1
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Xie SS, Duan CG. Epigenetic regulation of plant immunity: from chromatin codes to plant disease resistance. ABIOTECH 2023; 4:124-139. [PMID: 37581024 PMCID: PMC10423193 DOI: 10.1007/s42994-023-00101-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 08/16/2023]
Abstract
Facing a deteriorating natural environment and an increasing serious food crisis, bioengineering-based breeding is increasing in importance. To defend against pathogen infection, plants have evolved multiple defense mechanisms, including pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). A complex regulatory network acts downstream of these PTI and ETI pathways, including hormone signal transduction and transcriptional reprogramming. In recent years, increasing lines of evidence show that epigenetic factors act, as key regulators involved in the transcriptional reprogramming, to modulate plant immune responses. Here, we summarize current progress on the regulatory mechanism of DNA methylation and histone modifications in plant defense responses. In addition, we also discuss the application of epigenetic mechanism-based resistance strategies in plant disease breeding.
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Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
- University of the Chinese Academy of Sciences, Beijing, 100049 China
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2
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Kang H, Fan T, Wu J, Zhu Y, Shen WH. Histone modification and chromatin remodeling in plant response to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:986940. [PMID: 36262654 PMCID: PMC9574397 DOI: 10.3389/fpls.2022.986940] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Tianyi Fan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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3
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Azevedo V, Daddiego L, Cardone MF, Perrella G, Sousa L, Santos RB, Malhó R, Bergamini C, Marsico AD, Figueiredo A, Alagna F. Transcriptomic and methylation analysis of susceptible and tolerant grapevine genotypes following Plasmopara viticola infection. PHYSIOLOGIA PLANTARUM 2022; 174:e13771. [PMID: 36053855 PMCID: PMC9826190 DOI: 10.1111/ppl.13771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/05/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Downy mildew, caused by the biotrophic oomycete Plasmopara viticola, is one of the most economically significant grapevine diseases worldwide. Current strategies to cope with this threat rely on the massive use of chemical compounds during each cultivation season. The economic costs and negative environmental impact associated with these applications increased the urge to search for sustainable strategies of disease control. Improved knowledge of plant mechanisms to counteract pathogen infection may allow the development of alternative strategies for plant protection. Epigenetic regulation, in particular DNA methylation, is emerging as a key factor in the context of plant-pathogen interactions associated with the expression modulation of defence genes. To improve our understanding of the genetic and epigenetic mechanisms underpinning grapevine response to P. viticola, we studied the modulation of both 5-mC methylation and gene expression at 6 and 24 h post-infection (hpi). Leaves of two table grape genotypes (Vitis vinifera), selected by breeding activities for their contrasting level of susceptibility to the pathogen, were analysed. Following pathogen infection, we found variations in the 5-mC methylation level and the gene expression profile. The results indicate a genotype-specific response to pathogen infection. The tolerant genotype (N23/018) at 6 hpi exhibits a lower methylation level compared to the susceptible one (N20/020), and it shows an early modulation (at 6 hpi) of defence and epigenetic-related genes during P. viticola infection. These data suggest that the timing of response is an important mechanism to efficiently counteract the pathogen attack.
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Affiliation(s)
- Vanessa Azevedo
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Loretta Daddiego
- Energy Technologies and Renewable Sources DepartmentNational Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research CentreRotondellaMateraItaly
| | - Maria Francesca Cardone
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | | | - Lisete Sousa
- Department of Statistics and Operations Research, Faculdade de Ciências; Centre of Statistics and its Applications (CEAUL)Universidade de LisboaLisbonPortugal
| | - Rita B. Santos
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Rui Malhó
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Carlo Bergamini
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | - Antonio Domenico Marsico
- Research Centre for Viticulture and EnologyCouncil for Agricultural Research and Economics (CREA)TuriBariItaly
| | - Andreia Figueiredo
- Faculdade de Ciências, Plant Biology Department, Biosystems & Integrative Sciences Institute (BioISI)Universidade de LisboaLisbonPortugal
| | - Fiammetta Alagna
- Energy Technologies and Renewable Sources DepartmentNational Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research CentreRotondellaMateraItaly
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Cheng J, Xu L, Bergér V, Bruckmann A, Yang C, Schubert V, Grasser KD, Schnittger A, Zheng B, Jiang H. H3K9 demethylases IBM1 and JMJ27 are required for male meiosis in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 235:2252-2269. [PMID: 35638341 DOI: 10.1111/nph.18286] [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: 04/21/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Dimethylation of histone H3 lysine 9 (H3K9me2), a crucial modification for heterochromatin formation and transcriptional silencing, is essential for proper meiotic prophase progression in mammals. We analyzed meiotic defects and generated genome-wide profiles of H3K9me2 and transcriptomes for the mutants of H3K9 demethylases. Moreover, we also identified proteins interacting with H3K9 demethylases. H3K9me2 is usually found at transposable elements and repetitive sequences but is absent from the bodies of protein-coding genes. In this study, we show that the Arabidopsis thaliana H3K9 demethylases IBM1 and JMJ27 cooperatively regulate crossover formation and chromosome segregation. They protect thousands of protein-coding genes from ectopic H3K9me2, including genes essential for meiotic prophase progression. In addition to removing H3K9me2, IBM1 and JMJ27 interact with the Precocious Dissociation of Sisters 5 (PDS5) cohesin complex cofactors. The pds5 mutant shared similar transcriptional alterations with ibm1 jmj27, including meiosis-essential genes, yet without affecting H3K9me2 levels. Hence, PDS5s, together with IBM1 and JMJ27, regulate male meiosis and gene expression independently of H3K9 demethylation. These findings uncover a novel role of H3K9me2 removal in meiosis and a new function of H3K9 demethylases and cohesin cofactors in meiotic transcriptional regulation.
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Affiliation(s)
- Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Valentin Bergér
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Regensburg, 93053, Germany
| | - Astrid Bruckmann
- Department of Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, 93053, Germany
| | - Chao Yang
- Department of Developmental Biology, University of Hamburg, Hamburg, 20146, Germany
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Regensburg, 93053, Germany
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, Hamburg, 20146, Germany
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
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Lv S, Yang Y, Yu G, Peng L, Zheng S, Singh SK, Vílchez JI, Kaushal R, Zi H, Yi D, Wang Y, Luo S, Wu X, Zuo Z, Huang W, Liu R, Du J, Macho AP, Tang K, Zhang H. Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome. THE ISME JOURNAL 2022; 16:2513-2524. [PMID: 35908110 PMCID: PMC9561531 DOI: 10.1038/s41396-022-01297-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022]
Abstract
Root microbiota is important for plant growth and fitness. Little is known about whether and how the assembly of root microbiota may be controlled by epigenetic regulation, which is crucial for gene transcription and genome stability. Here we show that dysfunction of the histone demethylase IBM1 (INCREASE IN BONSAI METHYLATION 1) in Arabidopsis thaliana substantially reshaped the root microbiota, with the majority of the significant amplicon sequence variants (ASVs) being decreased. Transcriptome analyses of plants grown in soil and in sterile growth medium jointly disclosed salicylic acid (SA)-mediated autoimmunity and production of the defense metabolite camalexin in the ibm1 mutants. Analyses of genome-wide histone modifications and DNA methylation highlighted epigenetic modifications permissive for transcription at several important defense regulators. Consistently, ibm1 mutants showed increased resistance to the pathogen Pseudomonas syringae DC3000 with stronger immune responses. In addition, ibm1 showed substantially impaired plant growth promotion in response to beneficial bacteria; the impairment was partially mimicked by exogenous application of SA to wild-type plants, and by a null mutation of AGP19 that is important for cell expansion and that is repressed with DNA hypermethylation in ibm1. IBM1-dependent epigenetic regulation imposes strong and broad impacts on plant-microbe interactions and thereby shapes the assembly of root microbiota.
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6
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Mostafa S, Wang Y, Zeng W, Jin B. Plant Responses to Herbivory, Wounding, and Infection. Int J Mol Sci 2022; 23:ijms23137031. [PMID: 35806046 PMCID: PMC9266417 DOI: 10.3390/ijms23137031] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/26/2022] Open
Abstract
Plants have various self-defense mechanisms against biotic attacks, involving both physical and chemical barriers. Physical barriers include spines, trichomes, and cuticle layers, whereas chemical barriers include secondary metabolites (SMs) and volatile organic compounds (VOCs). Complex interactions between plants and herbivores occur. Plant responses to insect herbivory begin with the perception of physical stimuli, chemical compounds (orally secreted by insects and herbivore-induced VOCs) during feeding. Plant cell membranes then generate ion fluxes that create differences in plasma membrane potential (Vm), which provokes the initiation of signal transduction, the activation of various hormones (e.g., jasmonic acid, salicylic acid, and ethylene), and the release of VOCs and SMs. This review of recent studies of plant–herbivore–infection interactions focuses on early and late plant responses, including physical barriers, signal transduction, SM production as well as epigenetic regulation, and phytohormone responses.
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7
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Parween D, Sahu BB. An Arabidopsis nonhost resistance gene, IMPORTIN ALPHA 2 provides immunity against rice sheath blight pathogen, Rhizoctonia solani. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100109. [PMID: 35243446 PMCID: PMC8856995 DOI: 10.1016/j.crmicr.2022.100109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/06/2022] [Indexed: 12/23/2022] Open
Abstract
Rice sheath blight is caused by necrotrophic dreadful fungus Rhizoctonia solani. Forward genetics tools identified RSS1 (IMPA2; IMPORTIN ALPHA 2) as a NHR gene. Mutation in RSS1 at P65S in first exon compromise the immunity to R. solani. rss1 shows enhanced cell death, ROS, callose deposition and developmental defect. RSS1 activates early salicylic acid mediated defense response against R. solani.
There is neither resistant rice cultivar nor any control measure against Rhizoctonia solani AG-1 IA (RS), causal of sheath blight and a major threat to global rice production. Rice is a host and Arabidopsis is a nonhost with underlying nonhost resistance (NHR) gene which is largely untested. Using approaches of forward genetics and tools, cytology, and molecular biology, we identified homozygous mutants in Arabidopsis, mapped the NHR gene, and functionally characterized it in response to RS. Rss1 was mapped on Ch 4 between JAERI18 and Ch4_9.18 (844.6 Kb) and identified IMPORTIN ALPHA 2 as the candidate RSS1 gene. We found that breach of immunity in rss1 by RS activates defense responses whereas photosynthetic pigment biosynthesis and developmental processes are negatively regulated. In addition, a gradual decrease in PR1 by 3 dpi revealed that RSS1 positively regulated early SA-mediated resistance. Whereas increased expression of PDF1.2 by 3 dpi supported switching to necrotrophy, SA-mediated defense in Col-0 leading to immune response. Enhanced expression of ATG8a in rss1 supported autophagic cell death. IMPA2, IMPA1, and RAN1 function together to provide NHR against RS. These findings demonstrate that IMPA2 provides NHR against RS in Col-0 that evoke SA-mediated early immunity with boulevard for potential biotechnological application.
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Huang CY, Jin H. Coordinated Epigenetic Regulation in Plants: A Potent Managerial Tool to Conquer Biotic Stress. FRONTIERS IN PLANT SCIENCE 2022; 12:795274. [PMID: 35046981 PMCID: PMC8762163 DOI: 10.3389/fpls.2021.795274] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Plants have evolved variable phenotypic plasticity to counteract different pathogens and pests during immobile life. Microbial infection invokes multiple layers of host immune responses, and plant gene expression is swiftly and precisely reprogramed at both the transcriptional level and post-transcriptional level. Recently, the importance of epigenetic regulation in response to biotic stresses has been recognized. Changes in DNA methylation, histone modification, and chromatin structures have been observed after microbial infection. In addition, epigenetic modifications may be preserved as transgenerational memories to allow the progeny to better adapt to similar environments. Epigenetic regulation involves various regulatory components, including non-coding small RNAs, DNA methylation, histone modification, and chromatin remodelers. The crosstalk between these components allows precise fine-tuning of gene expression, giving plants the capability to fight infections and tolerant drastic environmental changes in nature. Fully unraveling epigenetic regulatory mechanisms could aid in the development of more efficient and eco-friendly strategies for crop protection in agricultural systems. In this review, we discuss the recent advances on the roles of epigenetic regulation in plant biotic stress responses.
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Affiliation(s)
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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9
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The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles. Int J Mol Sci 2021; 22:ijms22168618. [PMID: 34445323 PMCID: PMC8395315 DOI: 10.3390/ijms22168618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/03/2021] [Accepted: 08/08/2021] [Indexed: 11/17/2022] Open
Abstract
In plants, the gene expression and associated phenotypes can be modulated by dynamic changes in DNA methylation, occasionally being fixed in certain genomic loci and inherited stably as epialleles. Epiallelic variations in a population can occur as methylation changes at an individual cytosine position, methylation changes within a stretch of genomic regions, and chromatin changes in certain loci. Here, we focus on methylated regions, since it is unclear whether variations at individual methylated cytosines can serve any regulatory function, and the evidence for heritable chromatin changes independent of genetic changes is limited. While DNA methylation is known to affect and regulate wide arrays of plant phenotypes, most epialleles in the form of methylated regions have not been assigned any biological function. Here, we review how epialleles can be established in plants, serve a regulatory function, and are involved in adaptive processes. Recent studies suggest that most epialleles occur as byproducts of genetic variations, mainly from structural variants and Transposable Element (TE) activation. Nevertheless, epialleles that occur spontaneously independent of any genetic variations have also been described across different plant species. Here, we discuss how epialleles that are dependent and independent of genetic architecture are stabilized in the plant genome and how methylation can regulate a transcription relative to its genomic location.
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Islam MT, Wang LC, Chen IJ, Lo KL, Lo WS. Arabidopsis JMJ17 promotes cotyledon greening during de-etiolation by repressing genes involved in tetrapyrrole biosynthesis in etiolated seedlings. THE NEW PHYTOLOGIST 2021; 231:1023-1039. [PMID: 33666236 DOI: 10.1111/nph.17327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Arabidopsis histone H3 lysine 4 (H3K4) demethylases play crucial roles in several developmental processes, but their involvement in seedling establishment remain unexplored. Here, we show that Arabidopsis JUMONJI DOMAIN-CONTAINING PROTEIN17 (JMJ17), an H3K4me3 demethylase, is involved in cotyledon greening during seedling establishment. Dark-grown seedlings of jmj17 accumulated a high concentration of protochlorophyllide, an intermediate metabolite in the tetrapyrrole biosynthesis (TPB) pathway that generates chlorophyll (Chl) during photomorphogenesis. Upon light irradiation, jmj17 mutants displayed decreased cotyledon greening and reduced Chl level compared with the wild-type; overexpression of JMJ17 completely rescued the jmj17-5 phenotype. Transcriptomics analysis uncovered that several genes encoding key enzymes involved in TPB were upregulated in etiolated jmj17 seedlings. Consistently, chromatin immunoprecipitation-quantitative PCR revealed elevated H3K4me3 level at the promoters of target genes. Chromatin association of JMJ17 was diminished upon light exposure. Furthermore, JMJ17 interacted with PHYTOCHROME INTERACTING FACTOR1 in the yeast two-hybrid assay. JMJ17 binds directly to gene promoters to demethylate H3K4me3 to suppress PROTOCHLOROPHYLLIDE OXIDOREDUCTASE C expression and TPB in the dark. Light results in de-repression of gene expression to modulate seedling greening during de-etiolation. Our study reveals a new role for histone demethylase JMJ17 in controlling cotyledon greening in etiolated seedlings during the dark-to-light transition.
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Affiliation(s)
- Md Torikul Islam
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Long-Chi Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - I-Ju Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Lin Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
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11
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Ramos-Cruz D, Troyee AN, Becker C. Epigenetics in plant organismic interactions. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102060. [PMID: 34087759 DOI: 10.1016/j.pbi.2021.102060] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 05/26/2023]
Abstract
Plants are hubs of organismic interactions. They constantly engage in beneficial or competitive interactions with fungi, oomycetes, bacteria, insects, nematodes, and other plants. To adjust the molecular processes necessary for the establishment and maintenance of beneficial interactions and for the defense against pathogens and herbivores, plants have evolved intricate regulatory mechanisms. Besides the canonical plant immune system that acts as the primary defense, epigenetic mechanisms have started to emerge as another regulatory entity and as a target of pathogens trying to overcome the plant's defenses. In this review, we highlight recent advances in understanding the contribution of various epigenetic components and of epigenetic diversity to plant-organismic interactions.
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Affiliation(s)
- Daniela Ramos-Cruz
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - A Niloya Troyee
- Department of Evolutionary Ecology, Doñana Biological Station, CSIC, 41092 Sevilla, Spain
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria; Genetics, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany.
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12
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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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Zhi P, Chang C. Exploiting Epigenetic Variations for Crop Disease Resistance Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:692328. [PMID: 34149790 PMCID: PMC8212930 DOI: 10.3389/fpls.2021.692328] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/27/2021] [Indexed: 05/07/2023]
Abstract
Pathogen infections seriously threaten plant health and global crop production. Epigenetic processes such as DNA methylation, histone post-translational modifications, chromatin assembly and remodeling play important roles in transcriptional regulation of plant defense responses and could provide a new direction to drive breeding strategies for crop disease resistance improvement. Although past decades have seen unprecedented proceedings in understanding the epigenetic mechanism of plant defense response, most of these advances were derived from studies in model plants like Arabidopsis. In this review, we highlighted the recent epigenetic studies on crop-pathogen interactions and discussed the potentials, challenges, and strategies in exploiting epigenetic variations for crop disease resistance improvement.
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14
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Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet 2020; 16:e1008993. [PMID: 32925902 PMCID: PMC7529245 DOI: 10.1371/journal.pgen.1008993] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic “arms race” with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7-associated H3K9me2 is required for optimal expression of RPP7. By profiling of genome-wide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the “raw material” for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase. We previously found the Arabidopsis thaliana PHD-finger protein EDM2 to serve as a chromatin-associated factor controlling expression of the NLR-type immune receptor gene RPP7. EDM2 binds to the transposon-silencing signal H3K9me2 and affects levels of this epigenetic mark at various loci. By genome-wide profiling of transcript- and H3K9me2-levels we now found EDM2 to have a broader role in controlling NLR gene expression. In order to mitigate fitness costs caused by its promoting effects on RPP7 expression and that of several other NLR genes, EDM2 seems to suppress expression of many additional members of this gene family. This observation is in line with multiple reports demonstrating the need for balanced expression of NLRs, which can substantially reduce overall plant fitness, but need to be present at certain minimal levels to confer sufficient immune protection. Our previous results demonstrated that the influence of EDM2 on RPP7 expression was co-opted to this immune receptor gene by the insertion of an EDM2-controlled transposon. Here, we are providing additional examples for transposon-associated effects on NLR gene expression, suggesting that these mobile elements play an important role for NLR genes by equipping members of this rapidly evolving gene family with regulatory mechanisms needed for balanced expression.
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Affiliation(s)
- Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Xueqing Maggie Lu
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Songqin Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Jianqiang Wang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Wei Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne campus, United Kingdom
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Karine G. Le Roch
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
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Corrêa RL, Sanz-Carbonell A, Kogej Z, Müller SY, Ambrós S, López-Gomollón S, Gómez G, Baulcombe DC, Elena SF. Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants. Mol Biol Evol 2020; 37:1866-1881. [DOI: 10.1093/molbev/msaa091] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Although epigenetic factors may influence the expression of defense genes in plants, their role in antiviral responses and the impact of viral adaptation and evolution in shaping these interactions are still poorly explored. We used two isolates of turnip mosaic potyvirus with varying degrees of adaptation to Arabidopsis thaliana to address these issues. One of the isolates was experimentally evolved in the plant and presented increased load and virulence relative to the ancestral isolate. The magnitude of the transcriptomic responses was larger for the evolved isolate and indicated a role of innate immunity systems triggered by molecular patterns and effectors in the infection process. Several transposable elements located in different chromatin contexts and epigenetic-related genes were also affected. Correspondingly, mutant plants having loss or gain of repressive marks were, respectively, more tolerant and susceptible to turnip mosaic potyvirus, with a more efficient response against the ancestral isolate. In wild-type plants, both isolates induced similar levels of cytosine methylation changes, including in and around transposable elements and stress-related genes. Results collectively suggested that apart from RNA silencing and basal immunity systems, DNA methylation and histone modification pathways may also be required for mounting proper antiviral defenses and that the effectiveness of this type of regulation strongly depends on the degree of viral adaptation to the host.
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Affiliation(s)
- Régis L Corrêa
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
- Department of Genetics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alejandro Sanz-Carbonell
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Zala Kogej
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Sebastian Y Müller
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Ambrós
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - Sara López-Gomollón
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Gustavo Gómez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC)—Universitat de València, Paterna, Valencia, Spain
- The Santa Fe Institute, Santa Fe, NM
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