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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Ayyappan V, Sripathi VR, Xie S, Saha MC, Hayford R, Serba DD, Subramani M, Thimmapuram J, Todd A, Kalavacharla VK. Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass. BMC Genomics 2024; 25:223. [PMID: 38424499 PMCID: PMC10903042 DOI: 10.1186/s12864-024-10068-w] [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: 09/05/2022] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. RESULTS In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. CONCLUSION Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA.
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN, 47907, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Rita Hayford
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Desalegn D Serba
- USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA.
| | - Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
| | | | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
| | - Venu Kal Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
- Center for Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, DE, 19901, USA
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Wang J, Liang Y, Gong Z, Zheng J, Li Z, Zhou G, Xu Y, Li X. Genomic and epigenomic insights into the mechanism of cold response in upland cotton (Gossypium hirsutum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108206. [PMID: 38029617 DOI: 10.1016/j.plaphy.2023.108206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
Functional genome research, including gene transcriptional and posttranslational modifications of histones, can benefit greatly from a high-quality genome assembly. Histone modification plays a significant role in modulating the responses to abiotic stress in plants. However, there are limited reports on the involvement of dynamic changes in histone modification in cold stress response in upland cotton. In this study, the genome of an elite accession, YM11, with considerable cold stress tolerance was de novo assembled, which yielded a genome of 2343.06 Mb with a contig N50 of 88.96 Mb, and a total of 73,821 protein-coding gene models were annotated. Comparisons among YM11 and five Gossypium allopolyploid cotton assemblies highlighted a large amount of structural variations and presence/absence variations. We analyzed transcriptome and metabolome changes in YM11 seedlings subjected to cold stress. Using the CUT&Tag method, genome-wide H3K4me3 and H3K9ac modification patterns and effect of histone changes on gene expression were profiled during cold stress. Significant and consistently changing histone modifications and the gene expressions were screened, of which transcription factors (TFs) were highlighted. Our results suggest a positive correlation between the changes in H3K4me3, H3K9ac modifications and cold stress-responsive gene activation. This genome assembly and comprehensive analysis of genome-wide histone modifications and gene expression provide insights into the genomic variation and epigenetic responses to cold stress in upland cotton.
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Affiliation(s)
- Junduo Wang
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Yajun Liang
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Juyun Zheng
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi, 830022, Xinjiang, China
| | - Guohui Zhou
- Adsen Biotechnology Co., Ltd., Urumqi, 830022, Xinjiang, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumqi, 830022, Xinjiang, China.
| | - Xueyuan Li
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China.
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Ferrari M, Muto A, Bruno L, Cozza R. DNA Methylation in Algae and Its Impact on Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:241. [PMID: 36678953 PMCID: PMC9861306 DOI: 10.3390/plants12020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.
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Kourani M, Mohareb F, Rezwan FI, Anastasiadi M, Hammond JP. Genetic and Physiological Responses to Heat Stress in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:832147. [PMID: 35449889 PMCID: PMC9016328 DOI: 10.3389/fpls.2022.832147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 05/07/2023]
Abstract
Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.
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Affiliation(s)
- Mariam Kourani
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
- *Correspondence: Fady Mohareb,
| | - Faisal I. Rezwan
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Maria Anastasiadi
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
- John P. Hammond,
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Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021; 22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023] Open
Abstract
Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
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Rai KK, Pandey N, Meena RP, Rai SP. Biotechnological strategies for enhancing heavy metal tolerance in neglected and underutilized legume crops: A comprehensive review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111750. [PMID: 33396075 DOI: 10.1016/j.ecoenv.2020.111750] [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: 05/22/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 05/15/2023]
Abstract
Contamination of agricultural land and water by heavy metals due to rapid industrialization and urbanization including various natural processes have become one of the major constraints to crop growth and productivity. Several studies have reported that to counteract heavy metal stress, plants should be able to maneuver various physiological, biochemical and molecular processes to improve their growth and development under heavy metal stress. With the advent of modern biotechnological tools and techniques it is now possible to tailor legume and other plants overexpressing stress-induced genes, transcription factors, proteins, and metabolites that are directly involved in heavy metal stress tolerance. This review provides an in-depth overview of various biotechnological approaches and/or strategies that can be used for enhancing detoxification of the heavy metals by stimulating phytoremediation processes. Synthetic biology tools involved in the engineering of legume and other crop plants against heavy metal stress tolerance are also discussed herewith some pioneering examples where synthetic biology tools that have been used to modify plants for specific traits. Also, CRISPR based genetic engineering of plants, including their role in modulating the expression of several genes/ transcription factors in the improvement of abiotic stress tolerance and phytoremediation ability using knockdown and knockout strategies has also been critically discussed.
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Affiliation(s)
- Krishna Kumar Rai
- Centre of Advance Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Neha Pandey
- Centre of Advance Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi 221005, Uttar Pradesh, India; Department of Botany, CMP PG College, University of Allahabad, Prayagraj, India
| | - Ram Prasad Meena
- Centre of Advance Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi 221005, Uttar Pradesh, India; Department of Computer Science, IIT, Banaras Hindu University (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Shashi Pandey Rai
- Centre of Advance Study in Botany, Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi 221005, Uttar Pradesh, India.
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Zhu C, Zhang S, Zhou C, Chen L, Fu H, Li X, Lin Y, Lai Z, Guo Y. Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant ( Camellia sinensis) under abiotic stress and withering processing. PeerJ 2020; 8:e8432. [PMID: 31976183 PMCID: PMC6968495 DOI: 10.7717/peerj.8432] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants (Camellia sinensis) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET, CsCMT, CsDRM and CsDNMT2. The CsdMTase genes can be classified into CsROS, CsDME and CsDML. Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase. Furthermore, multiple cis-acting elements were observed in the CsC5-MTase and CsdMTase, including light responsiveness, phytohormone responsiveness, stress responsiveness, and plant growth and development-related elements. Then, we investigated the transcript abundance of CsC5-MTase and CsdMTase under abiotic stress (cold and drought) and withering processing (white tea and oolong tea). Notably, most CsC5-MTases, except for CsCMT1 and CsCMT2, were significantly downregulated under abiotic stress, while the transcript abundance of all four CsdMTase genes was significantly induced. Similarly, the same transcript abundance of CsC5-MTase and CsdMTase was found during withering processing of white tea and oolong tea, respectively. In total, our findings will provide a basis for the roles of CsC5-MTase and CsdMTase in response to abiotic stress and the potential functions of these two gene families in affecting tea flavor during tea withering processing.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Roy S, Kumar V, Bossier P, Norouzitallab P, Vanrompay D. Phloroglucinol Treatment Induces Transgenerational Epigenetic Inherited Resistance Against Vibrio Infections and Thermal Stress in a Brine Shrimp ( Artemia franciscana) Model. Front Immunol 2019; 10:2745. [PMID: 31827471 PMCID: PMC6890837 DOI: 10.3389/fimmu.2019.02745] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/08/2019] [Indexed: 01/05/2023] Open
Abstract
Emerging, infectious diseases in shrimp like acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus and mortality caused by other Vibrio species such as Vibrio harveyi are worldwide related to huge economic losses in industrial shrimp production. As a strategy to prevent disease outbreaks, a plant-based phenolic compound could be used as a biocontrol agent. Here, using the brine shrimp (Artemia franciscana) as a model system, we showed that phloroglucinol treatment of the parental animals at early life stages resulted in transgenerational inherited increased resistance in their progeny against biotic stress, i.e., bacteria (V. parahaemolyticus AHPND strain and V. harveyi) and abiotic stress, i.e., lethal heat shock. Increased resistance was recorded in three subsequent generations. Innate immune-related gene expression profiles and potential epigenetic mechanisms were studied to discover the underlying protective mechanisms. Our results showed that phloroglucinol treatment of the brine shrimp parents significantly (P < 0.05) enhanced the expression of a core set of innate immune genes (DSCAM, proPO, PXN, HSP90, HSP70, and LGBP) in subsequent generations. We also demonstrated that epigenetic mechanisms such as DNA methylation, m6A RNA methylation, and histone acetylation and methylation (active chromatin marker i.e., H3K4Me3, H3K4me1, H3K27me1, H3 hyperacetylation, H3K14ac and repression marker, i.e., H3K27me3, H4 hypoacetylation) might play a role in regulation of gene expression leading toward the observed transgenerational inheritance of the resistant brine shrimp progenies. To our knowledge, this is the first report on transgenerational inheritance of a compound-induced robust protected phenotype in brine shrimp, particularly protected against AHPND caused by V. parahaemolyticus and vibriosis caused by V. harveyi. Results showed that epigenetic reprogramming is likely to play a role in the underlying mechanism.
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Affiliation(s)
- Suvra Roy
- Laboratory of Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Vikash Kumar
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- ICAR-Central Inland Fisheries Research Institute, Barrackpore, India
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Parisa Norouzitallab
- Laboratory of Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Daisy Vanrompay
- Laboratory of Immunology and Animal Biotechnology, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Lee HG, Seo PJ. MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun 2019. [PMID: 30979883 DOI: 10.1038/s41467-019-09417-9411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Unlike activation of target genes in response to abscisic acid (ABA), how MYB96 transcription factor represses ABA-repressible genes to further enhance ABA responses remains unknown. Here, we show MYB96 interacts with the histone modifier HDA15 to suppress negative regulators of early ABA signaling. The MYB96-HDA15 complex co-binds to the promoters of a subset of RHO GTPASE OF PLANTS (ROP) genes, ROP6, ROP10, and ROP11, and represses their expression by removing acetyl groups of histone H3 and H4 from the cognate regions, particularly in the presence of ABA. In support, HDA15-deficient mutants display reduced ABA sensitivity and are susceptible to drought stress with derepression of the ROP genes, as observed in the myb96-1 mutant. Biochemical and genetic analyses show that MYB96 and HDA15 are interdependent in the regulation of ROP suppression. Thus, MYB96 confers maximal ABA sensitivity by regulating both positive and negative regulators of ABA signaling through distinctive molecular mechanisms.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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Lee HG, Seo PJ. MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun 2019; 10:1713. [PMID: 30979883 PMCID: PMC6461653 DOI: 10.1038/s41467-019-09417-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Unlike activation of target genes in response to abscisic acid (ABA), how MYB96 transcription factor represses ABA-repressible genes to further enhance ABA responses remains unknown. Here, we show MYB96 interacts with the histone modifier HDA15 to suppress negative regulators of early ABA signaling. The MYB96-HDA15 complex co-binds to the promoters of a subset of RHO GTPASE OF PLANTS (ROP) genes, ROP6, ROP10, and ROP11, and represses their expression by removing acetyl groups of histone H3 and H4 from the cognate regions, particularly in the presence of ABA. In support, HDA15-deficient mutants display reduced ABA sensitivity and are susceptible to drought stress with derepression of the ROP genes, as observed in the myb96-1 mutant. Biochemical and genetic analyses show that MYB96 and HDA15 are interdependent in the regulation of ROP suppression. Thus, MYB96 confers maximal ABA sensitivity by regulating both positive and negative regulators of ABA signaling through distinctive molecular mechanisms. MYB96 can regulate both positive and negative regulators of ABA signaling to maximize plant drought tolerance. Here, the authors show that MYB96 represses expression of ABA negative regulators in Arabidopsis by interacting with HDA15 and promoting histone deacetylation at the cognate regions.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea. .,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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Shokri-Gharelo R, Noparvar PM. Molecular response of canola to salt stress: insights on tolerance mechanisms. PeerJ 2018; 6:e4822. [PMID: 29844974 PMCID: PMC5969047 DOI: 10.7717/peerj.4822] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 01/16/2023] Open
Abstract
Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.
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Affiliation(s)
- Reza Shokri-Gharelo
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Pouya Motie Noparvar
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran.,Young Researchers and Elite Club, Islamic Azad University, Tabriz, Iran
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QTL Analysis for Drought Tolerance in Wheat: Present Status and Future Possibilities. AGRONOMY-BASEL 2017. [DOI: 10.3390/agronomy7010005] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Banerjee A, Wani SH, Roychoudhury A. Epigenetic Control of Plant Cold Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:1643. [PMID: 28983309 PMCID: PMC5613158 DOI: 10.3389/fpls.2017.01643] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/07/2017] [Indexed: 05/19/2023]
Affiliation(s)
- Aditya Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College-AutonomousKolkata, India
| | - Shabir H. Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of KashmirSrinagar, India
- Department of Plant Soil and Microbial Sciences, Michigan State UniversityEast Lansing, MI, United States
- *Correspondence: Shabir H. Wani
| | - Aryadeep Roychoudhury
- Post Graduate Department of Biotechnology, St. Xavier's College-AutonomousKolkata, India
- Aryadeep Roychoudhury
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Allu AD, Simancas B, Balazadeh S, Munné-Bosch S. Defense-Related Transcriptional Reprogramming in Vitamin E-Deficient Arabidopsis Mutants Exposed to Contrasting Phosphate Availability. FRONTIERS IN PLANT SCIENCE 2017; 8:1396. [PMID: 28848594 PMCID: PMC5554346 DOI: 10.3389/fpls.2017.01396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/26/2017] [Indexed: 05/06/2023]
Abstract
Vitamin E inhibits the propagation of lipid peroxidation and helps protecting photosystem II from photoinhibition, but little is known about its possible role in plant response to Pi availability. Here, we aimed at examining the effect of vitamin E deficiency in Arabidopsis thaliana vte mutants on phytohormone contents and the expression of transcription factors in plants exposed to contrasting Pi availability. Plants were subjected to two doses of Pi, either unprimed (controls) or previously exposed to low Pi (primed). In the wild type, α-tocopherol contents increased significantly in response to repeated periods of low Pi, which was paralleled by increased growth, indicative of a priming effect. This growth-stimulating effect was, however, abolished in vte mutants. Hormonal profiling revealed significant effects of Pi availability, priming and genotype on the contents of jasmonates and salicylates; remarkably, vte mutants showed enhanced accumulation of both hormones under low Pi. Furthermore, expression profiling of 1,880 transcription factors by qRT-PCR revealed a pronounced effect of priming on the transcript levels of 45 transcription factors mainly associated with growth and stress in wild-type plants in response to low Pi availability; while distinct differences in the transcriptional response were detected in vte mutants. We conclude that α-tocopherol plays a major role in the response of plants to Pi availability not only by protecting plants from photo-oxidative stress, but also by exerting a control over growth- and defense-related transcriptional reprogramming and hormonal modulation.
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Affiliation(s)
- Annapurna D. Allu
- Institute of Biochemistry and Biology, University of PotsdamPotsdam-Golm, Germany
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam, Germany
| | - Bárbara Simancas
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of BarcelonaBarcelona, Spain
| | - Salma Balazadeh
- Institute of Biochemistry and Biology, University of PotsdamPotsdam-Golm, Germany
- Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam, Germany
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of BarcelonaBarcelona, Spain
- *Correspondence: Sergi Munné-Bosch,
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Sharma R, Vishal P, Kaul S, Dhar MK. Epiallelic changes in known stress-responsive genes under extreme drought conditions in Brassica juncea (L.) Czern. PLANT CELL REPORTS 2017; 36:203-217. [PMID: 27844102 DOI: 10.1007/s00299-016-2072-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
Under severe drought conditions, Brassica juncea shows differential methylation and demethylation events, such that certain epialleles are silenced and some are activated. The plant employed avoidance strategy by delaying apoptosis through the activation of several genes. Harsh environmental conditions pose serious threat to normal growth and development of crops, sometimes leading to their death. However, plants have developed an essential mechanism of modulation of gene activities by epigenetic modifications. Brassica juncea is an important oilseed crop contributing effectively to the economy of India. In the present investigation, we studied the changes in the methylation level of various stress-responsive genes of B. juncea variety RH30 by methylation-dependent immune-precipitation-chip in response to severe drought. On the basis of changes in the number of differential methylation regions in response to drought, the promoter regions were designated as hypermethylated and hypomethylated. Gene body methylation increased in all the genes, whereas promoter methylation was dependent on the function of the gene. Overall, the genes responsible for delaying apoptosis were hypomethylated and many genes responsible for normal routine activities were hypermethylated at promoter regions, thereby suggesting that these may be suspending the activities under harsh conditions.
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Affiliation(s)
- Rahul Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Parivartan Vishal
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India.
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Abstract
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
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Pandey N, Pandey-Rai S. Deciphering UV-B-induced variation in DNA methylation pattern and its influence on regulation of DBR2 expression in Artemisia annua L. PLANTA 2015; 242:869-879. [PMID: 25998525 DOI: 10.1007/s00425-015-2323-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/03/2015] [Indexed: 06/04/2023]
Abstract
UV-B-caused DNA hypomethylation and UV-B-mediated epigenetic activation of additional WRKY-binding site(s) in the DBR2 promoter may contribute to the overexpression of the DBR2 gene in Artemisia annua. DNA methylation is one of the key mechanisms behind stress-induced transcriptional switch off/on. Here, we evaluate the DNA methylation level in response to UV-B radiation in Artemisia annua which produces artemisinin, a sesquiterpene that has been recommended by WHO for the frontline treatment of malaria. However, the drug is facing serious shortage due to its low concentration in plants. UV-B treatment (3 h) enhanced artemisinin concentration up to 1.91-fold as compared to control. A key regulatory gene of artemisinin biosynthesis, DBR2 was upregulated under UV-B. This study presents observations regarding contributions of DNA methylation to the gene regulation using DBR2 as an example. Restriction digestion of genomic DNA by isoschizomers (MspI and HpaII) suggested UV-B involvement in DNA hypomethylation in A. annua. The global level of DNA methylation (R) was 3.4 and 5.9% for UV-B treated and control plants, respectively, attesting hypomethylation of DNA in response to UV-B. Further bisulfite sequencing PCR showed demethylation at two CHG sites in 18S rRNA gene. Similarly, bisulfite sequencing of promoter region of DBR2 has demonstrated demethylation at 4 CG-, 4 CHH- and 2 CHG-sites. In silico analysis revealed UV-B-mediated demethylation at seven putative transcription factor binding sites including WRKY, which are positive regulators of artemisinin biosynthesis. UV-B treatment has resulted in activation of additional WRKY-binding site in UV-B-treated plants compared with single active WRKY-binding site in control and this could be the probable reason for overexpression of DBR2. It is suggested that DNA demethylation is an important epigenetic response to UV-B radiation in A. annua that surely will provide new horizons to further elucidate the mechanistic evidence of plant's responses to UV-B radiation.
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Affiliation(s)
- Neha Pandey
- Laboratory of Morphogenesis, Department of Botany, Faculty of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
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