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Sanjuan-Badillo A, P. Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2024; 19:2353536. [PMID: 38771929 PMCID: PMC11110687 DOI: 10.1080/15592324.2024.2353536] [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: 02/27/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.
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Affiliation(s)
- Andrea Sanjuan-Badillo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Programa de Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México, Ciudad de México, México
| | - León P. Martínez-Castilla
- Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | | | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, España
| | - Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Huang Y, Liu J, Cheng L, Xu D, Liu S, Hu H, Ling Y, Yang R, Zhang Y. Genome-Wide Analysis of the Histone Modification Gene ( HM) Family and Expression Investigation during Anther Development in Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:2496. [PMID: 39273980 PMCID: PMC11396841 DOI: 10.3390/plants13172496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
Histone modification plays a crucial role in chromatin remodeling and regulating gene expression, and participates in various biological processes, including plant development and responses to stress. Several gene families related to histone modification have been reported in various plant species. However, the identification of members and their functions in the rice (Oryza sativa L.) histone modification gene family (OsHM) at the whole-genome level remains unclear. In this study, a total of 130 OsHMs were identified through a genome-wide analysis. The OsHM gene family can be classified into 11 subfamilies based on a phylogenetic analysis. An analysis of the genes structures and conserved motifs indicates that members of each subfamily share specific conserved protein structures, suggesting their potential conserved functions. Molecular evolutionary analysis reveals that a significant number of OsHMs proteins originated from gene duplication events, particularly segmental duplications. Additionally, transcriptome analysis demonstrates that OsHMs are widely expressed in various tissues of rice and are responsive to multiple abiotic stresses. Fourteen OsHMs exhibit high expression in rice anthers and peaked at different pollen developmental stages. RT-qPCR results further elucidate the expression patterns of these 14 OsHMs during different developmental stages of anthers, highlighting their high expression during the meiosis and tetrad stages, as well as in the late stage of pollen development. Remarkably, OsSDG713 and OsSDG727 were further identified to be nucleus-localized. This study provides a fundamental framework for further exploring the gene functions of HMs in plants, particularly for researching their functions and potential applications in rice anthers' development and male sterility.
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Affiliation(s)
- Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jiawei Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Long Cheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Duo Xu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Sijia Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Hanqiao Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Rongchao Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
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Frings S, Schmidt-Schippers R, Lee WK. Epigenetic alterations in bioaccumulators of cadmium: Lessons from mammalian kidneys and plants. ENVIRONMENT INTERNATIONAL 2024; 191:109000. [PMID: 39278047 DOI: 10.1016/j.envint.2024.109000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 08/07/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024]
Abstract
Faced with unpredictable changes in global weather patterns, release and redistribution of metals through land erosion and water movements add to the increasing use of metals in industrial activities causing high levels of environmental pollution and concern to the health of all living organisms. Cadmium is released into the environment by smelting and mining, entering the food chain via contaminated soils, water, and phosphate fertilizers. Bioaccumulation of cadmium in plants represents the first major step into the human food chain and contributes to toxicity of several organs, especially the kidneys, where biomagnification of cadmium occurs over decades of exposure. Even in small amounts, cadmium brings about alterations at the molecular and cellular levels in eukaryotes through mutagenicity, molecular mimicry at metal binding sites and oxidative stress. The epigenome dictates expression of a gene's output through a number of regulatory steps involving chromatin remodeling, nucleosome unwinding, DNA accessibility, or nucleic acid modifications that ultimately impact the transcriptional and translational machinery. Several epigenetic enzymes exhibit zinc-dependence as zinc metalloenzymes and zinc finger proteins thus making them susceptible to deregulation through displacement by cadmium. In this review, we summarize the literature on cadmium-induced epigenetic mechanisms in mammalian kidneys and plants, compare similarities in the epigenetic defense between these bioaccumulators, and explore how future studies could advance our understanding of the cadmium-induced stress response and disruption to biological health.
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Affiliation(s)
- Stephanie Frings
- Center for Biotechnology, University of Bielefeld, 33615 Bielefeld, Germany; Plant Biotechnology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Romy Schmidt-Schippers
- Center for Biotechnology, University of Bielefeld, 33615 Bielefeld, Germany; Plant Biotechnology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wing-Kee Lee
- Physiology and Pathophysiology of Cells and Membranes, Medical School OWL, Bielefeld University, 33615 Bielefeld, Germany.
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Dard A, Van Breusegem F, Mhamdi A. Redox regulation of gene expression: proteomics reveals multiple previously undescribed redox-sensitive cysteines in transcription complexes and chromatin modifiers. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4476-4493. [PMID: 38642390 DOI: 10.1093/jxb/erae177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Redox signalling is crucial for regulating plant development and adaptation to environmental changes. Proteins with redox-sensitive cysteines can sense oxidative stress and modulate their functions. Recent proteomics efforts have comprehensively mapped the proteins targeted by oxidative modifications. The nucleus, the epicentre of transcriptional reprogramming, contains a large number of proteins that control gene expression. Specific redox-sensitive transcription factors have long been recognized as key players in decoding redox signals in the nucleus and thus in regulating transcriptional responses. Consequently, the redox regulation of the nuclear transcription machinery and its cofactors has received less attention. In this review, we screened proteomic datasets for redox-sensitive cysteines on proteins of the core transcription complexes and chromatin modifiers in Arabidopsis thaliana. Our analysis indicates that redox regulation affects every step of gene transcription, from initiation to elongation and termination. We report previously undescribed redox-sensitive subunits in transcription complexes and discuss the emerging challenges in unravelling the landscape of redox-regulated processes involved in nuclear gene transcription.
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Affiliation(s)
- Avilien Dard
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Amna Mhamdi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
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Wang F, Li CH, Liu Y, He LF, Li P, Guo JX, Zhang N, Zhao B, Guo YD. Plant responses to abiotic stress regulated by histone acetylation. FRONTIERS IN PLANT SCIENCE 2024; 15:1404977. [PMID: 39081527 PMCID: PMC11286584 DOI: 10.3389/fpls.2024.1404977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024]
Abstract
In eukaryotes, histone acetylation and deacetylation play an important role in the regulation of gene expression. Histone acetylation levels are reversibly regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Increasing evidence highlights histone acetylation plays essential roles in the regulation of gene expression in plant response to environmental stress. In this review, we discussed the recent advance of histone acetylation in the regulation of abiotic stress responses including temperature, light, salt and drought stress. This information will contribute to our understanding of how plants adapt to environmental changes. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in improvement of agricultural productivity.
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Affiliation(s)
- Fei Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Chong-Hua Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ying Liu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ling-Feng He
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ping Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jun-Xin Guo
- College of Horticulture, China Agricultural University, Beijing, China
| | - Na Zhang
- College of Horticulture, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Bing Zhao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yang-Dong Guo
- College of Horticulture, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
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Traubenik S, Charon C, Blein T. From environmental responses to adaptation: the roles of plant lncRNAs. PLANT PHYSIOLOGY 2024; 195:232-244. [PMID: 38246143 DOI: 10.1093/plphys/kiae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
As sessile organisms, plants are continuously exposed to heterogeneous and changing environments and constantly need to adapt their growth strategies. They have evolved complex mechanisms to recognize various stress factors, activate appropriate signaling pathways, and respond accordingly by reprogramming the expression of multiple genes at the transcriptional, post-transcriptional, and even epigenome levels to tolerate stressful conditions such as drought, high temperature, nutrient deficiency, and pathogenic interactions. Apart from protein-coding genes, long non-coding RNAs (lncRNAs) have emerged as key players in plant adaptation to environmental stresses. They are transcripts larger than 200 nucleotides without protein-coding potential. Still, they appear to regulate a wide range of processes, including epigenetic modifications and chromatin reorganization, as well as transcriptional and post-transcriptional modulation of gene expression, allowing plant adaptation to various environmental stresses. LncRNAs can positively or negatively modulate stress responses, affecting processes such as hormone signaling, temperature tolerance, and nutrient deficiency adaptation. Moreover, they also seem to play a role in stress memory, wherein prior exposure to mild stress enhances plant ability to adapt to subsequent stressful conditions. In this review, we summarize the contribution of lncRNAs in plant adaptation to biotic and abiotic stresses, as well as stress memory. The complex evolutionary conservation of lncRNAs is also discussed and provides insights into future research directions in this field.
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Affiliation(s)
- Soledad Traubenik
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Céline Charon
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Thomas Blein
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
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7
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Han J, Wang L, Tang X, Liu R, Shi L, Zhu J, Zhao M. Glsirt1-mediated deacetylation of GlCAT regulates intracellular ROS levels, affecting ganoderic acid biosynthesis in Ganoderma lucidum. Free Radic Biol Med 2024; 216:1-11. [PMID: 38458391 DOI: 10.1016/j.freeradbiomed.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Lysine acetylation is a reversible, dynamic protein modification regulated by lysine acetyltransferases and deacetylases. However, in Basidiomycetes, the extent of lysine acetylation of nonhistone proteins remains largely unknown. Recently, we identified the deacetylase Glsirt1 as a key regulator of the biosynthesis of ganoderic acid (GA), a key secondary metabolite of Ganoderma lucidum. To gain insight into the characteristics, extent, and biological function of Glsirt1-mediated lysine acetylation in G. lucidum, we aimed to identify additional Glsirt1 substrates via comparison of acetylomes between wild-type (WT) and Glsirt1-silenced mutants. A large amount of Glsirt1-dependent lysine acetylation occurs in G. lucidum according to the results of this omics analysis, involving energy metabolism, protein synthesis, the stress response and other pathways. Our results suggest that GlCAT is a direct target of Glsirt1 and that the deacetylation of GlCAT by Glsirt1 reduces catalase activity, thereby leading to the accumulation of intracellular reactive oxygen species (ROS) and positively regulating the biosynthesis of GA. Our findings provide evidence for the involvement of nonhistone lysine acetylation in the biological processes of G. lucidum and help elucidate the involvement of important ROS signaling molecules in regulating physiological and biochemical processes in this organism. In conclusion, this proteomic analysis reveals a striking breadth of cellular processes affected by lysine acetylation and provides new nodes of intervention in the biosynthesis of secondary metabolites in G. lucidum.
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Affiliation(s)
- Jing Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Lingshuai Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Xin Tang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Rui Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
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Cheng YJ, Wang JW, Ye R. Histone dynamics responding to internal and external cues underlying plant development. PLANT PHYSIOLOGY 2024; 194:1980-1997. [PMID: 38124490 DOI: 10.1093/plphys/kiad676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.
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Affiliation(s)
- Ying-Juan Cheng
- College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Ruiqiang Ye
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
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Bajpai SK, Nisha, Pandita S, Bahadur A, Verma PC. Recent advancements in the role of histone acetylation dynamics to improve stress responses in plants. Mol Biol Rep 2024; 51:413. [PMID: 38472555 DOI: 10.1007/s11033-024-09300-3] [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: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
In eukaryotes, transcriptional regulation is determined by the DNA sequence and is facilitated through sophisticated and complex chromatin alterations and histone remodelling. Recent research has shown that the histone acetylation dynamic, an intermittent and reversible substitution, constitutes a prerequisite for chromatin modification. These changes in chromatin structure modulate genome-wide and specific changes in response to external and internal cues like cell differentiation, development, growth, light temperature, and biotic stresses. Histone acetylation dynamics also control the cell cycle. HATs and HDACs play a critical role in gene expression modulation during plant growth and response to environmental circumstances. It has been well established that HATs and HDACs interact with various distinct transcription factors and chromatin-remodelling proteins (CRPs) involved in the transcriptional regulation of several developmental processes. This review explores recent research on histone acyltransferases and histone deacetylases, mainly focusing on their involvement in plant biotic stress responses. Moreover, we also emphasized the research gaps that must be filled to fully understand the complete function of histone acetylation dynamics during biotic stress responses in plants. A thorough understanding of histone acetylation will make it possible to enhance tolerance against various kinds of stress and decrease yield losses in many crops.
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Affiliation(s)
- Sanjay Kumar Bajpai
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Nisha
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Shivali Pandita
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Anand Bahadur
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh, 226007, India
| | - Praveen C Verma
- Molecular Biology & Biotechnology Division, CSIR-National Botanical Research Institute, (Council of Scientific and Industrial Research) Rana Pratap Marg, Lucknow, UP, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Chen CY, Shao Z, Wang G, Zhao B, Hardtke HA, Leong J, Zhou T, Zhang YJ, Qiao H. Histone acetyltransferase HAF2 associates with PDC to control H3K14ac and H3K23ac in ethylene response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573642. [PMID: 38260516 PMCID: PMC10802238 DOI: 10.1101/2023.12.31.573642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprogramming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. However, the histone acetyltransferase in this process remains unknown. Here, we identified histone acetyltransferase HAF2, and mutations in HAF2 confer plants with ethylene insensitivity. Furthermore, we found that HAF2 interacts with EIN2-C in response to ethylene. Biochemical assays demonstrated that the bromodomain of HAF2 binds to H3K14ac and H3K23ac peptides with a distinct affinity for H3K14ac; the HAT domain possesses acetyltransferase catalytic activity for H3K14 and H3K23 acetylation, with a preference for H3K14. ChIP-seq results provide additional evidence supporting the role of HAF2 in regulating H3K14ac and H3K23ac levels in response to ethylene. Finally, our findings revealed that HAF2 co-functions with pyruvate dehydrogenase complex (PDC) to regulate H3K14ac and H3K23ac in response to ethylene in an EIN2 dependent manner. Overall, this research reveals that HAF2 as a histone acetyltransferase that forms a complex with EIN2-C and PDC, collectively governing histone acetylation of H3H14ac and H3K23ac, preferentially for H3K14 in response to ethylene.
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Khan RA, Abbas N. Role of epigenetic and post-translational modifications in anthocyanin biosynthesis: A review. Gene 2023; 887:147694. [PMID: 37574116 DOI: 10.1016/j.gene.2023.147694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/18/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023]
Abstract
Anthocyanins are a class of flavonoids having antioxidant and anti-inflammatory properties. They defend plants against various biotic and abiotic stresses and are synthesized by a specific branch of the flavonoid biosynthetic pathway. Different regulatory mechanisms have been found to regulate anthocyanin biosynthesis in plants. These include the MYB-bHLH-WDR (MBW) MBW trimeric complex consisting of bHLH, R2R3 MYB, and WD40 transcription factors. Epigenetic and Post-translational modification (PTMs) of MBW complex and various other transcription factors play important role in both plant developmental processes and modulating plant response to different environmental conditions. Recent studies have broadened our understanding of the role of various epigenetic (methylation and histone modification) and PTMs (phosphorylation, acetylation, ubiquitylation, sumoylation, etc.) mechanisms in regulating anthocyanin biosynthesis in plants. In this review, we are updating various epigenetic and PTMs modifications of various transcription factors which regulate anthocyanin biosynthesis in various plants. In addition to this, we have also briefly discussed in which direction future research on epigenetic and PTMs can be taken so that we can engineer medicinal plants for enhanced secondary metabolite biosynthesis.
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Affiliation(s)
- Rameez Ahmad Khan
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K 190005, India; Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180001, India.
| | - Nazia Abbas
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, J&K 190005, India; Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi 180001, India.
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12
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Balbinott N, Margis R. The many faces of lysine acylation in proteins: Phytohormones as unexplored substrates. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111866. [PMID: 37714383 DOI: 10.1016/j.plantsci.2023.111866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Protein post-translational modification (PTM) is a ubiquitous process that occurs in most proteins. Lysine residues containing an ε-amino group are recognized as hotspots for the addition of different chemical groups. Lysine acetylation, extensively studied in histones, serves as an epigenetic hallmark capable of promoting changes in chromatin structure and availability. Acyl groups derived from molecules involved in carbohydrate and lipid metabolisms, such as lactate, succinate and hydroxybutyrate, were identified as lysine modifications of histones and other proteins. Lysine-acyltransferases do not exhibit significant substrate specificity concerning acyl donors. Furthermore, plant hormones harboring acyl groups often form conjugates with free amino acids to regulate their activity and function during plant physiological processes and responses, a process mediated by GH3 enzymes. Besides forming low-molecular weight conjugates, auxins have been shown to covalently modify proteins in bean seeds. Aside from auxins, other phytohormones with acyl groups are unexplored potential substrates for post-translational acylation of proteins. Using MS data searches, we revealed various proteins with lysine residues linked to auxin, abscisic acid, gibberellic acid, jasmonic acid, and salicylic acid. These findings raise compelling questions about the ability of plant hormones harboring carboxyl groups to serve as new candidates for protein acylation and acting in protein PTM and modulation.
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Affiliation(s)
- Natalia Balbinott
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rogerio Margis
- Programa de Pós-graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Programa de Pós-graduação em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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13
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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14
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Ivanova T, Dincheva I, Badjakov I, Iantcheva A. Transcriptional and Metabolic Profiling of Arabidopsis thaliana Transgenic Plants Expressing Histone Acetyltransferase HAC1 upon the Application of Abiotic Stress-Salt and Low Temperature. Metabolites 2023; 13:994. [PMID: 37755274 PMCID: PMC10536276 DOI: 10.3390/metabo13090994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023] Open
Abstract
Augmented knowledge of plant responses upon application of stress could help improve our understanding of plant tolerance under abiotic stress conditions. Histone acetylation plays an important role in gene expression regulation during plant growth and development and in the response of plants to abiotic stress. The current study examines the level of transcripts and free metabolite content in transgenic Arabidopsis thaliana plants expressing a gene encoding histone acetyltransferase from Medicago truncatula (MtHAC1) after its heterologous expression. Stable transgenic plants with HAC1 gain and loss of function were constructed, and their T5 generation was used. Transgenic lines with HAC1-modified expression showed a deviation in root growth dynamics and leaf area compared to the wild-type control. Transcriptional profiles were evaluated after the application of salinity stress caused by 150 mM NaCl at four different time points (0, 24, 48, and 72 h) in treated and non-treated transgenic and control plants. The content and quantity of free metabolites-amino acids, mono- and dicarbohydrates, organic acids, and fatty acids-were assessed at time points 0 h and 72 h in treated and non-treated transgenic and control plants. The obtained transcript profiles of HAC1 in transgenic plants with modified expression and control were assessed after application of cold stress (low temperature, 4 °C).
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Affiliation(s)
| | | | | | - Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tzankov 8, 1164 Sofia, Bulgaria; (T.I.); (I.D.); (I.B.)
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15
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Schott J, Jantzen F, Hilker M. Elm tree defences against a specialist herbivore are moderately primed by an infestation in the previous season. TREE PHYSIOLOGY 2023; 43:1218-1232. [PMID: 37010106 PMCID: PMC10335851 DOI: 10.1093/treephys/tpad038] [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: 09/02/2022] [Revised: 03/06/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
The studies of the long-term effects of insect infestations on plant anti-herbivore defences tend to focus on feeding-induced damage. Infestations by an entire insect generation, including egg depositions as well as the feeding insects, are often neglected. Whilst there is increasing evidence that the presence of insect eggs can intensify plants' anti-herbivore defences against hatching larvae in the short term, little is known about how insect infestations, including insect egg depositions, affect plant defences in the long term. We addressed this knowledge gap by investigating long-term effects of insect infestation on elm's (Ulmus minor Mill. cv. 'Dahlem') defences against subsequent infestation. In greenhouse experiments, elms were exposed to elm leaf beetle (ELB, Xanthogaleruca luteola) infestation (adults, eggs and larvae). Thereafter, the trees cast their leaves under simulated winter conditions and were re-infested with ELB after the regrowth of their leaves under simulated summer conditions. Elm leaf beetles performed moderately worse on previously infested elms with respect to several developmental parameters. The concentrations of the phenylpropanoids kaempferol and quercetin, which are involved in egg-mediated, short-term effects on elm defences, were slightly higher in the ELB-challenged leaves of previously infested trees than in the challenged leaves of naïve trees. The expression of several genes involved in the phenylpropanoid pathway, jasmonic acid signalling, and DNA and histone modifications appeared to be affected by ELB infestation; however, prior infestation did not alter the expression intensities of these genes. The concentrations of several phytohormones were similarly affected in the currently challenged leaves of previously infested trees and naïve trees. Our study shows that prior infestation of elms by a specialised insect leads to moderately improved defences against subsequent infestation in the following growing season. Prior infestation adds a long-term effect to the short-term enhancer effect that plants show in response to egg depositions when defending against hatching larvae.
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Affiliation(s)
- Johanna Schott
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Haderslebener Str. 9, 12163 Berlin, Germany
| | - Friederike Jantzen
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Haderslebener Str. 9, 12163 Berlin, Germany
| | - Monika Hilker
- Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Haderslebener Str. 9, 12163 Berlin, Germany
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16
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Lee SW, Choi D, Moon H, Kim S, Kang H, Paik I, Huq E, Kim DH. PHYTOCHROME-INTERACTING FACTORS are involved in starch degradation adjustment via inhibition of the carbon metabolic regulator QUA-QUINE STARCH in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:110-123. [PMID: 36710626 DOI: 10.1111/tpj.16124] [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: 04/27/2021] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
As sessile organisms, plants encounter dynamic and challenging environments daily, including abiotic/biotic stresses. The regulation of carbon and nitrogen allocations for the synthesis of plant proteins, carbohydrates, and lipids is fundamental for plant growth and adaption to its surroundings. Light, one of the essential environmental signals, exerts a substantial impact on plant metabolism and resource partitioning (i.e., starch). However, it is not fully understood how light signaling affects carbohydrate production and allocation in plant growth and development. An orphan gene unique to Arabidopsis thaliana, named QUA-QUINE STARCH (QQS) is involved in the metabolic processes for partitioning of carbon and nitrogen among proteins and carbohydrates, thus influencing leaf, seed composition, and plant defense in Arabidopsis. In this study, we show that PHYTOCHROME-INTERACTING bHLH TRANSCRIPTION FACTORS (PIFs), including PIF4, are required to suppress QQS during the period at dawn, thus preventing overconsumption of starch reserves. QQS expression is significantly de-repressed in pif4 and pifQ, while repressed by overexpression of PIF4, suggesting that PIF4 and its close homologs (PIF1, PIF3, and PIF5) act as negative regulators of QQS expression. In addition, we show that the evening complex, including ELF3 is required for active expression of QQS, thus playing a positive role in starch catabolism during night-time. Furthermore, QQS is epigenetically suppressed by DNA methylation machinery, whereas histone H3 K4 methyltransferases (e.g., ATX1, ATX2, and ATXR7) and H3 acetyltransferases (e.g., HAC1 and HAC5) are involved in the expression of QQS. This study demonstrates that PIF light signaling factors help plants utilize optimal amounts of starch during the night and prevent overconsumption of starch before its biosynthesis during the upcoming day.
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Affiliation(s)
- Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sujeong Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hajeong Kang
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Inyup Paik
- Department of Molecular Biosciences, the University of Texas at Austin, Texas, 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences, the University of Texas at Austin, Texas, 78712, USA
| | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
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17
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Wang T, Wang J, Chen L, Yao J, Yuan Z, Zhang D, Zhang WH. Reorganization of three-dimensional chromatin architecture in Medicago truncatula under phosphorus deficiency. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2005-2015. [PMID: 36573619 PMCID: PMC10049915 DOI: 10.1093/jxb/erac517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Emerging evidence reveals that the three-dimensional (3D) chromatin architecture plays a key regulatory role in various biological processes of plants. However, information on the 3D chromatin architecture of the legume model plant Medicago truncatula and its potential roles in the regulation of response to mineral nutrient deficiency are very limited. Using high-resolution chromosome conformation capture sequencing, we identified the 3D genome structure of M. truncatula in terms of A/B compartments, topologically associated domains (TADs) and chromatin loops. The gene density, expressional level, and active histone modification were higher in A compartments than in B compartments. Moreover, we analysed the 3D chromatin architecture reorganization in response to phosphorus (P) deficiency. The intra-chromosomal cis-interaction proportion was increased by P deficiency, and a total of 748 A/B compartment switch regions were detected. In these regions, density changes in H3K4me3 and H3K27ac modifications were associated with expression of P deficiency-responsive genes involved in root system architecture and hormonal responses. Furthermore, these genes enhanced P uptake and mobilization by increasing root surface area and strengthening signal transduction under P deficiency. These findings advance our understanding of the potential roles of 3D chromatin architecture in responses of plants in general, and in particular in M. truncatula, to P deficiency.
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Affiliation(s)
| | - Jing Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, P. R. China
- University of Chinese Academy of Sciences, the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Li Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, P. R. China
- University of Chinese Academy of Sciences, the Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiaying Yao
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Zan Yuan
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Dong Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Wen-Hao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, P. R. China
- University of Chinese Academy of Sciences, the Chinese Academy of Sciences, Beijing 100049, P. R. China
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18
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Guo Y, Tan Y, Qu M, Hong K, Zeng L, Wang L, Zhuang C, Qian Q, Hu J, Xiong G. OsWR2 recruits HDA704 to regulate the deacetylation of H4K8ac in the promoter of OsABI5 in response to drought stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36920174 DOI: 10.1111/jipb.13481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is a major environmental factor that limits the growth, development, and yield of rice (Oryza sativa L.). Histone deacetylases (HDACs) are involved in the regulation of drought stress responses. HDA704 is an RPD3/HDA1 class HDAC that mediates the deacetylation of H4K8 (lysine 8 of histone H4) for drought tolerance in rice. In this study, we show that plants overexpressing HDA704 (HDA704-OE) are resistant to drought stress and sensitive to abscisic acid (ABA), whereas HDA704 knockout mutant (hda704) plants displayed decreased drought tolerance and ABA sensitivity. Transcriptome analysis revealed that HDA704 regulates the expression of ABA-related genes in response to drought stress. Moreover, HDA704 was recruited by a drought-resistant transcription factor, WAX SYNTHESIS REGULATORY 2 (OsWR2), and co-regulated the expression of the ABA biosynthesis genes NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3), NCED4, and NCED5 under drought stress. HDA704 also repressed the expression of ABA-INSENSITIVE 5 (OsABI5) and DWARF AND SMALL SEED 1 (OsDSS1) by regulating H4K8ac levels in the promoter regions in response to polyethylene glycol 6000 treatment. In agreement, the loss of OsABI5 function increased resistance to dehydration stress in rice. Our results demonstrate that HDA704 is a positive regulator of the drought stress response and offers avenues for improving drought resistance in rice.
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Affiliation(s)
- Yalu Guo
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yiqing Tan
- Plant Phenomics Research Center, Academy of Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Minghao Qu
- College of Animal Science and Technology, Southwest University, Chongqing, 402460, China
| | - Kai Hong
- Plant Phenomics Research Center, Academy of Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Longjun Zeng
- Yichun Academy of Sciences, Yinchun, 336000, China
| | - Lei Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Chuxiong Zhuang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Guosheng Xiong
- Plant Phenomics Research Center, Academy of Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
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19
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Jiang K, Guo H, Zhai J. Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:381-398. [PMID: 36223083 DOI: 10.1111/jipb.13384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.
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Affiliation(s)
- Kai Jiang
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
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20
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Jia H, Zuo Q, Sadeghnezhad E, Zheng T, Chen X, Dong T, Fang J. HDAC19 recruits ERF4 to the MYB5a promoter and diminishes anthocyanin accumulation during grape ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:127-144. [PMID: 36423230 DOI: 10.1111/tpj.16040] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
DNA acetylation alters the expression of responsive genes during plant development. In grapes (Vitis vinifera), however, little is known about this regulatory mechanism. In the present study, 'Kyoho' grapes treated with trichostatin A (TSA, a deacetylase inhibitor) were used for transcriptome sequencing and quantitative proteomics analysis. We observed that acetylation was associated with anthocyanin accumulation and gene expression. Acetylation positively regulated phenylalanine metabolism and flavonoid biosynthesis pathways. Using omics analysis, we detected an increase in the levels of the AP2/EREBP transcription factor family after TSA treatment, indicating its association with acetylation-deacetylation dynamics in grapes. Furthermore, ethylene response factor 4 (ERF4) physically interacted with VvHDAC19, a histone deacetylase, which synergistically reduced the expression of target genes involved in anthocyanin biosynthesis owing to the binding of VvERF4 to the GCC-box cis-regulatory element in the VvMYB5a promoter. VvHDAC19 and VvERF4 also controlled anthocyanin biosynthesis and accumulation by regulating acetylation levels of histones H3 and H4. Therefore, alterations in histone modification can significantly regulate the expression of genes involved in anthocyanin biosynthesis and affect grape ripening.
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Affiliation(s)
- Haifeng Jia
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
- NJAU (Suqian) Academy of Protected Horticultures, Suqian, China
| | - Qianqian Zuo
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ehsan Sadeghnezhad
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Ting Zheng
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Xueqin Chen
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - Tianyu Dong
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
| | - JinggGui Fang
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, 1st Weigang Rd., Nanjing, 210095, China
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21
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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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Affiliation(s)
| | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Programa de Dinámica y Función del Genoma, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Programa de Dinámica y Función del Genoma, Madrid, Spain
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22
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Zhang Z, Yang W, Chu Y, Yin X, Liang Y, Wang Q, Wang L, Han Z. AtHD2D, a plant-specific histone deacetylase involved in abscisic acid response and lateral root development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7380-7400. [PMID: 36125085 DOI: 10.1093/jxb/erac381] [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: 02/07/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
In eukaryotes, histone acetylation levels directly regulate downstream gene expression. As a plant-specific histone deacetylase (HDAC), HD2D is involved in plant development and abiotic stress. However, the response of HD2D to drought stress and its interacting proteins, is still unclear. In this study, we analysed HD2D gene expression patterns in Arabidopsis, revealing that HD2D gene was highly expressed in roots and rosette leaves, but poorly expressed in other tissues such as stems, flowers, and young siliques. The HD2D gene expression was induced by d-mannitol. We investigated the responses to drought stress in the wild-type plant, HD2D overexpression lines, and hd2d mutants. HD2D-overexpressing lines showed abscisic acid (ABA) hypersensitivity and drought tolerance, and these phenotypes were not present in hd2d mutants. RNA-seq analysis revealed the transcriptome changes caused by HD2D under drought stress, and showed that HD2D responded to drought stress via the ABA signalling pathway. In addition, we demonstrated that CASEIN KINASE II (CKA4) directly interacted with HD2D. The phosphorylation of Ser residues on HD2D by CKA4 enhanced HD2D enzymatic activity. Furthermore, the phosphorylation of HD2D was shown to contribute to lateral root development and ABA sensing in Arabidopsis, but, these phenotypes could not be reproduced by the overexpression of Ser-phospho-null HD2D lines. Collectively, this study suggests that HD2D responded to drought stress by regulating the ABA signalling pathway, and the expression of drought stress-related genes. The regulatory mechanism of HD2D mediated by CKII phosphorylation provides new insights into the ABA response and lateral root development in Arabidopsis.
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Affiliation(s)
- Zhaochen Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Weixia Yang
- College of Chemistry & Pharmacy, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueqi Liang
- College of Innovation and Experiment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Qiuping Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Lei Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
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23
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Histone Deacetylase HDA15 Restrains PHYB-Dependent Seed Germination via Directly Repressing GA20ox1/2 Gene Expression. Cells 2022; 11:cells11233788. [PMID: 36497048 PMCID: PMC9735612 DOI: 10.3390/cells11233788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/12/2022] [Accepted: 11/20/2022] [Indexed: 11/29/2022] Open
Abstract
Seed germination is essential for the colonization of the land plants. Light is a major environmental factor affecting seed germination, which is predominantly regulated by photoreceptor phytochrome B (PHYB). PHYB is activated by red light (designated as PHYB-on) whereas it is inactivated by far-red light (referred as PHYB-off). We previously reported that Arabidopsis histone deacetylase HDA15 interacts with phytochrome-interacting factor1 (PIF1) to repress seed germination under PHYB-off conditions. Here, we show that HDA15 plays a negative role in regulating seed germination under PHYB-on conditions. Overexpression of HDA15 in Arabidopsis restrains PHYB-dependent seed germination, while gibberellin (GA) relieves the repressive role of HDA15 under PHYB-off conditions. We further show that HDA15 directly binds to GA20ox1 and GA20ox2, two key GA biosynthesis genes and represses their expression by removal of histone H3 and H4 acetylation. Moreover, the levels of HDA15 transcript and HDA15 protein are up-regulated in the phyB mutant. Collectively, our work proposes that HDA15 acts as a negative regulator of PHYB-dependent seed germination by directly repressing GA20ox1/2 gene expression.
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Patitaki E, Schivre G, Zioutopoulou A, Perrella G, Bourbousse C, Barneche F, Kaiserli E. Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:333-349. [PMID: 35949052 PMCID: PMC9826491 DOI: 10.1111/nph.18424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/26/2022] [Indexed: 05/31/2023]
Abstract
The plant nucleus provides a major hub for environmental signal integration at the chromatin level. Multiple light signaling pathways operate and exchange information by regulating a large repertoire of gene targets that shape plant responses to a changing environment. In addition to the established role of transcription factors in triggering photoregulated changes in gene expression, there are eminent reports on the significance of chromatin regulators and nuclear scaffold dynamics in promoting light-induced plant responses. Here, we report and discuss recent advances in chromatin-regulatory mechanisms modulating plant architecture and development in response to light, including the molecular and physiological roles of key modifications such as DNA, RNA and histone methylation, and/or acetylation. The significance of the formation of biomolecular condensates of key light signaling components is discussed and potential applications to agricultural practices overviewed.
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Affiliation(s)
- Eirini Patitaki
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Geoffrey Schivre
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
- Université Paris‐SaclayOrsay91400France
| | - Anna Zioutopoulou
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Giorgio Perrella
- Department of BiosciencesUniversity of MilanVia Giovanni Celoria, 2620133MilanItaly
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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Liao HS, Yang CC, Hsieh MH. Nitrogen deficiency- and sucrose-induced anthocyanin biosynthesis is modulated by HISTONE DEACETYLASE15 in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3726-3742. [PMID: 35182426 DOI: 10.1093/jxb/erac067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Anthocyanin accumulation is a hallmark response to nitrogen (N) deficiency in Arabidopsis. Although the regulation of anthocyanin biosynthesis has been extensively studied, the roles of chromatin modification in this process are largely unknown. In this study we show that anthocyanin accumulation induced by N deficiency is modulated by HISTONE DEACETYLASE15 (HDA15) in Arabidopsis seedlings. The hda15-1 T-DNA insertion mutant accumulated more anthocyanins than the wild-type when the N supply was limited, and this was caused by up-regulation of anthocyanin biosynthetic and regulatory genes in the mutant. The up-regulated genes also had increased levels of histone acetylation in the mutant. The accumulation of anthocyanins induced by sucrose and methyl jasmonate, but not that induced by H2O2 and phosphate starvation, was also greater in the hda15-1 mutant. While sucrose increased histone acetylation in the hda15-1 mutant in genes in a similar manner to that caused by N deficiency, methyl jasmonate only enhanced histone acetylation in the genes involved in anthocyanin biosynthesis. Our results suggest that different stresses act through distinct regulatory modules to activate anthocyanin biosynthesis, and that HDA15-mediated histone modification modulates the expression of anthocyanin biosynthetic and regulatory genes to avoid overaccumulation in response to N deficiency and other stresses.
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Affiliation(s)
- Hong-Sheng Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
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Chu L, Yang C, Zhuang F, Gao Y, Luo M. The HDA9‐HY5 module epigenetically regulates flowering time in
Arabidopsis thaliana. J Cell Physiol 2022; 237:2961-2968. [DOI: 10.1002/jcp.30761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 01/20/2023]
Affiliation(s)
- Liutian Chu
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
| | - Feng Zhuang
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Yingmiao Gao
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany & Agriculture and Biotechnology Research Center South China Botanical Garden, Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences Guangzhou China
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Popular Science Guangzhou China
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Chen Q, Zhang J, Li G. Dynamic epigenetic modifications in plant sugar signal transduction. TRENDS IN PLANT SCIENCE 2022; 27:379-390. [PMID: 34865981 DOI: 10.1016/j.tplants.2021.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 05/21/2023]
Abstract
In eukaryotes, dynamic chromatin states are closely related to changes in gene expression. Epigenetic modifications help plants adapt to their ever-changing environment by modulating gene expression via covalent modification at specific sites on DNA or histones. Sugars provide energy, but also function as signaling molecules to control plant growth and development. Various epigenetic modifications participate in sensing and transmitting sugar signals. Here we summarize recent progress in uncovering the epigenetic mechanisms involved in sugar signal transduction, including histone acetylation and deacetylation, histone methylation and demethylation, and DNA methylation. We also highlight changes in chromatin marks when crosstalk occurs between sugar signaling and the light, temperature, and phytohormone signaling pathways, and describe potential questions and approaches for future research.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, Shandong, China; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, Shandong, China.
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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González-Grandío E, Álamos S, Zhang Y, Dalton-Roesler J, Niyogi KK, García HG, Quail PH. Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light. FRONTIERS IN PLANT SCIENCE 2022; 13:803441. [PMID: 35251080 PMCID: PMC8891703 DOI: 10.3389/fpls.2022.803441] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/27/2022] [Indexed: 05/11/2023]
Abstract
As sessile organisms, plants must adapt to a changing environment, sensing variations in resource availability and modifying their development in response. Light is one of the most important resources for plants, and its perception by sensory photoreceptors (e.g., phytochromes) and subsequent transduction into long-term transcriptional reprogramming have been well characterized. Chromatin changes have been shown to be involved in photomorphogenesis. However, the initial short-term transcriptional changes produced by light and what factors enable these rapid changes are not well studied. Here, we define rapidly light-responsive, Phytochrome Interacting Factor (PIF) direct-target genes (LRP-DTGs). We found that a majority of these genes also show rapid changes in Histone 3 Lysine-9 acetylation (H3K9ac) in response to the light signal. Detailed time-course analysis of transcript and chromatin changes showed that, for light-repressed genes, H3K9 deacetylation parallels light-triggered transcriptional repression, while for light-induced genes, H3K9 acetylation appeared to somewhat precede light-activated transcript accumulation. However, direct, real-time imaging of transcript elongation in the nucleus revealed that, in fact, transcriptional induction actually parallels H3K9 acetylation. Collectively, the data raise the possibility that light-induced transcriptional and chromatin-remodeling processes are mechanistically intertwined. Histone modifying proteins involved in long term light responses do not seem to have a role in this fast response, indicating that different factors might act at different stages of the light response. This work not only advances our understanding of plant responses to light, but also unveils a system in which rapid chromatin changes in reaction to an external signal can be studied under natural conditions.
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Affiliation(s)
- Eduardo González-Grandío
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
- *Correspondence: Eduardo González-Grandío,
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, United States
| | - Yu Zhang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Jutta Dalton-Roesler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Hernán G. García
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Physics, University of California, Berkeley, Berkeley, CA, United States
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, United States
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, United States
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
- Peter H. Quail,
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Zhao H, Bao Y. PIF4: Integrator of light and temperature cues in plant growth. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111086. [PMID: 34763871 DOI: 10.1016/j.plantsci.2021.111086] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/18/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Plants are sessile and lack behavioural responses to avoid extreme environmental changes linked to annual seasons. For survival, they have evolved elaborate sensory systems coordinating their architecture and physiology with fluctuating diurnal and seasonal temperatures. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) was initially identified as a key component of the Arabidopsis thaliana phytochrome signalling pathway. It was then identified as playing a central role in promoting plant hypocotyl growth via the activation of auxin synthesis and signalling-related genes. Recent studies expanded its known regulatory functions to thermomorphogenesis and defined PIF4 as a central molecular hub for the integration of environmental light and temperature cues. The present review comprehensively summarizes recent progress in our understanding of PIF4 function in Arabidopsis thaliana, including PIF4-mediated photomorphogenesis and thermomorphogenesis, and the contribution of PIF4 to plant growth via the integration of environmental light and temperature cues. Remaining questions and possible directions for future research on PIF4 are also discussed.
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Affiliation(s)
- Hang Zhao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China.
| | - Ying Bao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China
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Gao S, Zeng X, Wang J, Xu Y, Yu C, Huang Y, Wang F, Wu K, Yang S. Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering. Cells 2021; 10:cells10113001. [PMID: 34831226 PMCID: PMC8616286 DOI: 10.3390/cells10113001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/31/2021] [Indexed: 01/12/2023] Open
Abstract
The changes in histone acetylation mediated by histone deacetylases (HDAC) play a crucial role in plant development and response to environmental changes. Mammalian HDACs are regulated by post-translational modifications (PTM), such as phosphorylation, acetylation, ubiquitination and small ubiquitin-like modifier (SUMO) modification (SUMOylation), which affect enzymatic activity and transcriptional repression. Whether PTMs of plant HDACs alter their functions are largely unknown. In this study, we demonstrated that the Arabidopsis SUMO E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HISTONE DEACETYLASE 6 (HDA6) both in vitro and in vivo. Biochemical analyses indicated that HDA6 is not modified by SUMO1. Overexpression of HDA6 in siz1-3 background results in a decreased level of histone H3 acetylation, indicating that the activity of HDA6 is increased in siz1-3 plants. Chromatin immunoprecipitation (ChIP) assays showed that SIZ1 represses HDA6 binding to its target genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING 4 (MAF4), resulting in the upregulation of FLC and MAF4 by increasing the level of histone H3 acetylation. Together, these findings indicate that the Arabidopsis SUMO E3 ligase SIZ1 interacts with HDA6 and negatively regulates HDA6 function.
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Affiliation(s)
- Sujuan Gao
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Ministry of Agriculture, Guangzhou 510225, China;
| | - Xueqin Zeng
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510000, China;
| | - Yingchao Xu
- 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; (Y.X.); (Y.H.)
| | - Chunwei Yu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Yishui Huang
- 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; (Y.X.); (Y.H.)
| | - Feng Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
- Correspondence: (K.W.); (S.Y.)
| | - Songguang Yang
- 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; (Y.X.); (Y.H.)
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (K.W.); (S.Y.)
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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Li S, He X, Gao Y, Zhou C, Chiang VL, Li W. Histone Acetylation Changes in Plant Response to Drought Stress. Genes (Basel) 2021; 12:genes12091409. [PMID: 34573391 PMCID: PMC8468061 DOI: 10.3390/genes12091409] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Drought stress causes recurrent damage to a healthy ecosystem because it has major adverse effects on the growth and productivity of plants. However, plants have developed drought avoidance and resilience for survival through many strategies, such as increasing water absorption and conduction, reducing water loss and conversing growth stages. Understanding how plants respond and regulate drought stress would be important for creating and breeding better plants to help maintain a sound ecosystem. Epigenetic marks are a group of regulators affecting drought response and resilience in plants through modification of chromatin structure to control the transcription of pertinent genes. Histone acetylation is an ubiquitous epigenetic mark. The level of histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines whether the chromatin is open or closed, thereby controlling access of DNA-binding proteins for transcriptional activation. In this review, we summarize histone acetylation changes in plant response to drought stress, and review the functions of HATs and HDACs in drought response and resistance.
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Affiliation(s)
- Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
- Correspondence: ; Tel.: +86-15114585206
| | - Xu He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Yuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
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Smolikova G, Strygina K, Krylova E, Leonova T, Frolov A, Khlestkina E, Medvedev S. Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:1884. [PMID: 34579418 PMCID: PMC8467299 DOI: 10.3390/plants10091884] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023]
Abstract
Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ksenia Strygina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Ekaterina Krylova
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Khlestkina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
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Barrero-Gil J, Mouriz A, Piqueras R, Salinas J, Jarillo JA, Piñeiro M. A MRG-operated chromatin switch at SOC1 attenuates abiotic stress responses during the floral transition. PLANT PHYSIOLOGY 2021; 187:462-471. [PMID: 34618146 PMCID: PMC8418395 DOI: 10.1093/plphys/kiab275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Plants react to environmental challenges by integrating external cues with endogenous signals to optimize survival and reproductive success. However, the mechanisms underlying this integration remain obscure. While stress conditions are known to impact plant development, how developmental transitions influence responses to adverse conditions has not been addressed. Here, we reveal a molecular mechanism of stress response attenuation during the onset of flowering in Arabidopsis (Arabidopsis thaliana). We show that Arabidopsis MORF-RELATED GENE (MRG) proteins, components of the NuA4 histone acetyltransferase complex that bind trimethylated-lysine 36 in histone H3 (H3K36me3), function as a chromatin switch on the floral integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) to coordinate flowering initiation with plant responsiveness to hostile environments. MRG proteins are required to activate SOC1 expression during flowering induction by promoting histone H4 acetylation. In turn, SOC1 represses a broad array of genes that mediate abiotic stress responses. We propose that during the transition from vegetative to reproductive growth, the MRG-SOC1 module constitutes a central hub in a mechanism that tunes down stress responses to enhance the reproductive success and plant fitness at the expense of costly efforts for adaptation to challenging environments.
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Affiliation(s)
- Javier Barrero-Gil
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Raquel Piqueras
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - José A. Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
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Vall-Llaura N, Torres R, Lindo-García V, Muñoz P, Munné-Bosch S, Larrigaudière C, Teixidó N, Giné-Bordonaba J. PbSRT1 and PbSRT2 regulate pear growth and ripening yet displaying a species-specific regulation in comparison to other Rosaceae spp. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110925. [PMID: 34034873 DOI: 10.1016/j.plantsci.2021.110925] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/15/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic regulation is crucial to ensure a coordinated control of the different events that occur during fruit development and ripening. Sirtuins are NAD+-dependent histone deacetylases involved in the regulation of gene expression of many biological processes. However, their implications in the Rosaceae family remains unexplored. Accordingly, in this work, we demonstrated the phylogenetic divergence of both sirtuins among Rosaceae species. We then characterized the expression pattern of both SRT1 and SRT2 in selected pome and stone fruit species. Both SRT1 and SRT2 significantly changed during the fruit development and ripening of apple, nectarine and pear fruit, displaying a different expression profile. Such differences could explain in part their different ripening behaviour. To further unravel the role of sirtuins on the fruit development and ripening processes, a deeper analysis was performed using pear as a fruit model. In pear, PbSRT1 gene expression levels were negatively correlated with specific hormones (i.e. abscisic acid, indole-3-acetic acid, gibberellin A1 and zeatin) during the first phases of fruit development. PbSRT2 seemed to directly mediate pear ripening in an ethylene-independent manner. This hypothesis was further reinforced by treating the fruit with the ethylene inhibitor 1-methylcyclopropene (1-MCP). Instead, enhanced PbSRT2 along pear growth/ripening positively correlated with the accumulation of major sugars (R2 > 0.94), reinforcing the idea that sugar metabolism may be a target of epigenetic modifications during fruit ripening. Overall, the results from this study point out, for the first time, the importance that sirtuins have in the regulation of fruit growth and ripening of pear fruit by likely regulating hormonal and sugar metabolism.
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Affiliation(s)
- Núria Vall-Llaura
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Rosario Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Violeta Lindo-García
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Paula Muñoz
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, 08028, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), University of Barcelona, Barcelona, 08028, Spain.
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, 08028, Spain; Institut de Nutrició i Seguretat Alimentària (INSA), University of Barcelona, Barcelona, 08028, Spain.
| | - Christian Larrigaudière
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Neus Teixidó
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
| | - Jordi Giné-Bordonaba
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Catalonia, 25003, Spain.
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Niekerk LA, Carelse MF, Bakare OO, Mavumengwana V, Keyster M, Gokul A. The Relationship between Cadmium Toxicity and the Modulation of Epigenetic Traits in Plants. Int J Mol Sci 2021; 22:ijms22137046. [PMID: 34209014 PMCID: PMC8268939 DOI: 10.3390/ijms22137046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 01/17/2023] Open
Abstract
Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort to improve Cd tolerance, studies have identified genetic mechanisms which could be important for conferring stress tolerance. In recent years epigenetic studies have garnered much attention and hold great potential in both improving the understanding of Cd stress in plants as well as revealing candidate mechanisms for future work. This review describes some of the main epigenetic mechanisms involved in Cd stress responses. We summarize recent literature and data pertaining to chromatin remodeling, DNA methylation, histone acetylation and miRNAs in order to understand the role these epigenetic traits play in cadmium tolerance. The review aims to provide the framework for future studies where these epigenetic traits may be used in plant breeding and molecular studies in order to improve Cd tolerance.
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Affiliation(s)
- Lee-Ann Niekerk
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Mogamat Fahiem Carelse
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Olalekan Olanrewaju Bakare
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
| | - Vuyo Mavumengwana
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Tygerberg Campus, Stellenbosch University, Cape Town 7505, South Africa;
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (M.F.C.); (O.O.B.)
- Correspondence: (M.K.); (A.G.); Tel.: +27-587185392 (M.K. & A.G.)
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthadithjaba 9866, South Africa
- Correspondence: (M.K.); (A.G.); Tel.: +27-587185392 (M.K. & A.G.)
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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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Vlachonasios KE. Histone acetylation: a requirement for petunia floral scent. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3493-3495. [PMID: 33948651 PMCID: PMC8096597 DOI: 10.1093/jxb/erab092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article comments on: Patrick RM, Huang X-Q, Dudareva N, Li Y. 2021. Dynamic histone acetylation in floral volatile synthesis and emission in petunia flowers. Journal of Experimental Botany 72, 3704–3722.
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Affiliation(s)
- Konstantinos E Vlachonasios
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, Greece
- Natural Products Research Centre of Excellence (NatPro-AUTh), Center of Interdisciplinary Research and Innovation of Aristotle University of Thessaloniki (CIRI-AUTh), Thessaloniki, Greece
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42
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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43
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Liu H, Timko MP. Jasmonic Acid Signaling and Molecular Crosstalk with Other Phytohormones. Int J Mol Sci 2021; 22:ijms22062914. [PMID: 33805647 PMCID: PMC8000993 DOI: 10.3390/ijms22062914] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Plants continually monitor their innate developmental status and external environment and make adjustments to balance growth, differentiation and stress responses using a complex and highly interconnected regulatory network composed of various signaling molecules and regulatory proteins. Phytohormones are an essential group of signaling molecules that work through a variety of different pathways conferring plasticity to adapt to the everchanging developmental and environmental cues. Of these, jasmonic acid (JA), a lipid-derived molecule, plays an essential function in controlling many different plant developmental and stress responses. In the past decades, significant progress has been made in our understanding of the molecular mechanisms that underlie JA metabolism, perception, signal transduction and its crosstalk with other phytohormone signaling pathways. In this review, we discuss the JA signaling pathways starting from its biosynthesis to JA-responsive gene expression, highlighting recent advances made in defining the key transcription factors and transcriptional regulatory proteins involved. We also discuss the nature and degree of crosstalk between JA and other phytohormone signaling pathways, highlighting recent breakthroughs that broaden our knowledge of the molecular bases underlying JA-regulated processes during plant development and biotic stress responses.
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44
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Genome-Wide Identification and Expression Analysis of the Histone Deacetylase Gene Family in Wheat ( Triticum aestivum L.). PLANTS 2020; 10:plants10010019. [PMID: 33374252 PMCID: PMC7823868 DOI: 10.3390/plants10010019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 12/16/2022]
Abstract
Histone acetylation is a dynamic modification process co-regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDACs play vital roles in abiotic or biotic stress responses, their members in Triticumaestivum and their response to plant viruses remain unknown. Here, we identified and characterized 49 T. aestivumHDACs (TaHDACs) at the whole-genome level. Based on phylogenetic analyses, TaHDACs could be divided into 5 clades, and their protein spatial structure was integral and conserved. Chromosomal location and synteny analyses showed that TaHDACs were widely distributed on wheat chromosomes, and gene duplication has accelerated the TaHDAC gene family evolution. The cis-acting element analysis indicated that TaHDACs were involved in hormone response, light response, abiotic stress, growth, and development. Heatmaps analysis of RNA-sequencing data showed that TaHDAC genes were involved in biotic or abiotic stress response. Selected TaHDACs were differentially expressed in diverse tissues or under varying temperature conditions. All selected TaHDACs were significantly upregulated following infection with the barley stripe mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV), and wheat yellow mosaic virus (WYMV), suggesting their involvement in response to viral infections. Furthermore, TaSRT1-silenced contributed to increasing wheat resistance against CWMV infection. In summary, these findings could help deepen the understanding of the structure and characteristics of the HDAC gene family in wheat and lay the foundation for exploring the function of TaHDACs in plants resistant to viral infections.
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45
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Parry G, Pradillo M, Probst AV, Tatout C. Untangling chromatin interactions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5115-5118. [PMID: 32803270 DOI: 10.1093/jxb/eraa334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
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Grasser KD, Rubio V, Barneche F. Multifaceted activities of the plant SAGA complex. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194613. [PMID: 32745625 DOI: 10.1016/j.bbagrm.2020.194613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Abstract
From yeast to human, the Spt-Ada-GCN5-acetyltransferase (SAGA) gigantic complex modifies chromatin during RNA polymerase II initiation and elongation steps to facilitate transcription. Its enzymatic activity involves a histone acetyltransferase module (HATm) that acetylates multiple lysine residues on the N-terminal tails of histones H2B and H3 and a deubiquitination module (DUBm) that triggers co-transcriptional deubiquitination of histone H2B. With a few notable exceptions described in this review, most SAGA subunits identified in yeast and metazoa are present in plants. Studies from the last 20 years have unveiled that different SAGA subunits are involved in gene expression regulation during the plant life cycle and in response to various types of stress or environmental cues. Their functional analysis in the Arabidopsis thaliana model species is increasingly shedding light on their intrinsic properties and how they can themselves be regulated during plant adaptive responses. Recent biochemical studies have also uncovered multiple associations between plant SAGA and chromatin machineries linked to RNA Pol II transcription. Still, considerably less is known about the molecular links between SAGA or SAGA-like complexes and chromatin dynamics during transcription in Arabidopsis and other plant species. We summarize the emerging knowledge on plant SAGA complex composition and activity, with a particular focus on the best-characterized subunits from its HAT (such as GCN5) and DUB (such as UBP22) modules, and implication of these ensembles in plant development and adaptive responses.
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Affiliation(s)
- Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
| | - Vicente Rubio
- Plant Molecular Genetics Dept., Centro Nacional de Biotecnología (CNB-CSIC), Darwin, 3, 28049 Madrid, Spain.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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