integrates this with suggested strategies to enhance crop tolerance under HT stress conditions at the reproductive stage.
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Affiliation(s)
- Aamir Hamid Khan
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Muhammad Zeeshan
- Guangxi Key Laboratory for Agro‐Environment and Agro‐Product Safety, Guangxi Colleges and Universities Key Laboratory of Crop Cultivation and Tillage, College of AgricultureGuanxi UniversityNanningChina
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement & Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanChina
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BRM Complex in Arabidopsis Adopts ncBAF-like Composition and Requires BRD Subunits for Assembly and Stability. Int J Mol Sci 2023; 24:ijms24043917. [PMID: 36835328 PMCID: PMC9967331 DOI: 10.3390/ijms24043917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
ATP-dependent SWI/SNF chromatin remodelling complexes are conserved multi-subunit assemblies that control genome activity. Functions of SWI/SNF complexes in plant development and growth have been well established, but the architecture of particular assemblies is unclear. In this study, we elucidate the organization of Arabidopsis SWI/SNF complexes formed around a BRM catalytic subunit, and define the requirement of bromodomain-containing proteins BRD1/2/13 for the formation and stability of the entire complex. Using affinity purification followed by mass spectrometry, we identify a set of BRM-associated subunits and demonstrate that the BRM complexes strongly resemble mammalian non-canonical BAF complexes. Furthermore, we identify BDH1 and 2 proteins as components of the BRM complex and, using mutant analyses, show that BDH1/2 are important for vegetative and generative development, as well as hormonal responses. We further show that BRD1/2/13 represent unique subunits of the BRM complexes, and their depletion severely affects the integrity of the complex, resulting in the formation of residual assemblies. Finally, analyses of BRM complexes after proteasome inhibition revealed the existence of a module consisting of the ATPase, ARP, and BDH proteins, assembled with other subunits in a BRD-dependent manner. Together, our results suggest modular organization of plant SWI/SNF complexes and provide a biochemical explanation for mutant phenotypes.
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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12
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Shu J, Ding N, Liu J, Cui Y, Chen C. Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis. Nucleic Acids Res 2022; 50:12754-12767. [PMID: 36453990 PMCID: PMC9825159 DOI: 10.1093/nar/gkac1126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.
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Affiliation(s)
- Jie Shu
- 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, Guangdong 510650, China
| | - Ning Ding
- 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, Guangdong 510650, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Chen Chen
- To whom correspondence should be addressed. Tel: +86 20 37252711;
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13
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Bobde RC, Kumar A, Vasudevan D. Plant-specific HDT family histone deacetylases are nucleoplasmins. THE PLANT CELL 2022; 34:4760-4777. [PMID: 36069647 PMCID: PMC9709999 DOI: 10.1093/plcell/koac275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.
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Affiliation(s)
- Ruchir C Bobde
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
- Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Ashish Kumar
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
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14
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Tahir MS, Karagiannis J, Tian L. HD2A and HD2C co-regulate drought stress response by modulating stomatal closure and root growth in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1062722. [PMID: 36507458 PMCID: PMC9727301 DOI: 10.3389/fpls.2022.1062722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Histone deacetylase 2 (HD2) is a unique family of histone deacetylases (HDACs) in plants. Despite evidence that certain HD2 family HDACs play an important role in plant growth and stress response, the coordination of HD2s in these processes remains largely unknown. We found that HD2-type, HD2A and HD2C coordinate to play a role in drought stress response in Arabidopsis. We showed that the hd2a.hd2c double mutant (Mac16) exhibit decreased drought survival and increased water loss as compared to the single mutants, hd2a and hd2c. Gene expression analysis showed that the ABI1 and ABI2 genes were upregulated and SLAC1 was downregulated which led to the modified stomatal functioning in the Mac16 as compared to the single mutants. Overexpression of HD2A and HD2C showed enhanced drought survival and decreased water loss. We also showed that the GA2ox1 and GA2ox2 genes, which are involved in the catabolism of bioactive gibberellic acids, were upregulated in the Mac16 as compared to the single mutants, which led to a decreased root growth in the Mac16. Furthermore, we showed that HD2A and HD2C can physically interact and increased genome-wide H3K9 acetylation was observed in the Mac16, compared to the single mutants. Overall, our investigation revealed that HD2A and HD2C coordinate to play a cumulative role in drought stress response and root growth in Arabidopsis.
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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
| | - Jim Karagiannis
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lining Tian
- Department of Biology, University of Western Ontario, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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15
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Molecular and epigenetic basis of heat stress responses and acclimatization in plants. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00400-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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16
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Shekhawat K, Almeida-Trapp M, García-Ramírez GX, Hirt H. Beat the heat: plant- and microbe-mediated strategies for crop thermotolerance. TRENDS IN PLANT SCIENCE 2022; 27:802-813. [PMID: 35331665 DOI: 10.1016/j.tplants.2022.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/30/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Heat stress (HS) affects plant growth and development, and reduces crop yield. To combat HS, plants have evolved several sophisticated strategies. The primary HS response in plants involves the activation of heat-shock transcription factors and heat-shock proteins (HSPs). Plants also deploy more advanced epigenetic mechanisms in response to recurring HS conditions. In addition, beneficial microbes can reprogram the plant epitranscriptome to induce thermotolerance, and have the potential to improve crop yield productivity by mitigating HS-induced inhibition of growth and development. We summarize the latest advances in plant epigenetic regulation and highlight microbe-mediated thermotolerance in plants.
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Affiliation(s)
- Kirti Shekhawat
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Marilia Almeida-Trapp
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Gabriel X García-Ramírez
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia; Max Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria.
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17
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Li B, Yang C, An B, Wang H, Albaqami M, Abou-Elwafa SF, Xu L, Xu Y. Comparative transcriptomic and epigenetic analyses reveal conserved and divergent regulatory pathways in barley response to temperature stresses. PHYSIOLOGIA PLANTARUM 2022; 174:e13727. [PMID: 35657636 DOI: 10.1111/ppl.13727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation and histone modification enable plants to rapidly adapt to adverse temperature stresses, including low temperature (LT) and high temperature (HT) stress. In this study, we conducted physiological, epigenetic, and transcriptomic analyses of barley seedlings grown under control (22°C), mild low temperature (MLT, 14°C) and HT (38°C) conditions to elucidate the underlying molecular mechanisms. Compared to MLT, HT implies greater deleterious effects on barley seedlings' growth. The methylation-sensitive amplification polymorphism analysis showed that MLT induced more DNA methylation and HT more DNA demethylation compared to control. Besides, the higher levels of H3K9ac and H3K4me3 under HT compared to MLT stresses might lead to the loosening of chromatin and, subsequently, the activation of gene expression. Consistently, the transcriptome analysis revealed that there were more differentially expressed genes (DEGs) in plants subjected to HT stress than MLT stress compared to control. The common and unique pathways of these DEGs between MLT and HT were also analyzed. Transcription factors, such as ERF, bHLH, NAC, HSF, and MYB, were most involved in MLT and HT stress. The underlying gene regulation networks of epigenetic modulation-related genes were further explored by weight gene co-expression network analysis. Our study provides new insights into the understanding of epigenetic regulation responses to temperature stress in barley, which will lead to improved strategies for the development of cold- and heat-tolerant barley varieties for sustainable barley production in a climate-changing world.
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Affiliation(s)
- Bo Li
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Caixian Yang
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Bingzhuang An
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Hongpan Wang
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Mohammed Albaqami
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Le Xu
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
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18
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Hernández-García J, Diego-Martin B, Kuo PH, Jami-Alahmadi Y, Vashisht AA, Wohlschlegel J, Jacobsen SE, Blázquez MA, Gallego-Bartolomé J. Comprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant components. Commun Biol 2022; 5:549. [PMID: 35668117 PMCID: PMC9170682 DOI: 10.1038/s42003-022-03490-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/16/2022] [Indexed: 01/19/2023] Open
Abstract
Over millions of years, eukaryotes evolved from unicellular to multicellular organisms with increasingly complex genomes and sophisticated gene expression networks. Consequently, chromatin regulators evolved to support this increased complexity. The ATP-dependent chromatin remodelers of the SWI/SNF family are multiprotein complexes that modulate nucleosome positioning and appear under different configurations, which perform distinct functions. While the composition, architecture, and activity of these subclasses are well understood in a limited number of fungal and animal model organisms, the lack of comprehensive information in other eukaryotic organisms precludes the identification of a reliable evolutionary model of SWI/SNF complexes. Here, we performed a systematic analysis using 36 species from animal, fungal, and plant lineages to assess the conservation of known SWI/SNF subunits across eukaryotes. We identified evolutionary relationships that allowed us to propose the composition of a hypothetical ancestral SWI/SNF complex in the last eukaryotic common ancestor. This last common ancestor appears to have undergone several rounds of lineage-specific subunit gains and losses, shaping the current conformation of the known subclasses in animals and fungi. In addition, our results unravel a plant SWI/SNF complex, reminiscent of the animal BAF subclass, which incorporates a set of plant-specific subunits of still unknown function.
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Affiliation(s)
- Jorge Hernández-García
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
- Laboratory of Biochemistry, Wageningen University & Research, 6703 WE, Stippeneng 4, Wageningen, The Netherlands
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Peggy Hsuanyu Kuo
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, 90095, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, 90095, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, 90095, CA, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, 90095, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, 90095, CA, USA
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain.
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19
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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.
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20
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Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:1449. [PMID: 35684223 PMCID: PMC9182740 DOI: 10.3390/plants11111449] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Plants' stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory non-coding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.
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Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
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21
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Ji SX, Wang XD, Lin ZK, Wan FH, Lü ZC, Liu WX. Characterization of Chromatin Remodeling Genes Involved in Thermal Tolerance of Biologically Invasive Bemisia tabaci. Front Physiol 2022; 13:865172. [PMID: 35669578 PMCID: PMC9163341 DOI: 10.3389/fphys.2022.865172] [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: 02/06/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
As an invasive species, Bemisia tabaci Mediterranean (MED) has notable potential to adapt to a wide range of environmental temperatures, which enables it to successfully spread after invasion and occupy habitats over a wide latitude range. It has been postulated that chromatin remodeling mechanisms are related to the rapid acquisition of adaptive traits and thermal resistance in invasive species; however, relevant experimental evidence is scarce. To identify the molecular characteristics and assess the role of chromatin remodelers in thermal stress within invasive MED and native Asia II 1 of the B. tabaci species complex, we identified 13 switching defective/sucrose non-fermenting (SWI/SNF) and 10 imitation switch (ISWI) family members in the B. tabaci genome, analyzed their molecular characteristics and structures, and identified key mutation sites between MED and Asia II 1, then cloned the catalytic subunits, and revealed the difference in thermal tolerance function. The results showed that the expression levels of Bt-BRM-1 and Bt-BRM-2 were significantly higher in MED than in Asia II 1 during heat stress, and Bt-BRM-2 expression was significantly higher during cold stress. In addition, RNA interference results indicated that the two target genes had similar temperature tolerance function in the both two cryptic species. This study is the first to identify and analyze the molecular characteristics of SWI/SNF and ISWI family members and reveal their potential key roles in temperature tolerance in poikilothermic ectotherms. The results will assist in understanding the underlying temperature adaptation mechanism of invasive insects and will enrich stress adaptation research systems from an epigenetic perspective.
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Affiliation(s)
- Shun-Xia Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Di Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ze-Kai Lin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fang-Hao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Chuang Lü
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Zhi-Chuang Lü,
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Lan W, Zheng S, Yang P, Qiu Y, Xu Y, Miao Y. Establishment of a Landscape of UPL5-Ubiquitinated on Multiple Subcellular Components of Leaf Senescence Cell in Arabidopsis. Int J Mol Sci 2022; 23:ijms23105754. [PMID: 35628561 PMCID: PMC9145402 DOI: 10.3390/ijms23105754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Catabolism of macromolecules is a major event in senescent cells, especially involving proteolysis of organelles and abnormally aggregated proteins, circulation of nutrients, and precise control of intracellular environmental balance. Proteasomes are distributed in the nucleus and cytoplasm; however, proteasomes in organelles are limited. In this study, multi-omics proteomic analyses of ubiquitinated proteins enriched by using antibody against “di-Gly-Lys” via a free labeling were used to investigate the global changes of protein levels and ubiquitination modification levels of upl5 mutant relative to wild-type plant; subcellular localization analysis of UPL5 was found to be located in the nucleus, cytoplasm, and plastid within the cell; and the direct lysine site patterns of UPL5 were screened by the H89R substitution in the tagged ubiquitinated assay. It suggests that UPL5 acting as a candidate of organelle E3 ligase either in the nucleus or cytoplasm or plastid modifies numerous targets related to nuclear transcription and plastid photosynthesis involving in Ca2+ and hormone signaling pathway in plant senescence and in response to (a)biotic stress protection.
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Affiliation(s)
| | | | | | | | | | - Ying Miao
- Correspondence: ; Tel.: +86-59186392987
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23
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Ramakrishnan M, Papolu PK, Satish L, Vinod KK, Wei Q, Sharma A, Emamverdian A, Zou LH, Zhou M. Redox status of the plant cell determines epigenetic modifications under abiotic stress conditions and during developmental processes. J Adv Res 2022; 42:99-116. [PMID: 35690579 PMCID: PMC9788946 DOI: 10.1016/j.jare.2022.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The oxidation-reduction (redox) status of the cell influences or regulates transcription factors and enzymes involved in epigenetic changes, such as DNA methylation, histone protein modifications, and chromatin structure and remodeling. These changes are crucial regulators of chromatin architecture, leading to differential gene expression in eukaryotes. But the cell's redox homeostasis is difficult to sustain since the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) is not equal in plants at different developmental stages and under abiotic stress conditions. Exceeding optimum ROS and RNS levels leads to oxidative stress and thus alters the redox status of the cell. Consequently, this alteration modulates intracellular epigenetic modifications that either mitigate or mediate the plant growth and stress response. AIM OF REVIEW Recent studies suggest that the altered redox status of the cell reform the cellular functions and epigenetic changes. Recent high-throughput techniques have also greatly advanced redox-mediated gene expression discovery, but the integrated view of the redox status, and its associations with epigenetic changes and subsequent gene expression in plants are still scarce. In this review, we accordingly focus on how the redox status of the cell affects epigenetic modifications in plants under abiotic stress conditions and during developmental processes. This is a first comprehensive review on the redox status of the cell covering the redox components and signaling, redox status alters the post-translational modification of proteins, intracellular epigenetic modifications, redox interplay during DNA methylation, redox regulation of histone acetylation and methylation, redox regulation of miRNA biogenesis, redox regulation of chromatin structure and remodeling and conclusion, future perspectives and biotechnological opportunities for the future development of the plants. KEY SCIENTIFIC CONCEPTS OF REVIEW The interaction of redox mediators such as ROS, RNS and antioxidants regulates redox homeostasis and redox-mediated epigenetic changes. We discuss how redox mediators modulate epigenetic changes and show the opportunities for smart use of the redox status of the cell in plant development and abiotic stress adaptation. However, how a redox mediator triggers epigenetic modification without activating other redox mediators remains yet unknown.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Lakkakula Satish
- Department of Biotechnology Engineering, & The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva - 84105, Israel; Applied Phycology and Biotechnology Division, Marine Algal Research Station, CSIR - Central Salt and Marine Chemicals Research Institute, Mandapam 623519, Tamil Nadu, India
| | | | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Abolghassem Emamverdian
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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Post-translational modification: a strategic response to high temperature in plants. ABIOTECH 2022; 3:49-64. [PMID: 36304199 PMCID: PMC9590526 DOI: 10.1007/s42994-021-00067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022]
Abstract
With the increasing global warming, high-temperature stress is affecting plant growth and development with greater frequency. Therefore, an increasing number of studies examining the mechanism of temperature response contribute to a more optimal understanding of plant growth under environmental pressure. Post-translational modification (PTM) provides the rapid reconnection of transcriptional programs including transcription factors and signaling proteins. It is vital that plants quickly respond to changes in the environment in order to survive under stressful situations. Herein, we discuss several types of PTMs that occur in response to warm-temperature and high-temperature stress, including ubiquitination, SUMOylation, phosphorylation, histone methylation, and acetylation. This review provides a valuable resolution to this issue to enable increased crop productivity at high temperatures.
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Liu J, Chang C. Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122766. [PMID: 34961235 PMCID: PMC8705648 DOI: 10.3390/plants10122766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 05/26/2023]
Abstract
Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.
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Zioutopoulou A, Patitaki E, Xu T, Kaiserli E. The Epigenetic Mechanisms Underlying Thermomorphogenesis and Heat Stress Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112439. [PMID: 34834802 PMCID: PMC8624032 DOI: 10.3390/plants10112439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 05/28/2023]
Abstract
Integration of temperature cues is crucial for plant survival and adaptation. Global warming is a prevalent issue, especially in modern agriculture, since the global rise in average temperature is expected to impact crop productivity worldwide. Hence, better understanding of the mechanisms by which plants respond to warmer temperatures is very important. This review focuses on the epigenetic mechanisms implicated in plant responses to high temperature and distinguishes the different epigenetic events that occur at warmer average temperatures, leading to thermomorphogenic responses, or subjected to extreme warm temperatures, leading to heat stress.
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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Li S, Lyu S, Liu Y, Luo M, Shi S, Deng S. Cauliflower mosaic virus P6 Dysfunctions Histone Deacetylase HD2C to Promote Virus Infection. Cells 2021; 10:2278. [PMID: 34571927 PMCID: PMC8464784 DOI: 10.3390/cells10092278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/16/2021] [Accepted: 08/29/2021] [Indexed: 12/30/2022] Open
Abstract
Histone deacetylases (HDACs) are vital epigenetic modifiers not only in regulating plant development but also in abiotic- and biotic-stress responses. Though to date, the functions of HD2C-an HD2-type HDAC-In plant development and abiotic stress have been intensively explored, its function in biotic stress remains unknown. In this study, we have identified HD2C as an interaction partner of the Cauliflower mosaic virus (CaMV) P6 protein. It functions as a positive regulator in defending against CaMV infection. The hd2c mutants show enhanced susceptibility to CaMV infection. In support, the accumulation of viral DNA, viral transcripts, and the deposition of histone acetylation on the viral minichromosomes are increased in hd2c mutants. P6 interferes with the interaction between HD2C and HDA6, and P6 overexpression lines have similar phenotypes with hd2c mutants. In further investigations, P6 overexpression lines, together with CaMV infection plants, are more sensitive to ABA and NaCl with a concomitant increasing expression of ABA/NaCl-regulated genes. Moreover, the global levels of histone acetylation are increased in P6 overexpression lines and CaMV infection plants. Collectively, our results suggest that P6 dysfunctions histone deacetylase HD2C by physical interaction to promote CaMV infection.
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Affiliation(s)
- Shun Li
- Guangdong Provincial Key Laboratory of Applied Botany & CAS Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (S.L.); (S.L.); (M.L.)
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Shanwu Lyu
- Guangdong Provincial Key Laboratory of Applied Botany & CAS Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (S.L.); (S.L.); (M.L.)
| | - Yujuan Liu
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & CAS Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (S.L.); (S.L.); (M.L.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China;
| | - Shulin Deng
- Guangdong Provincial Key Laboratory of Applied Botany & CAS Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (S.L.); (S.L.); (M.L.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
- National Engineering Research Center of Navel Orange, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China
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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.
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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
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Banerjee S, Roy S. An insight into understanding the coupling between homologous recombination mediated DNA repair and chromatin remodeling mechanisms in plant genome: an update. Cell Cycle 2021; 20:1760-1784. [PMID: 34437813 DOI: 10.1080/15384101.2021.1966584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Plants, with their obligatory immobility, are vastly exposed to a wide range of environmental agents and also various endogenous processes, which frequently cause damage to DNA and impose genotoxic stress. These factors subsequently increase genome instability, thus affecting plant growth and productivity. Therefore, to survive under frequent and extreme environmental stress conditions, plants have developed highly efficient and powerful defense mechanisms to repair the damages in the genome for maintaining genome stability. Such multi-dimensional signaling response, activated in presence of damage in the DNA, is collectively known as DNA Damage Response (DDR). DDR plays a crucial role in the remarkably efficient detection, signaling, and repair of damages in the genome for maintaining plant genome stability and normal growth responses. Like other highly advanced eukaryotic systems, chromatin dynamics play a key role in regulating cell cycle progression in plants through remarkable orchestration of environmental and developmental signals. The regulation of chromatin architecture and nucleosomal organization in DDR is mainly modulated by the ATP dependent chromatin remodelers (ACRs), chromatin modifiers, and histone chaperones. ACRs are mainly responsible for transcriptional regulation of several homologous recombination (HR) repair genes in plants under genotoxic stress. The HR-based repair of DNA damage has been considered as the most error-free mechanism of repair and represents one of the essential sources of genetic diversity and new allelic combinations in plants. The initiation of DDR signaling and DNA damage repair pathway requires recruitment of epigenetic modifiers for remodeling of the damaged chromatin while accumulating evidence has shown that chromatin remodeling and DDR share part of the similar signaling pathway through the altered epigenetic status of the associated chromatin region. In this review, we have integrated information to provide an overview on the association between chromatin remodeling mediated regulation of chromatin structure stability and DDR signaling in plants, with emphasis on the scope of the utilization of the available knowledge for the improvement of plant health and productivity.Abbreviation: ADH: Alcohol Dehydrogenase; AGO2: Argonaute 2; ARP: Actin-Related Protein; ASF:1- Anti-Silencing Function-1; ATM: Ataxia Telangiectasia Mutated; ATR: ATM and Rad3- Related; AtSWI3c: Arabidopsis thaliana Switch 3c; ATXR5: Arabidopsis Trithorax-Related5; ATXR6: Arabidopsis Trithorax-Related6; BER: Base Excision Repair; BRCA1: Breast Cancer Associated 1; BRM: BRAHMA; BRU1: BRUSHY1; CAF:1- Chromatin Assembly Factor-1; CHD: Chromodomain Helicase DNA; CHR5: Chromatin Remodeling Protein 5; CHR11/17: Chromatin Remodeling Protein 11/17; CIPK11- CBL- Interacting Protein Kinase 11; CLF: Curly Leaf; CMT3: Chromomethylase 3; COR15A: Cold Regulated 15A; COR47: Cold Regulated 47; CRISPR: Clustered Regulatory Interspaced Short Palindromic Repeats; DDM1: Decreased DNA Methylation1; DRR: DNA Repair and Recombination; DSBs: Double-Strand Breaks; DDR: DNA Damage Response; EXO1: Exonuclease 1; FAS1/2: Fasciata1/2; FACT: Facilitates Chromatin Transcription; FT: Flowering Locus T; GMI1: Gamma-Irradiation And Mitomycin C Induced 1; HAC1: Histone Acetyltransferase of the CBP Family 1; HAM1: Histone Acetyltransferase of the MYST Family 1; HAM2: Histone Acetyltransferase of the MYST Family 2; HAF1: Histone Acetyltransferase of the TAF Family 1; HAT: Histone Acetyl Transferase; HDA1: Histone Deacetylase 1; HDA6: Histone Deacetylase 6; HIRA: Histone Regulatory Homolog A; HR- Homologous recombination; HAS: Helicase SANT Associated; HSS: HAND-SLANT-SLIDE; ICE1: Inducer of CBF Expression 1; INO80: Inositol Requiring Mutant 80; ISW1: Imitation Switch 1; KIN1/2: Kinase 1 /2; MET1: Methyltransferase 1; MET2: Methyltransferase 2; MINU: MINUSCULE; MMS: Methyl Methane Sulfonate; MMS21: Methyl Methane Sulfonate Sensitivity 21; MRN: MRE11, RAD50 and NBS1; MSI1: Multicopy Suppressor Of Ira1; NAP1: Nucleosome Assembly Protein 1; NRP1/NRP2: NAP1-Related Protein; NER: Nucleotide Excision Repair; NHEJ: Non-Homologous End Joining; PARP1: Poly-ADP Ribose Polymerase; PIE1: Photoperiod Independent Early Flowering 1; PIKK: Phosphoinositide 3-Kinase-Like Kinase; PKL: PICKLE; PKR1/2: PICKLE Related 1/2; RAD: Radiation Sensitive Mutant; RD22: Responsive To Desiccation 22; RD29A: Responsive To Desiccation 29A; ROS: Reactive Oxygen Species; ROS1: Repressor of Silencing 1; RPA1E: Replication Protein A 1E; SANT: Swi3, Ada2, N-Cor and TFIIIB; SEP3: SEPALLATA3; SCC3: Sister Chromatid Cohesion Protein 3; SMC1: Structural Maintenance of Chromosomes Protein 1; SMC3: Structural Maintenance of Chromosomes Protein 3; SOG1: Suppressor of Gamma Response 1; SWC6: SWR1 Complex Subunit 6; SWR1: SWI2/SNF2-Related 1; SYD: SPLAYED; SMC5: Structural Maintenance of Chromosome 5; SWI/SNF: Switch/Sucrose Non-Fermentable; TALENs: Transcription Activators Like Effector Nucleases; TRRAP: Transformation/Transactivation Domain-Associated Protein; ZFNs: Zinc Finger Nucleases.
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Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
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Singh RK, Prasad M. Delineating the epigenetic regulation of heat and drought response in plants. Crit Rev Biotechnol 2021; 42:548-561. [PMID: 34289772 DOI: 10.1080/07388551.2021.1946004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
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Affiliation(s)
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
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Jarończyk K, Sosnowska K, Zaborowski A, Pupel P, Bucholc M, Małecka E, Siwirykow N, Stachula P, Iwanicka-Nowicka R, Koblowska M, Jerzmanowski A, Archacki R. Bromodomain-containing subunits BRD1, BRD2, and BRD13 are required for proper functioning of SWI/SNF complexes in Arabidopsis. PLANT COMMUNICATIONS 2021; 2:100174. [PMID: 34327319 PMCID: PMC8299063 DOI: 10.1016/j.xplc.2021.100174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 05/26/2023]
Abstract
SWI/SNF chromatin remodelers are evolutionarily conserved multiprotein complexes that use the energy of ATP hydrolysis to change chromatin structure. A characteristic feature of SWI/SNF remodelers is the occurrence in both the catalytic ATPase subunit and some auxiliary subunits, of bromodomains, the protein motifs capable of binding acetylated histones. Here, we report that the Arabidopsis bromodomain-containing proteins BRD1, BRD2, and BRD13 are likely true SWI/SNF subunits that interact with the core SWI/SNF components SWI3C and SWP73B. Loss of function of each single BRD protein caused early flowering but had a negligible effect on other developmental pathways. By contrast, a brd triple mutation (brdx3) led to more pronounced developmental abnormalities, indicating functional redundancy among the BRD proteins. The brdx3 phenotypes, including hypersensitivity to abscisic acid and the gibberellin biosynthesis inhibitor paclobutrazol, resembled those of swi/snf mutants. Furthermore, the BRM protein level and occupancy at the direct target loci SCL3, ABI5, and SVP were reduced in the brdx3 mutant background. Finally, a brdx3 brm-3 quadruple mutant, in which SWI/SNF complexes were devoid of all constituent bromodomains, phenocopied a loss-of-function mutation in BRM. Taken together, our results demonstrate the relevance of BRDs as SWI/SNF subunits and suggest their cooperation with the bromodomain of BRM ATPase.
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Affiliation(s)
- Kamila Jarończyk
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | | | - Adam Zaborowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Piotr Pupel
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
| | - Maria Bucholc
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Ewelina Małecka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Nina Siwirykow
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Paulina Stachula
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Andrzej Jerzmanowski
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
| | - Rafał Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, 02-106 Warsaw, Poland
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33
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Blanco-Pastor JL, Liberal IM, Sakiroglu M, Wei Y, Brummer EC, Andrew RL, Pfeil BE. Annual and perennial Medicago show signatures of parallel adaptation to climate and soil in highly conserved genes. Mol Ecol 2021; 30:4448-4465. [PMID: 34217151 DOI: 10.1111/mec.16061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
Human induced environmental change may require rapid adaptation of plant populations and crops, but the genomic basis of environmental adaptation remain poorly understood. We analysed polymorphic loci from the perennial crop Medicago sativa (alfalfa or lucerne) and the annual legume model species M. truncatula to search for a common set of candidate genes that might contribute to adaptation to abiotic stress in both annual and perennial Medicago species. We identified a set of candidate genes of adaptation associated with environmental gradients along the distribution of the two Medicago species. Candidate genes for each species were detected in homologous genomic linkage blocks using genome-environment (GEA) and genome-phenotype association analyses. Hundreds of GEA candidate genes were species-specific, of these, 13.4% (M. sativa) and 24% (M. truncatula) were also significantly associated with phenotypic traits. A set of 168 GEA candidates were shared by both species, which was 25.4% more than expected by chance. When combined, they explained a high proportion of variance for certain phenotypic traits associated with adaptation. Genes with highly conserved functions dominated among the shared candidates and were enriched in gene ontology terms that have shown to play a central role in drought avoidance and tolerance mechanisms by means of cellular shape modifications and other functions associated with cell homeostasis. Our results point to the existence of a molecular basis of adaptation to abiotic stress in Medicago determined by highly conserved genes and gene functions. We discuss these results in light of the recently proposed omnigenic model of complex traits.
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Affiliation(s)
- José Luis Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,INRAE, Centre Nouvelle-Aquitaine-Poitiers, UR4 (URP3F), Lusignan, France
| | - Isabel M Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.,Real Jardín Botánico de Madrid (RJB-CSIC), Madrid, Spain
| | - Muhammet Sakiroglu
- Department of Bioengineering, Adana Alparslan Turkes Science and Technology University, Adana, Turkey
| | - Yanling Wei
- Plant Breeding Center, Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - E Charles Brummer
- Plant Breeding Center, Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Bernard E Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
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Marchetti F, Cainzos M, Cascallares M, Distéfano AM, Setzes N, López GA, Zabaleta E, Pagnussat GC. Heat stress in Marchantia polymorpha: Sensing and mechanisms underlying a dynamic response. PLANT, CELL & ENVIRONMENT 2021; 44:2134-2149. [PMID: 33058168 DOI: 10.1111/pce.13914] [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: 07/29/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Sensing and response to high temperatures are crucial to prevent heat-related damage and to preserve cellular and metabolic functions. The response to heat stress is a complex and coordinated process that involves several subcellular compartments and multi-level regulatory networks that are synchronized to avoid cell damage while maintaining cellular homeostasis. In this review, we provide an insight into the most recent advances in elucidating the molecular mechanisms involved in heat stress sensing and response in Marchantia polymorpha. Based on the signaling pathways and genes that were identified in Marchantia, our analyses indicate that although with specific particularities, the core components of the heat stress response seem conserved in bryophytes and angiosperms. Liverworts not only constitute a powerful tool to study heat stress response and signaling pathways during plant evolution, but also provide key and simple mechanisms to cope with extreme temperatures. Given the increasing prevalence of high temperatures around the world as a result of global warming, this knowledge provides a new set of molecular tools with potential agronomical applications.
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Affiliation(s)
- Fernanda Marchetti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Maximiliano Cainzos
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Milagros Cascallares
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Ayelén Mariana Distéfano
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Nicolás Setzes
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Gabriel Alejandro López
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Eduardo Zabaleta
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Gabriela Carolina Pagnussat
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
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35
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Ramirez-Prado JS, Benhamed M. New partners for old friends: Plant SWI/SNF complexes. MOLECULAR PLANT 2021; 14:870-872. [PMID: 34015459 DOI: 10.1016/j.molp.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 05/15/2023]
Affiliation(s)
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay 91405, France; Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay (IPS2) 91405, France; Institut Universitaire de France (IUF), France.
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36
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Liao X, Li Y, Hu Z, Lin Y, Zheng B, Ding J. Poplar acetylome profiling reveals lysine acetylation dynamics in seasonal bud dormancy release. PLANT, CELL & ENVIRONMENT 2021; 44:1830-1845. [PMID: 33675080 DOI: 10.1111/pce.14040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 05/06/2023]
Abstract
For perennials in boreal and temperate ecosystems, bud dormancy is crucial for survival in harsh winter. Dormancy is released by prolonged exposure to low temperatures and is followed by reactive growth in the spring. Lysine acetylation (Kac) is one of the major post-translational modifications (PTMs) that are involved in plant response to environmental signals. However, little information is available on the effects of Kac modification on bud dormancy release. Here, we report the dynamics of lysine acetylome in hybrid poplar (Populus tremula × Populus alba) dormant buds. A total of 7,594 acetyl-sites from 3,281 acetyl-proteins were identified, representing a large dataset of lysine acetylome in plants. Of them, 229 proteins were differentially acetylated during bud dormancy release and were mainly involved in the primary metabolic pathways. Site-directed mutagenesis enzymatic assays showed that Kac strongly modified the activities of two key enzymes of primary metabolism, pyruvate dehydrogenase (PDH) and isocitrate dehydrogenase (IDH). We thus propose that Kac of enzymes could be an important strategy for reconfiguration of metabolic processes during bud dormancy release. In all, our results reveal the importance of Kac in bud dormancy release and provide a new perspective to understand the molecular mechanisms of seasonal growth of trees.
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Affiliation(s)
- Xiaoli Liao
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Yue Li
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Zhenzhu Hu
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Ying Lin
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Bo Zheng
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Jihua Ding
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
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Srivastava AK, Suresh Kumar J, Suprasanna P. Seed 'primeomics': plants memorize their germination under stress. Biol Rev Camb Philos Soc 2021; 96:1723-1743. [PMID: 33961327 DOI: 10.1111/brv.12722] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl2 and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.
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Affiliation(s)
- Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Jisha Suresh Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
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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.
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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.
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Song ZT, Liu JX, Han JJ. Chromatin remodeling factors regulate environmental stress responses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:438-450. [PMID: 33421288 DOI: 10.1111/jipb.13064] [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: 09/26/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality. As sessile organisms, plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes. In eukaryotes, nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation. To enable dynamic access to packaged DNA, eukaryotes have evolved Snf2 (sucrose nonfermenting 2) family proteins as chromatin remodeling factors (CHRs) that modulate the position of nucleosomes on chromatin. During plant stress responses, CHRs are recruited to specific genomic loci, where they regulate the distribution or composition of nucleosomes, which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery. Moreover, CHRs interplay with other epigenetic mechanisms, including DNA methylation, histone modifications, and deposition of histone variants. CHRs are also involved in RNA processing at the post-transcriptional level. In this review, we discuss major advances in our understanding of the mechanisms by which CHRs function during plants' response to environmental stress.
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Affiliation(s)
- Ze-Ting Song
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500, China
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Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021; 22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023] Open
Abstract
Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
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Bhadouriya SL, Mehrotra S, Basantani MK, Loake GJ, Mehrotra R. Role of Chromatin Architecture in Plant Stress Responses: An Update. FRONTIERS IN PLANT SCIENCE 2021; 11:603380. [PMID: 33510748 PMCID: PMC7835326 DOI: 10.3389/fpls.2020.603380] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 05/08/2023]
Abstract
Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression. DNA methylation and histone modification are crucial for genome reprogramming for tissue-specific gene expression and global gene silencing. Different classes of chromatin remodelers including SWI/SNF, ISWI, INO80, and CHD are reported to act upon chromatin in different organisms, under diverse stresses, to convert chromatin from a transcriptionally inactive to a transcriptionally active state. The architecture of chromatin at a given promoter is crucial for determining the transcriptional readout. Further, the connection between somatic memory and chromatin modifications may suggest a mechanistic basis for a stress memory. Studies have suggested that there is a functional connection between changes in nuclear organization and stress conditions. In this review, we discuss the role of chromatin architecture in different stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Sneha Lata Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Mahesh K. Basantani
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow, India
| | - Gary J. Loake
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburg, Edinburg, United Kingdom
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
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Nishad A, Nandi AK. Recent advances in plant thermomemory. PLANT CELL REPORTS 2021; 40:19-27. [PMID: 32975635 DOI: 10.1007/s00299-020-02604-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/13/2020] [Indexed: 05/04/2023]
Abstract
This review summarizes the process of thermal acquired tolerance in plants and the knowledge gap compared to systemic acquired resistance that a plant shows after pathogen inoculation. Plants are continuously challenged by several biotic stresses such as pests and pathogens, or abiotic stresses like high light, UV radiation, drought, salt, and very high or low temperature. Interestingly, for most stresses, prior exposure makes plants more tolerant during the subsequent exposures, which is often referred to as acclimatization. Research of the last two decades reveals that the memory of most of the stresses is associated with epigenetic changes. Heat stress causes damage to membrane proteins, denaturation and inactivation of various enzymes, and accumulation of reactive oxygen species leading to cell injury and death. Plants are equipped with thermosensors that can recognize certain specific changes and activate protection machinery. Phytochrome and calcium signaling play critical roles in sensing sudden changes in temperature and activate cascades of signaling, leading to the production of heat shock proteins (HSPs) that keep protein-unfolding under control. Heat shock factors (HSFs) are the transcription factors that read the activation of thermosensors and induce the expression of HSPs. Epigenetic modifications of HSFs are likely to be the key component of thermal acquired tolerance (TAT). Despite the advances in understanding the process of thermomemory generation, it is not known whether plants are equipped with systemic activation thermal protection, as happens in the form of systemic acquired resistance (SAR) upon pathogen infection. This review describes the recent advances in the understanding of thermomemory development in plants and the knowledge gap in comparison with SAR.
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Affiliation(s)
- Anand Nishad
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India
| | - Ashis Kumar Nandi
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India.
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43
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Zhang YM, Guo P, Xia X, Guo H, Li Z. Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives. FRONTIERS IN PLANT SCIENCE 2021; 12:788996. [PMID: 34938309 PMCID: PMC8685244 DOI: 10.3389/fpls.2021.788996] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 05/22/2023]
Abstract
Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.
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Affiliation(s)
- Yue-Mei Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pengru Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhonghai Li,
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Plant Responses to Heat Stress: Physiology, Transcription, Noncoding RNAs, and Epigenetics. Int J Mol Sci 2020; 22:ijms22010117. [PMID: 33374376 PMCID: PMC7795586 DOI: 10.3390/ijms22010117] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 01/05/2023] Open
Abstract
Global warming has increased the frequency of extreme high temperature events. High temperature is a major abiotic stress that limits the growth and production of plants. Therefore, the plant response to heat stress (HS) has been a focus of research. However, the plant response to HS involves complex physiological traits and molecular or gene networks that are not fully understood. Here, we review recent progress in the physiological (photosynthesis, cell membrane thermostability, oxidative damage, and others), transcriptional, and post-transcriptional (noncoding RNAs) regulation of the plant response to HS. We also summarize advances in understanding of the epigenetic regulation (DNA methylation, histone modification, and chromatin remodeling) and epigenetic memory underlying plant–heat interactions. Finally, we discuss the challenges and opportunities of future research in the plant response to HS.
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Epigenetics and epigenomics: underlying mechanisms, relevance, and implications in crop improvement. Funct Integr Genomics 2020; 20:739-761. [PMID: 33089419 DOI: 10.1007/s10142-020-00756-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023]
Abstract
Epigenetics is defined as changes in gene expression that are not associated with changes in DNA sequence but due to the result of methylation of DNA and post-translational modifications to the histones. These epigenetic modifications are known to regulate gene expression by bringing changes in the chromatin state, which underlies plant development and shapes phenotypic plasticity in responses to the environment and internal cues. This review articulates the role of histone modifications and DNA methylation in modulating biotic and abiotic stresses, as well as crop improvement. It also highlights the possibility of engineering epigenomes and epigenome-based predictive models for improving agronomic traits.
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Guo Z, Li Z, Liu Y, An Z, Peng M, Shen WH, Dong A, Yu Y. MRG1/2 histone methylation readers and HD2C histone deacetylase associate in repression of the florigen gene FT to set a proper flowering time in response to day-length changes. THE NEW PHYTOLOGIST 2020; 227:1453-1466. [PMID: 32315442 DOI: 10.1111/nph.16616] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/07/2020] [Indexed: 05/26/2023]
Abstract
Day-length changes represent an important cue for modulating flowering time. In Arabidopsis, the expression of the florigen gene FLOWERING LOCUS T (FT) exhibits a 24-h circadian rhythm under long-day (LD) conditions. Here we focus on the chromatin-based mechanism regarding the control of FT expression. We conducted co-immunoprecipitation assays along with LC-MS/MS analysis and identified HD2C histone deacetylase as the binding protein of the H3K4/H3K36 methylation reader MRG2. HD2C and MRG1/2 regulate flowering time under LD conditions, but not under short-day conditions. Moreover, HD2C functions as an effective deacetylase in planta, mainly targeting H3K9ac, H3K23ac and H3K27ac. At dusk, HD2C is recruited to FT to deacetylate histones and repress transcription in an MRG1/2-dependent manner. More importantly, HD2C competes with CO for the binding of MRG2, and the accumulation of HD2C at the FT locus occurs at the end of the day. Our findings not only reveal a histone deacetylation mechanism contributing to prevent FT overexpression and precocious flowering, but also support the model in which the histone methylation readers MRG1/2 provide a platform on chromatin for connecting regulatory factors involved in activating FT expression in response to daylight and decreasing FT expression around dusk under long days.
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Affiliation(s)
- Zhihao Guo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zepeng Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- CNRS, IBMP UPR 2357, Université de Strasbourg, Strasbourg, F-67000, France
| | - Yuhao Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zengxuan An
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Maolin Peng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- CNRS, IBMP UPR 2357, Université de Strasbourg, Strasbourg, F-67000, France
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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Chen J, Clinton M, Qi G, Wang D, Liu F, Fu ZQ. Reprogramming and remodeling: transcriptional and epigenetic regulation of salicylic acid-mediated plant defense. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5256-5268. [PMID: 32060527 DOI: 10.1093/jxb/eraa072] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/11/2020] [Indexed: 05/13/2023]
Abstract
As a plant hormone, salicylic acid (SA) plays essential roles in plant defense against biotrophic and hemibiotrophic pathogens. Significant progress has been made in understanding the SA biosynthesis pathways and SA-mediated defense signaling networks in the past two decades. Plant defense responses involve rapid and massive transcriptional reprogramming upon the recognition of pathogens. Plant transcription factors and their co-regulators are critical players in establishing a transcription regulatory network and boosting plant immunity. A multitude of transcription factors and epigenetic regulators have been discovered, and their roles in SA-mediated defense responses have been reported. However, our understanding of plant transcriptional networks is still limited. As such, novel genomic tools and bioinformatic techniques will be necessary if we are to fully understand the mechanisms behind plant immunity. Here, we discuss current knowledge, provide an update on the SA biosynthesis pathway, and describe the transcriptional and epigenetic regulation of SA-mediated plant immune responses.
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Affiliation(s)
- Jian Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, P. R. China
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Michael Clinton
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Guang Qi
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
- State Key Laboratory of Wheat and Maize Crop Science and College of Agronomy, Henan Agricultural University, Zhengzhou, P. R. China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science and College of Agronomy, Henan Agricultural University, Zhengzhou, P. R. China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, P. R. China
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
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48
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Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
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Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
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Yu Y, Liang Z, Song X, Fu W, Xu J, Lei Y, Yuan L, Ruan J, Chen C, Fu W, Cui Y, Huang S, Li C. BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes. NATURE PLANTS 2020; 6:996-1007. [PMID: 32747760 DOI: 10.1038/s41477-020-0734-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/29/2020] [Indexed: 05/22/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodelling complexes are multi-protein machineries that control gene expression by regulating chromatin structure in eukaryotes. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we report that in Arabidopsis thaliana, two homologous glioma tumour suppressor candidate region domain-containing proteins, named BRAHMA-interacting proteins 1 (BRIP1) and BRIP2, are core subunits of plant SWI/SNF complexes. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome remarkably similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and BRIP2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and BRIP2 physically interact with BRM-containing SWI/SNF complexes and extensively co-localize with BRM on chromatin. Simultaneous mutation of BRIP1 and BRIP2 results in decreased BRM occupancy at almost all BRM target loci and substantially reduced abundance of the SWI/SNF assemblies. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants and uncovers the essential role of these subunits in maintaining the abundance of SWI/SNF complexes in plants.
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Affiliation(s)
- Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yawen Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chen Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Wenqun Fu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
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50
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Kong L, Liu Y, Wang X, Chang C. Insight into the Role of Epigenetic Processes in Abiotic and Biotic Stress Response in Wheat and Barley. Int J Mol Sci 2020; 21:ijms21041480. [PMID: 32098241 PMCID: PMC7073019 DOI: 10.3390/ijms21041480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Environmental stresses such as salinity, drought, heat, freezing, heavy metal and even pathogen infections seriously threaten the growth and yield of important cereal crops including wheat and barley. There is growing evidence indicating that plants employ sophisticated epigenetic mechanisms to fine-tune their responses to environmental stresses. Here, we provide an overview of recent developments in understanding the epigenetic processes and elements—such as DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs—involved in plant responses to abiotic and biotic stresses in wheat and barley. Potentials of exploiting epigenetic variation for the improvement of wheat and barley are discussed.
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Affiliation(s)
- Lingyao Kong
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Yanna Liu
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- Correspondence: ; Tel.: +86-532-85953227
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