1
|
Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [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: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
Collapse
Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
| |
Collapse
|
2
|
Gohari G, Jiang M, Manganaris GA, Zhou J, Fotopoulos V. Next generation chemical priming: with a little help from our nanocarrier friends. TRENDS IN PLANT SCIENCE 2024; 29:150-166. [PMID: 38233253 DOI: 10.1016/j.tplants.2023.11.024] [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: 10/03/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Plants are exposed to multiple threats linked to climate change which can cause critical yield losses. Therefore, designing novel crop management tools is crucial. Chemical priming has recently emerged as an effective technology for improving tolerance to stress factors. Several compounds such as phytohormones, reactive species, and synthetic chimeras have been identified as promising priming agents. Following remarkable developments in nanotechnology, several unique nanocarriers (NCs) have been engineered that can act as smart delivery systems. These provide an eco-friendly, next-generation method for chemical priming, leading to increased efficiency and reduced overall chemical usage. We review novel engineered NCs (NENCs) as vehicles for chemical agents in advanced priming strategies, and address challenges and opportunities to be met towards achieving sustainable agriculture.
Collapse
Affiliation(s)
- Gholamreza Gohari
- Department of Agricultural Sciences Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus; Department of Horticulture, Faculty of Horticulture, University of Maragheh, Maragheh, Iran
| | - Meng Jiang
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, PR China
| | - George A Manganaris
- Department of Agricultural Sciences Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Jie Zhou
- Hainan Institute, Zhejiang University, Yazhou Bay Sci-Tech City, Sanya, PR China; Department of Horticulture, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, PR China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences Biotechnology and Food Science, Cyprus University of Technology, Lemesos, Cyprus.
| |
Collapse
|
3
|
Lempe J, Flachowsky H, Peil A. Exploring epigenetic variation for breeding climate resilient apple crops. PHYSIOLOGIA PLANTARUM 2022; 174:e13782. [PMID: 36151889 DOI: 10.1111/ppl.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/10/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Climate change with warmer winter and spring temperatures poses major challenges to apple fruit production. Long-term observations confirm the trend toward earlier flowering, which leads to an increased risk of frost damage. New breeding strategies are needed to generate cultivars that are able to stay largely unaffected by warmer temperatures. Recently, epigenetic variation has been proposed as a new resource for breeding purposes and seems suitable in principle for apple breeding. However, to serve as a new resource for apple breeding, it is necessary to clarify whether epigenetic variation can be induced by the environment, whether it can create phenotypic variation, and whether this variation is stable across generations. In this brief review, we summarize the impact of climate change on the timing of apple phenology, highlight how epigenetic variation can potentially support novel breeding strategies, and point out important features of epigenetic variation that are required for its application in breeding programs.
Collapse
Affiliation(s)
- Janne Lempe
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| | - Andreas Peil
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Dresden, Germany
| |
Collapse
|
4
|
Nair AU, Bhukya DPN, Sunkar R, Chavali S, Allu AD. Molecular basis of priming-induced acquired tolerance to multiple abiotic stresses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3355-3371. [PMID: 35274680 DOI: 10.1093/jxb/erac089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/04/2022] [Indexed: 05/04/2023]
Abstract
The growth, survival, and productivity of plants are constantly challenged by diverse abiotic stresses. When plants are exposed to stress for the first time, they can capture molecular information and store it as a form of memory, which enables them to competently and rapidly respond to subsequent stress(es). This process is referred to as a priming-induced or acquired stress response. In this review, we discuss how (i) the storage and retrieval of the information from stress memory modulates plant physiological, cellular, and molecular processes in response to subsequent stress(es), (ii) the intensity, recurrence, and duration of priming stimuli influences the outcomes of the stress response, and (iii) the varying responses at different plant developmental stages. We highlight current understanding of the distinct and common molecular processes manifested at the epigenetic, (post-)transcriptional, and post-translational levels mediated by stress-associated molecules and metabolites, including phytohormones. We conclude by emphasizing how unravelling the molecular circuitry underlying diverse priming-stimuli-induced stress responses could propel the use of priming as a management practice for crop plants. This practice, in combination with precision agriculture, could aid in increasing yield quantity and quality to meet the rapidly rising demand for food.
Collapse
Affiliation(s)
- Akshay U Nair
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Durga Prasad Naik Bhukya
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Annapurna Devi Allu
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| |
Collapse
|
5
|
Kang JE, Yoo N, Jeon BJ, Kim BS, Chung EH. Resveratrol Oligomers, Plant-Produced Natural Products With Anti-virulence and Plant Immune-Priming Roles. FRONTIERS IN PLANT SCIENCE 2022; 13:885625. [PMID: 35712595 PMCID: PMC9197177 DOI: 10.3389/fpls.2022.885625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance has become increasingly prevalent in the environment. Many alternative strategies have been proposed for the treatment and prevention of diverse diseases in agriculture. Among them, the modulation of bacterial virulence to bypass antibiotic resistance or boost plant innate immunity can be considered a promising drug target. Plant-produced natural products offer a broad spectrum of stereochemistry and a wide range of pharmacophores, providing a great diversity of biological activities. Here, we present a perspective on the putative role of plant-produced resveratrol oligomers as anti-virulence and plant-immune priming agents for efficient disease management. Resveratrol oligomers can decrease (1) bacterial motility directly and (2) indirectly by attenuating the bacterial type III secretion system (TT3S). They induce enhanced local immune responses mediated by two-layered plant innate immunity, demonstrating (3) a putative plant immune priming role.
Collapse
Affiliation(s)
- Ji Eun Kang
- Institute of Life Science and Natural Resources, Korea University, Seoul, South Korea
| | - Nayeon Yoo
- Department of Plant Biotechnology, Graduate School, Korea University, Seoul, South Korea
| | - Byeong Jun Jeon
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung Institute, Gangneung, South Korea
| | - Beom Seok Kim
- Institute of Life Science and Natural Resources, Korea University, Seoul, South Korea
- Department of Plant Biotechnology, Graduate School, Korea University, Seoul, South Korea
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Eui-Hwan Chung
- Institute of Life Science and Natural Resources, Korea University, Seoul, South Korea
- Department of Plant Biotechnology, Graduate School, Korea University, Seoul, South Korea
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| |
Collapse
|
6
|
Soudani S, Poza-Carrión C, De la Cruz Gómez N, González-Coloma A, Andrés MF, Berrocal-Lobo M. Essential Oils Prime Epigenetic and Metabolomic Changes in Tomato Defense Against Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2022; 13:804104. [PMID: 35422834 PMCID: PMC9002333 DOI: 10.3389/fpls.2022.804104] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/07/2022] [Indexed: 05/10/2023]
Abstract
In this work, we studied the direct and indirect plant protection effects of an Artemisia absinthium essential oil (AEO) on tomato seedlings against Fusarium oxysporum sp. oxysporum radicis lycopersici (Fol). AEO exhibited a toxic effect in vitro against Fol. Additionally, tomato seedlings germinated from seeds pretreated with AEO and grown hydroponically were protected against Fol. Plant disease symptoms, including, water and fresh weight loss, tissue necrosis, and chlorosis were less pronounced in AEO-treated seedlings. AEO also contributed to plant defenses by increasing callose deposition and the production of reactive oxygen species (ROS) on seed surfaces without affecting seed germination or plant development. The essential oil seed coating also primed a durable tomato seedling defense against the fungus at later stages of plant development. RNA-seq and metabolomic analysis performed on seedlings after 12 days showed that the AEO treatment on seeds induced transcriptomic and metabolic changes. The metabolomic analysis showed an induction of vanillic acid, coumarin, lycopene, oleamide, and an unknown metabolite of m/z 529 in the presence of Fol. The StNRPD2 gene, the second largest component of RNA polymerases IV and V directly involved in de novo cytosine methylation by RNA-directed DNA methylation (RdDM), was highly induced in the presence of AEO. The host methionine cycle (MTC) controlling trans-methylation reactions, was also altered by AEO through the high induction of S-adenosyl methionine transferases (SAMts). Our results suggest that AEO treatment could induce de novo epigenetic changes in tomato, modulating the speed and extent of its immune response to Fol. The EO-seed coating could be a new strategy to prime durable tomato resistance, compatible with other environmentally friendly biopesticides.
Collapse
Affiliation(s)
- Serine Soudani
- Department of Systems and Natural Resources, School of Forestry Engineering and Natural Environment, Polytechnical University of Madrid, Madrid, Spain
| | - César Poza-Carrión
- Department of Systems and Natural Resources, School of Forestry Engineering and Natural Environment, Polytechnical University of Madrid, Madrid, Spain
| | - Noelia De la Cruz Gómez
- Department of Systems and Natural Resources, School of Forestry Engineering and Natural Environment, Polytechnical University of Madrid, Madrid, Spain
| | - Azucena González-Coloma
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - María Fé Andrés
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Marta Berrocal-Lobo
- Department of Systems and Natural Resources, School of Forestry Engineering and Natural Environment, Polytechnical University of Madrid, Madrid, Spain
- *Correspondence: Marta Berrocal-Lobo,
| |
Collapse
|
7
|
Bhar A, Chakraborty A, Roy A. Plant Responses to Biotic Stress: Old Memories Matter. PLANTS (BASEL, SWITZERLAND) 2021; 11:84. [PMID: 35009087 PMCID: PMC8747260 DOI: 10.3390/plants11010084] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 05/20/2023]
Abstract
Plants are fascinating organisms present in most ecosystems and a model system for studying different facets of ecological interactions on Earth. In the environment, plants constantly encounter a multitude of abiotic and biotic stresses. The zero-avoidance phenomena make them more resilient to such environmental odds. Plants combat biotic stress or pathogenic ingression through a complex orchestration of intracellular signalling cascades. The plant-microbe interaction primarily relies on acquired immune response due to the absence of any specialised immunogenic cells for adaptive immune response. The generation of immune memory is mainly carried out by T cells as part of the humoral immune response in animals. Recently, prodigious advancements in our understanding of epigenetic regulations in plants invoke the "plant memory" theory afresh. Current innovations in cutting-edge genomic tools have revealed stress-associated genomic alterations and strengthened the idea of transgenerational memory in plants. In plants, stress signalling events are transferred as genomic imprints in successive generations, even without any stress. Such immunogenic priming of plants against biotic stresses is crucial for their eco-evolutionary success. However, there is limited literature capturing the current knowledge of the transgenerational memory of plants boosting biotic stress responses. In this context, the present review focuses on the general concept of memory in plants, recent advancements in this field and comprehensive implications in biotic stress tolerance with future perspectives.
Collapse
Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata 700118, West Bengal, India
| | - Amrita Chakraborty
- EVA4.0-Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, 16500 Prague, Czech Republic
| | - Amit Roy
- EVA4.0-Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, 16500 Prague, Czech Republic
| |
Collapse
|
8
|
Srivastava AK, Suresh Kumar J, Suprasanna P. Seed 'primeomics': plants memorize their germination under stress. Biol Rev Camb Philos Soc 2021; 96:1723-1743. [PMID: 33961327 DOI: 10.1111/brv.12722] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl2 and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.
Collapse
Affiliation(s)
- Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Jisha Suresh Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| |
Collapse
|
9
|
Latzel V, Münzbergová Z, Skuhrovec J, Novák O, Strnad M. Effect of experimental DNA demethylation on phytohormones production and palatability of a clonal plant after induction via jasmonic acid. OIKOS 2020. [DOI: 10.1111/oik.07302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vít Latzel
- Inst. of Botany, Czech Academy of Sciences, Dept of Population Ecology Zámek 1 CZ‐252 43 Průhonice Czech Republic
| | - Zuzana Münzbergová
- Inst. of Botany, Czech Academy of Sciences, Dept of Population Ecology Zámek 1 CZ‐252 43 Průhonice Czech Republic
- Dept of Botany, Faculty of Science, Charles Univ. Prague Czech Republic
| | | | - Ondřej Novák
- Laboratory of Growth Regulators, Czech Academy of Sciences, Inst. of Experimental Botany and Palacký Univ. Olomouc Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Czech Academy of Sciences, Inst. of Experimental Botany and Palacký Univ. Olomouc Czech Republic
| |
Collapse
|
10
|
Turgut-Kara N, Arikan B, Celik H. Epigenetic memory and priming in plants. Genetica 2020; 148:47-54. [PMID: 32356021 DOI: 10.1007/s10709-020-00093-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/16/2020] [Indexed: 12/17/2022]
Abstract
In nature, plants are regularly exposed to biotic and abiotic stress conditions. These conditions create potential risks for survival. Plants have evolved in order to compete with these stress conditions through physiological adjustments that are based on epigenetic background. Thus, the ecological signals create different levels of stress memory. Recent studies have shown that this stress-induced environmental memory is mediated by epigenetic mechanisms that have fundamental roles in the aspect of controlling gene expression via DNA methylation, histone modifications and, small RNAs and these modifications could be transmitted to the next generations. Thus, they provide alternative mechanisms to constitute stress memories in plants. In this review, we summarized the epigenetic memory mechanisms related with biotic and abiotic stress conditions, and relationship between priming and epigenetic memory in plants by believing that it can be useful for analyzing memory mechanisms and see what is missing out in order to develop plants more resistant and productive under diverse environmental cues.
Collapse
Affiliation(s)
- Neslihan Turgut-Kara
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
| | - Burcu Arikan
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Haluk Celik
- Program of Molecular Biology and Genetics, Institute of Science, Istanbul University, Istanbul, Turkey
| |
Collapse
|