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
|
Soto-Cardinault C, Childs KL, Góngora-Castillo E. Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana. Genes (Basel) 2023; 14:2223. [PMID: 38137044 PMCID: PMC10743233 DOI: 10.3390/genes14122223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Fungal pathogens can have devastating effects on global crop production, leading to annual economic losses ranging from 10% to 23%. In light of climate change-related challenges, researchers anticipate an increase in fungal infections as a result of shifting environmental conditions. However, plants have developed intricate molecular mechanisms for effective defense against fungal attacks. Understanding these mechanisms is essential to the development of new strategies for protecting crops from multiple fungi threats. Public omics databases provide valuable resources for research on plant-pathogen interactions; however, integrating data from different studies can be challenging due to experimental variation. In this study, we aimed to identify the core genes that defend against the pathogenic fungi Colletotrichum higginsianum and Botrytis cinerea in Arabidopsis thaliana. Using a custom framework to control batch effects and construct Gene Co-expression Networks in publicly available RNA-seq dataset from infected A. thaliana plants, we successfully identified a gene module that was responsive to both pathogens. We also performed gene annotation to reveal the roles of previously unknown protein-coding genes in plant defenses against fungal infections. This research demonstrates the potential of publicly available RNA-seq data for identifying the core genes involved in defending against multiple fungal pathogens.
Collapse
Affiliation(s)
- Cynthia Soto-Cardinault
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico;
| | - Kevin L. Childs
- Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA;
| | - Elsa Góngora-Castillo
- CONAHCYT-Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
| |
Collapse
|
3
|
Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
Collapse
Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| |
Collapse
|
4
|
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
| |
Collapse
|
5
|
|
6
|
Rodrigues da Silva A, da Costa Silva D, Dos Santos Pinto KN, Santos Filho HP, Coelho Filho MA, Dos Santos Soares Filho W, Ferreira CF, da Silva Gesteira A. Epigenetic responses to Phytophthora citrophthora gummosis in citrus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 313:111082. [PMID: 34763867 DOI: 10.1016/j.plantsci.2021.111082] [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: 08/16/2021] [Revised: 09/28/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
Studies show that DNA methylation is associated with plant immunity but little is known as to how this epigenetic mechanism assists plants in adjusting their responses to biotic stress, especially when interacting with an hemibiotrophic pathogen such as citrus Phytophthora. The aim of the present study was to assess the effects of scion-rootstock interaction on plant resistance to P. citrophthora infection and DNA methylation patterns in 'Pera' sweet orange and 'Tahiti' acid lime grafted onto 'Rangpur' lime and 'Tropical' sunki rootstocks reinoculated with P. citrophthora. Results showed that reinoculated plants of the 'Pera' sweet orange/'Rangpur' lime and 'Tahiti' acid lime/'Tropical' sunki combinations with more and less sensitive varieties to Phytophthora, presented smaller stem lesions and increased frequency of full methylation and hemimethylation rates, compared to inoculated plants. In contrast, 'Tahiti' acid lime/'Rangpur' lime, two highly sensitive varieties, and 'Pera'/'Tropical' sunki, two much less sensitive varieties, showed high increases in the frequency of hemimethylation and non-methylation levels. Results suggest that in citrus, both the scion-rootstock interaction and DNA methylation affect the response to P. citrophthora infection. Reinoculated plants, depending on the combination, showed changes in intracellular hyphae growth through the formation of sets of fibers and crystal accumulation in the periderm, cortex, and phloem. In addition, starch grain concentration was higher in reinoculated plants in comparison to inoculated plants. These findings support the assumption that DNA methylation is a plant defense mechanism and therefore may be exploited to improve the response of plants to the gummosis of P. citrophthora in citrus.
Collapse
Affiliation(s)
- Adielle Rodrigues da Silva
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | - Delmira da Costa Silva
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | | | | | | | | | | | - Abelmon da Silva Gesteira
- Departamento de Biologia, Centro de Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil; Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia, 44380-000, Brazil.
| |
Collapse
|
7
|
Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
Collapse
|
8
|
Martínez-Aguilar K, Hernández-Chávez JL, Alvarez-Venegas R. Priming of seeds with INA and its transgenerational effect in common bean (Phaseolus vulgaris L.) plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110834. [PMID: 33691968 DOI: 10.1016/j.plantsci.2021.110834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/04/2021] [Accepted: 01/30/2021] [Indexed: 05/14/2023]
Abstract
Priming is a mechanism of defense that prepares the plant's immune system for a faster and/or stronger activation of cellular defenses against future exposure to different types of stress. This enhanced resistance can be achieved by using inorganic and organic compounds which imitate the biological induction of systemic acquired resistance. INA (2,6 dichloro-isonicotinic acid) was the first synthetic compound created as a resistance inducer for plant-pathogen interactions. However, the use of INA to activate primed resistance in common bean, at the seed stage and during germination, remains experimentally unexplored. Here, we test the hypothesis that INA-seed treatment would induce resistance in common bean plants to Pseudomonas syringae pv. phaseolicola, and that the increased resistance is not accompanied by a tradeoff between plant defense and growth. Additionally, it was hypothesized that treating seeds with INA has a transgenerational priming effect. We provide evidence that seed treatment activates a primed state for disease resistance, in which low nucleosome enrichment and reduced histone activation marks during the priming phase, are associated with a defense-resistant phenotype, characterized by symptom appearance, pathogen accumulation, yield, and changes in gene expression. In addition, the priming status for induced resistance can be inherited to its offspring.
Collapse
|
9
|
Yamashita F, Rodrigues AL, Rodrigues TM, Palermo FH, Baluška F, de Almeida LFR. Potential Plant-Plant Communication Induced by Infochemical Methyl Jasmonate in Sorghum ( Sorghum bicolor). PLANTS 2021; 10:plants10030485. [PMID: 33806670 PMCID: PMC8001897 DOI: 10.3390/plants10030485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/25/2022]
Abstract
Despite the fact that they are sessile organisms, plants actively move their organs and also use these movements to manipulate the surrounding biotic and abiotic environments. Plants maintain communication with neighboring plants, herbivores, and predators through the emission of diverse chemical compounds by their shoots and roots. These infochemicals modify the environment occupied by plants. Moreover, some infochemicals may induce morphophysiological changes of neighboring plants. We have used methyl-jasmonate (MeJa), a plant natural infochemical, to trigger communication between emitters and receivers Sorghum bicolor plants. The split roots of two plants were allocated to three different pots, with the middle pot containing the roots of both plants. We scored low stomatal conductance (gS) and low CO2 net assimilation (A) using the plants that had contact with the infochemical for the first time. During the second contact, these parameters showed no significant differences, indicating a memory effect. We also observed that the plants that had direct leaf contact with MeJa transmitted sensory information through their roots to neighboring plants. This resulted in higher maximum fluorescence (FM) and structural changes in root anatomy. In conclusion, MeJa emerges as possible trigger for communication between neighboring sorghum plants, in response to the environmental challenges.
Collapse
Affiliation(s)
- Felipe Yamashita
- Section of Plant Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.L.R.); (T.M.R.); (F.H.P.); (L.F.R.d.A.)
- Institute of Cellular and Molecular Botany, University of Bonn, 53115 Bonn, Germany;
- Correspondence:
| | - Angélica Lino Rodrigues
- Section of Plant Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.L.R.); (T.M.R.); (F.H.P.); (L.F.R.d.A.)
| | - Tatiane Maria Rodrigues
- Section of Plant Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.L.R.); (T.M.R.); (F.H.P.); (L.F.R.d.A.)
| | - Fernanda Helena Palermo
- Section of Plant Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.L.R.); (T.M.R.); (F.H.P.); (L.F.R.d.A.)
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, 53115 Bonn, Germany;
| | - Luiz Fernando Rolim de Almeida
- Section of Plant Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil; (A.L.R.); (T.M.R.); (F.H.P.); (L.F.R.d.A.)
| |
Collapse
|
10
|
Sousa AO, Camillo LR, Assis ETCM, Lima NS, Silva GO, Kirch RP, Silva DC, Ferraz A, Pasquali G, Costa MGC. EgPHI-1, a PHOSPHATE-INDUCED-1 gene from Eucalyptus globulus, is involved in shoot growth, xylem fiber length and secondary cell wall properties. PLANTA 2020; 252:45. [PMID: 32880001 DOI: 10.1007/s00425-020-03450-x] [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: 05/30/2020] [Accepted: 08/27/2020] [Indexed: 05/15/2023]
Abstract
MAIN CONCLUSION EgPHI-1 is a member of PHI-1/EXO/EXL protein family. Its overexpression in tobacco resulted in changes in biomass partitioning, xylem fiber length, secondary cell wall thickening and composition, and lignification. Here, we report the functional characterization of a PHOSPHATE-INDUCED PROTEIN 1 homologue showing differential expression in xylem cells from Eucalyptus species of contrasting phenotypes for wood quality and growth traits. Our results indicated that this gene is a member of the PHI-1/EXO/EXL family. Analysis of the promoter cis-acting regulatory elements and expression responses to different treatments revealed that the Eucalyptus globulus PHI-1 (EgPHI-1) is transcriptionally regulated by auxin, cytokinin, wounding and drought. EgPHI-1 overexpression in transgenic tobacco changed the partitioning of biomass, favoring its allocation to shoots in detriment of roots. The stem of the transgenic plants showed longer xylem fibers and reduced cellulose content, while the leaf xylem had enhanced secondary cell wall thickness. UV microspectrophotometry of individual cell wall layers of fibers and vessels has shown that the transgenic plants exhibit differences in the lignification of S2 layer in both cell types. Taken together, the results suggest that EgPHI-1 mediates the elongation of secondary xylem fibers, secondary cell wall thickening and composition, and lignification, making it an attractive target for biotechnological applications in forestry and biofuel crops.
Collapse
Affiliation(s)
- Aurizangela O Sousa
- Centro Multidisciplinar do Campus de Luís Eduardo Magalhães, Universidade Federal do Oeste da Bahia, Luís Eduardo Magalhães, Bahia, 47850-000, Brazil
| | - Luciana R Camillo
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | - Elza Thaynara C M Assis
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | - Nathália S Lima
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | - Genilson O Silva
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | - Rochele P Kirch
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | - Delmira C Silva
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil
| | - André Ferraz
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo- USP, Lorena, São Paulo, 12602-810, Brazil
| | - Giancarlo Pasquali
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | - Marcio G C Costa
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, 45662-900, Brazil.
| |
Collapse
|
11
|
Whole-genome landscape of H3K4me3, H3K36me3 and H3K9ac and their association with gene expression during Paulownia witches' broom disease infection and recovery processes. 3 Biotech 2020; 10:336. [PMID: 32670736 DOI: 10.1007/s13205-020-02331-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
Histone methylation and acetylation participate in the modulation of gene expression. Here, chromatin immunoprecipitation sequencing (ChIP-Seq) was used to determine genome-wide patterns of three histone modifications, H3K4me3, H3K36me3, and H3K9ac (associated with actively expressed genes) and their associations with gene expression in Paulownia fortunei following phytoplasma infection and recovery from Paulownia witches' broom (PaWB) disease after methyl methane sulfonate treatment. The three histone marks were preferentially deposited in genic regions, especially downstream of transcription start sites, and were highly concurrent with gene expression. Genes with all three histone marks exhibited the highest expression levels. Based on the comparison scheme, we detected 365, 2244, and 752 PaWB-associated genes with H3K4me3, H3K36me3, and H3K9ac marks, separately. KEGG pathway analysis showed that these genes were involved in plant-pathogen interaction, plant hormone signal transduction, and starch and sucrose metabolism. A small proportion of differentially modified genes showed changes in expression in response to phytoplasma infection, including genes involved in calcium ion signal transduction, abscisic acid signal transduction, and ethylene biosynthesis. This comprehensive analysis of genome-wide histone modifications and gene expression in Paulownia following phytoplasma infection provides new insights into the epigenetic responses to phytoplasma infection and will be useful for further studies on epigenetic regulation mechanisms in plants under biotic stress.
Collapse
|
12
|
Crespo-Salvador Ó, Sánchez-Giménez L, López-Galiano MJ, Fernández-Crespo E, Schalschi L, García-Robles I, Rausell C, Real MD, González-Bosch C. The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation. PLANTS 2020; 9:plants9030300. [PMID: 32121544 PMCID: PMC7154849 DOI: 10.3390/plants9030300] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
Abstract
Research into the relationship between epigenetic regulation and resistance to biotic stresses provides alternatives for plant protection and crop improvement. To unravel the mechanisms underlying tomato responses to Botrytis cinerea, we performed a chromatin immunoprecipitation (ChIP) analysis showing the increase in H3K9ac mark along the early induced genes SlyDES, SlyDOX1, and SlyLoxD encoding oxylipin-pathway enzymes, and SlyWRKY75 coding for a transcriptional regulator of hormonal signaling. This histone mark showed a more distinct distribution than the previously studied H3K4me3. The RNAPol-ChIP analysis reflected the actual gene transcription associated with increased histone modifications. A different pattern of marks in the oxylipin-related genes against P. syringae supported a pathogen-specific profile, while no significant differences occurred in SlyWRKY75. The epigenetic regulation of SlyWRKY75 by the intron-binding miR1127-3p was supported by the presence of SlyWRKY75 pre-mRNA in control plants. Interestingly, mRNA was found to be accumulated in response to B. cinerea and P. syringae, while reduction in miRNA only occurred against B. cinerea. The intronic region presented a similar pattern of marks than the rest of the gene in both pathosystems, except for H3K4me3 in the miRNA binding site upon B. cinerea. We located the gene encoding Sly-miR1127-3p, which presented reduced H3K4me3 on its promoter against B. cinerea.
Collapse
Affiliation(s)
- Óscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
| | - Lorena Sánchez-Giménez
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
| | - Mª José López-Galiano
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Emma Fernández-Crespo
- Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain; (E.F.-C.); (L.S.)
| | - Loredana Schalschi
- Plant Physiology Area, Biochemistry and Biotechnology Group, Department CAMN, University Jaume I, 12071 Castellón, Spain; (E.F.-C.); (L.S.)
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - M Dolores Real
- Department of Genetics, University of Valencia, Burjassot, 46100 Valencia, Spain; (M.J.L.-G.); (I.G.-R.); (C.R.); (M.D.R.)
| | - Carmen González-Bosch
- Department of Biochemistry and Molecular Biology, University of Valencia, Agrochemical and Food Technology Institute (CSIC), 46980 Paterna, Valencia, Spain; (Ó.C.-S.); (L.S.-G.)
- Correspondence: ; Tel.: +34-963900022
| |
Collapse
|
13
|
Sham A, Al-Ashram H, Whitley K, Iratni R, El-Tarabily KA, AbuQamar SF. Metatranscriptomic Analysis of Multiple Environmental Stresses Identifies RAP2.4 Gene Associated with Arabidopsis Immunity to Botrytis cinerea. Sci Rep 2019; 9:17010. [PMID: 31740741 PMCID: PMC6861241 DOI: 10.1038/s41598-019-53694-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/24/2019] [Indexed: 01/18/2023] Open
Abstract
In this study, we aimed to identify common genetic components during stress response responsible for crosstalk among stresses, and to determine the role of differentially expressed genes in Arabidopsis-Botrytis cinerea interaction. Of 1,554 B. cinerea up-regulated genes, 24%, 1.4% and 14% were induced by biotic, abiotic and hormonal treatments, respectively. About 18%, 2.5% and 22% of B. cinerea down-regulated genes were also repressed by the same stress groups. Our transcriptomic analysis indicates that plant responses to all tested stresses can be mediated by commonly regulated genes; and protein-protein interaction network confirms the cross-interaction between proteins regulated by these genes. Upon challenges to individual or multiple stress(es), accumulation of signaling molecules (e.g. hormones) plays a major role in the activation of downstream defense responses. In silico gene analyses enabled us to assess the involvement of RAP2.4 (related to AP2.4) in plant immunity. Arabidopsis RAP2.4 was repressed by B. cinerea, and its mutants enhanced resistance to the same pathogen. To the best of our knowledge, this is the first report demonstrating the role of RAP2.4 in plant defense against B. cinerea. This research can provide a basis for breeding programs to increase tolerance and improve yield performance in crops.
Collapse
Affiliation(s)
- Arjun Sham
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE
| | | | - Kenna Whitley
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE
| | - Rabah Iratni
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE
| | - Khaled A El-Tarabily
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE. .,School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, 6150, Australia.
| | - Synan F AbuQamar
- Department of Biology, United Arab Emirates University, 15551, Al-Ain, UAE.
| |
Collapse
|
14
|
Alonso C, Ramos‐Cruz D, Becker C. The role of plant epigenetics in biotic interactions. THE NEW PHYTOLOGIST 2019; 221:731-737. [PMID: 30156271 PMCID: PMC6726468 DOI: 10.1111/nph.15408] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/22/2018] [Indexed: 05/07/2023]
Abstract
Contents Summary 731 I. Biotic interactions in the context of genetic, epigenetic and environmental diversity 731 II. Biotic interactions affect epigenetic configuration 732 III. Plant epigenetic configuration influences biotic interactions 733 IV. Epigenetic memory in the context of biotic interactions 734 V. Conclusions and future research 735 Acknowledgements 735 Author contributions 735 References 735 SUMMARY: Plants are hubs of a wide range of biotic interactions with mutualist and antagonist animals, microbes and neighboring plants. Because the quality and intensity of those relationships can change over time, a fast and reversible response to stress is required. Here, we review recent studies on the role of epigenetic factors such as DNA methylation and histone modifications in modulating plant biotic interactions, and discuss the state of knowledge regarding their potential role in memory and priming. Moreover, we provide an overview of strategies to investigate the contribution of epigenetics to environmentally induced phenotypic changes in an ecological context, highlighting possible transitions from whole-genome high-resolution analyses in plant model organisms to informative reduced representation analyses in genomically less accessible species.
Collapse
Affiliation(s)
- Conchita Alonso
- Estación Biológica de DoñanaConsejo Superior de Investigaciones Científicas (CSIC)Av. Américo Vespucio 26Sevilla41092Spain
| | - Daniela Ramos‐Cruz
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr Gasse 3Vienna1030Austria
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr Gasse 3Vienna1030Austria
| |
Collapse
|
15
|
Meller B, Kuźnicki D, Arasimowicz-Jelonek M, Deckert J, Floryszak-Wieczorek J. BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2018; 9:1228. [PMID: 30233606 PMCID: PMC6135045 DOI: 10.3389/fpls.2018.01228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 05/23/2023]
Abstract
In this paper we analyzed β-aminobutyric acid (BABA)-primed epigenetic adjustment of potato cv. "Sarpo Mira" to Phytophthora infestans. The first stress-free generation of the potato genotype obtained from BABA-primed parent plants via tubers and seeds showed pronounced resistance to the pathogen, which was tuned with the transcriptional memory of SA-responsive genes. During the early priming phase before the triggering stress, we found robust bistable deposition of histone marks (H3K4me2 and H3K27me3) on the NPR1 (Non-expressor of PR genes) and the SNI1 gene (Suppressor of NPR1, Inducible), in which transcription antagonized silencing. Switchable chromatin states of these adverse systemic acquired resistance (SAR) regulators probably reprogrammed responsiveness of the PR1 and PR2 genes and contributed to stress imprinting. The elevated levels of heritable H3K4me2 tag in the absence of transcription on SA-dependent genes in BABA-primed (F0) and its vegetative and generative progeny (F1) before pathogen challenge provided evidence for the epigenetic mark for intergenerational memory in potato. Moreover, our study revealed that histone acetylation was not critical for maintaining BABA-primed defense information until the plants were triggered with the virulent pathogen when rapid and boosted PRs gene expression probably required histone acetyltransferase (HAT) activity both in F0 and F1 progeny.
Collapse
Affiliation(s)
- Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Joanna Deckert
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | |
Collapse
|
16
|
Hewezi T. Editorial: epigenetic regulation of plant development and stress responses. PLANT CELL REPORTS 2018; 37:1-2. [PMID: 29159566 DOI: 10.1007/s00299-017-2233-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/05/2017] [Indexed: 05/25/2023]
Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
| |
Collapse
|
17
|
López-Galiano MJ, González-Hernández AI, Crespo-Salvador O, Rausell C, Real MD, Escamilla M, Camañes G, García-Agustín P, González-Bosch C, García-Robles I. Epigenetic regulation of the expression of WRKY75 transcription factor in response to biotic and abiotic stresses in Solanaceae plants. PLANT CELL REPORTS 2018; 37:167-176. [PMID: 29079899 DOI: 10.1007/s00299-017-2219-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/05/2017] [Indexed: 05/12/2023]
Abstract
SlyWRKY75: gene expression was induced in response to biotic stresses, especially in Botrytis cinerea-infected tomato plants, in which Sly-miR1127-3p is a putative SlyWRKY75 regulator and epigenetic marks were detected. WRKY75 transcription factor involved in Pi homeostasis was recently found also induced in defense against necrotrophic pathogens. In this study, we analyzed by RT-qPCR the expression of SlyWRKY75 gene in tomato plants in response to abiotic stresses (drought or heat) and biotic stresses (Colorado potato beetle larvae infestation, Pseudomonas syringae or Botrytis cinerea infection) being only differentially expressed following biotic stresses, especially upon B. cinerea infection (55-fold induction). JA and JA-Ile levels were significantly increased in tomato plants under biotic stresses compared with control plants, indicating that SlyWRKY75 might be a transcriptional regulator of the JA pathway. The contribution of miRNAs and epigenetic molecular mechanisms to the regulation of this gene in B. cinerea-infected tomato plants was explored. We identified a putative Sly-miR1127-3p miRNA predicted to bind the intronic region of the SlyWRKY75 genomic sequence. Sly-miR1127-3p miRNA was repressed in infected plants (0.4-fold) supporting that it might act as an epigenetic regulation factor of SlyWRKY75 gene expression rather than via the post-transcriptional mechanisms of canonical miRNAs. It has been proposed that certain miRNAs can mediate DNA methylation in the plant nucleus broadening miRNA functions with transcriptional gene silencing by targeting intron-containing pre-mRNAs. Histone modifications analysis by chromatin immunoprecipitation (ChIP) demonstrated the presence of the activator histone modification H3K4me3 on SlyWRKY75 transcription start site and gene body. The induction of this gene in response to B. cinerea correlates with the presence of an activator mark. Thus, miRNAs and chromatin modifications might cooperate as epigenetic factors to modulate SlyWRKY75 gene expression.
Collapse
Affiliation(s)
- María José López-Galiano
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Ana I González-Hernández
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Oscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - M Dolores Real
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Mónica Escamilla
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Gemma Camañes
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Pilar García-Agustín
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071, Castellón, Spain
| | - Carmen González-Bosch
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980, Paterna, Valencia, Spain
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain.
| |
Collapse
|