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Mierziak J, Wojtasik W. Epigenetic weapons of plants against fungal pathogens. BMC PLANT BIOLOGY 2024; 24:175. [PMID: 38443788 PMCID: PMC10916060 DOI: 10.1186/s12870-024-04829-8] [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: 07/14/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.
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Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland.
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Liu H, Li J, Wang S, Hua J, Zou B. CHROMATIN REMODELING 11-dependent nucleosome occupancy affects disease resistance in rice. PLANT PHYSIOLOGY 2023; 193:1635-1651. [PMID: 37403194 DOI: 10.1093/plphys/kiad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023]
Abstract
Plant immune responses involve transcriptional reprograming of defense response genes, and chromatin remodeling is important for transcriptional regulation. However, nucleosome dynamics induced by pathogen infection and its association with gene transcription are largely unexplored in plants. Here, we investigated the role of the rice (Oryza sativa) gene CHROMATIN REMODELING 11 (OsCHR11) in nucleosome dynamics and disease resistance. Nucleosome profiling revealed that OsCHR11 is required for the maintaining of genome-wide nucleosome occupancy in rice. Nucleosome occupancy of 14% of the genome was regulated by OsCHR11. Infection of bacterial leaf blight Xoo (Xanthomonas oryzae pv. oryzae) repressed genome-wide nucleosome occupancy, and this process depended on OsCHR11 function. Furthermore, OsCHR11/Xoo-dependent chromatin accessibility correlated with gene transcript induction by Xoo. In addition, accompanied by increased resistance to Xoo, several defense response genes were differentially expressed in oschr11 after Xoo infection. Overall, this study reports the genome-wide effects of pathogen infection on nucleosome occupancy, its regulation, and its contribution to disease resistance in rice.
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Affiliation(s)
- He Liu
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Li
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Baohong Zou
- The State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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Meher J, Sarkar A, Sarma BK. Binding of stress-responsive OsWRKY proteins through WRKYGQK heptapeptide residue with the promoter region of two rice blast disease resistance genes Pi2 and Pi54 is important for development of blast resistance. 3 Biotech 2023; 13:294. [PMID: 37560615 PMCID: PMC10407006 DOI: 10.1007/s13205-023-03711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Molecular docking was done to investigate the interactions between five differentially expressed rice WRKY proteins when challenged with the rice blast disease caused by Magnaporthe oryzae and drought stresses applied either individually or overlapped, with the promoter region of two blast resistance genes (Pi2 and Pi54). Molecular docking was performed using the HDOCK server. Initially, the homology models for each of the five rice WRKY proteins were prepared using I-TASSER server, and then the secondary structure as well as the DNA-binding pockets were predicted using PSIPRED and BindUP servers, respectively. The molecular docking study revealed a differential binding pattern of the rice WRKYs with the two blast resistance genes. The WRKY proteins (OsWRKY88 and OsWRKY102), whose transcript levels decrease when drought and blast stresses are overlapped, interact with the two resistance genes mostly involving the residues of the zinc finger structure. On the other hand, the WRKY proteins (OsWRKY53-1 and OsWRKY113), whose transcript levels did not reduce significantly when challenged by drought and blast overlapped condition compared to individual treatment of blast, interact mostly involving the residues of the conserved WRKYGQK heptapeptide sequence. Interestingly, the protein OsWRKY74 whose transcript levels are unaffected in both individual and overlapped stresses, interacts with both the blast resistance genes involving few residues of both WRKYGQK heptapeptide and the zinc finger structure. The findings thus indicate that the interaction of OsWRKY proteins involving the conserved WRKYGQK heptapeptide sequence with the blast resistance genes Pi2 and Pi54 is important to mitigate the blast challenge in rice even during overlapping challenges of drought. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03711-y.
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Affiliation(s)
- Jhumishree Meher
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Ankita Sarkar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005 India
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Wu X, Zhang X, Huang B, Han J, Fang H. Advances in biological functions and mechanisms of histone variants in plants. Front Genet 2023; 14:1229782. [PMID: 37588047 PMCID: PMC10426802 DOI: 10.3389/fgene.2023.1229782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Nucleosome is the basic subunit of chromatin, consisting of approximately 147bp DNA wrapped around a histone octamer, containing two copies of H2A, H2B, H3 and H4. A linker histone H1 can bind nucleosomes through its conserved GH1 domain, which may promote chromatin folding into higher-order structures. Therefore, the complexity of histones act importantly for specifying chromatin and gene activities. Histone variants, encoded by separate genes and characterized by only a few amino acids differences, can affect nucleosome packaging and stability, and then modify the chromatin properties. Serving as carriers of pivotal genetic and epigenetic information, histone variants have profound significance in regulating plant growth and development, response to both biotic and abiotic stresses. At present, the biological functions of histone variants in plant have become a research hotspot. Here, we summarize recent researches on the biological functions, molecular chaperons and regulatory mechanisms of histone variants in plant, and propose some novel research directions for further study of plant histone variants research field. Our study will provide some enlightens for studying and understanding the epigenetic regulation and chromatin specialization mediated by histone variant in plant.
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Affiliation(s)
- Xi Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xu Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Borong Huang
- Developmental Biology, Laboratory of Plant Molecular and Zhejiang A & F University, Hangzhou, China
| | - Junyou Han
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Huihui Fang
- Developmental Biology, Laboratory of Plant Molecular and Zhejiang A & F University, Hangzhou, China
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Zarreen F, Karim MJ, Chakraborty S. The diverse roles of histone 2B monoubiquitination in the life of plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3854-3865. [PMID: 35348666 DOI: 10.1093/jxb/erac120] [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: 10/07/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Covalent modification of histones is an important tool for gene transcriptional control in eukaryotes, which coordinates growth, development, and adaptation to environmental changes. In recent years, an important role for monoubiquitination of histone 2B (H2B) has emerged in plants, where it is associated with transcriptional activation. In this review, we discuss the dynamics of the H2B monoubiquitination system in plants and its role in regulating developmental processes including flowering, circadian rhythm, photomorphogenesis, and the response to abiotic and biotic stress including drought, salinity, and fungal, bacterial, and viral pathogens. Furthermore, we highlight the crosstalk between H2B monoubiquitination and other histone modifications which fine-tunes transcription and ensures developmental plasticity. Finally, we put into perspective how this versatile regulatory mechanism can be developed as a useful tool for crop improvement.
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Affiliation(s)
- Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mir Jishan Karim
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Guo M, Zhao H, He Z, Zhang W, She Z, Mohammadi MA, Shi C, Yan M, Tian D, Qin Y. Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:910663. [PMID: 35712583 PMCID: PMC9194907 DOI: 10.3389/fpls.2022.910663] [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: 04/01/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aqa Mohammadi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Dagang Tian
- Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
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Guo M, Zhang W, Mohammadi MA, He Z, She Z, Yan M, Shi C, Lin L, Wang A, Liu J, Tian D, Zhao H, Qin Y. OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:873993. [PMID: 35463416 PMCID: PMC9024357 DOI: 10.3389/fpls.2022.873993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aqa Mohammadi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingwei Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aqiong Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jindian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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CaSWC4 regulates the immunity-thermotolerance tradeoff by recruiting CabZIP63/CaWRKY40 to target genes and activating chromatin in pepper. PLoS Genet 2022; 18:e1010023. [PMID: 35226664 PMCID: PMC8884482 DOI: 10.1371/journal.pgen.1010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
Pepper (Capsicum annuum) responds differently to high temperature stress (HTS) and Ralstonia solanacearum infection (RSI) but employs some shared transcription factors (TFs), such as CabZIP63 and CaWRKY40, in both cases. How the plant activates and balances these distinct responses, however, was unclear. Here, we show that the protein CaSWC4 interacts with CaRUVBL2 and CaTAF14b and they all act positively in pepper response to RSI and thermotolerance. CaSWC4 activates chromatin of immunity or thermotolerance related target genes of CaWRKY40 or CabZIP63 by promoting deposition of H2A.Z, H3K9ac and H4K5ac, simultaneously recruits CabZIP63 and CaWRKY40 through physical interaction and brings them to their targets (immunity- or thermotolerance-related genes) via binding AT-rich DNA element. The above process relies on the recruitment of CaRUVBL2 and TAF14 by CaSWC4 via physical interaction, which occurs at loci of immunity related target genes only when the plants are challenged with RSI, and at loci of thermotolerance related target genes only upon HTS. Collectively, our data suggest that CaSWC4 regulates rapid, accurate responses to both RSI and HTS by modulating chromatin of specific target genes opening and recruiting the TFs, CaRUVBL2 and CaTAF14b to the specific target genes, thereby helping achieve the balance between immunity and thermotolerance.
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Hannan Parker A, Wilkinson SW, Ton J. Epigenetics: a catalyst of plant immunity against pathogens. THE NEW PHYTOLOGIST 2022; 233:66-83. [PMID: 34455592 DOI: 10.1111/nph.17699] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/20/2021] [Indexed: 05/11/2023]
Abstract
The plant immune system protects against pests and diseases. The recognition of stress-related molecular patterns triggers localised immune responses, which are often followed by longer-lasting systemic priming and/or up-regulation of defences. In some cases, this induced resistance (IR) can be transmitted to following generations. Such transgenerational IR is gradually reversed in the absence of stress at a rate that is proportional to the severity of disease experienced in previous generations. This review outlines the mechanisms by which epigenetic responses to pathogen infection shape the plant immune system across expanding time scales. We review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, we explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes. This raises questions about the long-term evolutionary consequences of stress-induced diversification of the plant immune system in relation to the long-held dichotomy between Darwinian and Lamarckian evolution.
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Affiliation(s)
- Adam Hannan Parker
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Samuel W Wilkinson
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jurriaan Ton
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
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Yang Z, Zhi P, Chang C. Priming seeds for the future: Plant immune memory and application in crop protection. FRONTIERS IN PLANT SCIENCE 2022; 13:961840. [PMID: 35968080 PMCID: PMC9372760 DOI: 10.3389/fpls.2022.961840] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/13/2022] [Indexed: 05/12/2023]
Abstract
Plants have evolved adaptive strategies to cope with pathogen infections that seriously threaten plant viability and crop productivity. Upon the perception of invading pathogens, the plant immune system is primed, establishing an immune memory that allows primed plants to respond more efficiently to the upcoming pathogen attacks. Physiological, transcriptional, metabolic, and epigenetic changes are induced during defense priming, which is essential to the establishment and maintenance of plant immune memory. As an environmental-friendly technique in crop protection, seed priming could effectively induce plant immune memory. In this review, we highlighted the recent advances in the establishment and maintenance mechanisms of plant defense priming and the immune memory associated, and discussed strategies and challenges in exploiting seed priming on crops to enhance disease resistance.
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Ding X, Jia X, Xiang Y, Jiang W. Histone Modification and Chromatin Remodeling During the Seed Life Cycle. FRONTIERS IN PLANT SCIENCE 2022; 13:865361. [PMID: 35548305 PMCID: PMC9083068 DOI: 10.3389/fpls.2022.865361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Seeds are essential for the reproduction and dispersion of spermatophytes. The seed life cycle from seed development to seedling establishment proceeds through a series of defined stages regulated by distinctive physiological and biochemical mechanisms. The role of histone modification and chromatin remodeling in seed behavior has been intensively studied in recent years. In this review, we summarize progress in elucidating the regulatory network of these two kinds of epigenetic regulation during the seed life cycle, especially in two model plants, rice and Arabidopsis. Particular emphasis is placed on epigenetic effects on primary tissue formation (e.g., the organized development of embryo and endosperm), pivotal downstream gene expression (e.g., transcription of DOG1 in seed dormancy and repression of seed maturation genes in seed-to-seedling transition), and environmental responses (e.g., seed germination in response to different environmental cues). Future prospects for understanding of intricate interplay of epigenetic pathways and the epigenetic mechanisms in other commercial species are also proposed.
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Affiliation(s)
- Xiali Ding
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Xuhui Jia
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yong Xiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Wenhui Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- *Correspondence: Wenhui Jiang,
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Jian Y, Shim WB, Ma Z. Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions. STRESS BIOLOGY 2021; 1:18. [PMID: 37676626 PMCID: PMC10442046 DOI: 10.1007/s44154-021-00019-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 09/08/2023]
Abstract
The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events. Studies in animals, plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses. In this review, we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription, mRNA splicing, and DNA damage response. Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis. Finally, the potentials in exploiting chromatin remodeling for management of crop disease are presented.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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Wang J, Wang J, Li J, Shang H, Chen X, Hu X. The RLK protein TaCRK10 activates wheat high-temperature seedling-plant resistance to stripe rust through interacting with TaH2A.1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1241-1255. [PMID: 34583419 DOI: 10.1111/tpj.15513] [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: 11/08/2020] [Accepted: 09/22/2021] [Indexed: 05/27/2023]
Abstract
Plants sense various pathogens and activate immunity responses through receptor-like kinases (RLKs). Cysteine-rich receptor-like kinases (CRKs) are involved in massive transduction pathways upon perception of a pathogen. However, the roles of CRKs in response to stripe rust are unclear. In the present study, we identified a CRK gene (designated TaCRK10) from wheat variety Xiaoyan 6 (XY6) that harbors high-temperature seedling-plant (HTSP) resistance to stripe rust caused by fungal pathogen Puccinia striiformis f. sp. tritici (Pst). The expression level of TaCRK10 was induced by Pst inoculation and high temperature treatment. Knockdown of TaCRK10 by virus-induced gene silencing resulted in attenuated wheat HTSP resistance to Pst, whereas there is no effect on Pst development and host responses under normal temperatures. Notably, overexpression of TaCRK10 in susceptible variety Fielder provided resistance only under normal temperatures at 14 days with reactive oxygen species accumulation and defense-related gene expression of the salicylic acid pathway. Moreover, TaCRK10 physically interacted with and phosphorylated a histone variant TaH2A.1, which belongs to the H2A.W group. Silencing of TaH2A.1 suppressed wheat resistance to Pst, indicating that TaH2A.1 plays a positive role in wheat resistance to Pst. Thus, TaCRK10 serves as an important sensor of Pst infection and high temperatures, and it activates wheat resistance to Pst through regulating nuclear processes. This knowledge helps elucidate the molecular mechanism of wheat HTSP resistance to Pst and promotes efforts in developing wheat varieties with resistance to stripe rust.
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Affiliation(s)
- Jiahui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
| | - Jingjing Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
| | - Juan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
| | - Hongsheng Shang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
| | - Xianming Chen
- Agricultural Research Service, United States Department of Agriculture and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, 712100, China
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14
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Xiao S, Jiang L, Wang C, Ow DW. Arabidopsis OXS3 family proteins repress ABA signaling through interactions with AFP1 in the regulation of ABI4 expression. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5721-5734. [PMID: 34037750 DOI: 10.1093/jxb/erab237] [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: 11/30/2020] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Abscisic acid (ABA) and the AP2/ERF (APETALA2/ETHYLENE-RESPONSIVE FACTOR)-type transcription factor called ABA INSENSITIVE 4 (ABI4) play pivotal roles in plant growth responses to environmental stress. An analysis of seedling development in Arabidopsis ABA hypersensitive mutants suggested that OXS3 (OXIDATIVE STRESS 3), OXS3b, O3L3 (OXS3 LIKE 3), O3L4, and O3L6 were negative regulators of ABI4 expression. We therefore characterized the roles of the OXS3 family members in ABA signaling. All the above five OXS3 proteins were found to interact with AFP1 (ABI FIVE BINDING PROTEIN 1) in yeast two hybrid assays. Seven OXS3 family members including two other members O3L1 and O3L5 were found to interact with histone H2A.X, although OXS3b, O3L3, and O3L5 showed weaker interactions. ChIP-qPCR analysis showed that the absence of some of these OXS3 family proteins was associated with increased occupancy of histone γ-H2A.X at the ABI4 promoter, which also corresponded with de-repression of ABI4 expression. Repression of ABI4 expression, however, required both AFP1 and OXS3, OXS3b or O3L6. We conclude that in the absence of stress, OXS3 family proteins regulate γ-H2A.X deposition at the ABI4 promoter and that together with AFP1, OXS3 family proteins function to prevent ABA-induced growth arrest by co-repressing ABI4 through decreased promoter occupancy of histone γ-H2A.X.
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Affiliation(s)
- Shimin Xiao
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Jiang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changhu Wang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - David W Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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15
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Lai F, Cheng Y, Zou J, Wang H, Zhu W, Wang X, Cheng H, Zhou R. Identification of Histone Modifications Reveals a Role of H2b Monoubiquitination in Transcriptional Regulation of dmrt1 in Monopterus albus. Int J Biol Sci 2021; 17:2009-2020. [PMID: 34131402 PMCID: PMC8193266 DOI: 10.7150/ijbs.59347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 01/14/2023] Open
Abstract
Gonadal trans-differentiation from ovary to testis occurs in a same individual, suggesting a role of epigenetic regulation. However, histone modifications concerning the sex reversal process remain elusive. We analyzed histone modifications using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology was used to test chromatin immunoprecipitation of gonads. Western blot analysis was performed to analyze protein expression. Immunofluorescence analysis was conducted to localize proteins in gonadal tissues. Here, we report a developmental atlas of histone modifications in the gonadal differentiation, including acetylation, methylation, and ubiquitination. We provided a detail distribution map of these modification sites including novel histone modifications along histones H2a, H2b, H3, and H4, and revealed their relationship with types of gonadal differentiation. We then determined a testis-enriched histone modification site, H2b monoubiquitination at K120, and its association with spermatogenesis. ChIP-seq demonstrated that the modification was highly enriched in the male sex-determining gene dmrt1 (doublesex and mab-3 related transcription factor 1), in particular, in its exon regions, suggesting its role in transcriptional regulation of dmrt1 in testis. Together, these data not only provide a new resource for epigenetic study in gonadal development, but also define an association of histone modifications with gonadal differentiation from ovary to testis.
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Affiliation(s)
- Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yibin Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Juan Zou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Haoyu Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wang Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
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16
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Pardal AJ, Piquerez SJM, Dominguez-Ferreras A, Frungillo L, Mastorakis E, Reilly E, Latrasse D, Concia L, Gimenez-Ibanez S, Spoel SH, Benhamed M, Ntoukakis V. Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLoS Pathog 2021; 17:e1009572. [PMID: 34015058 PMCID: PMC8171942 DOI: 10.1371/journal.ppat.1009572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/02/2021] [Accepted: 04/19/2021] [Indexed: 01/23/2023] Open
Abstract
Perception of microbes by plants leads to dynamic reprogramming of the transcriptome, which is essential for plant health. The appropriate amplitude of this transcriptional response can be regulated at multiple levels, including chromatin. However, the mechanisms underlying the interplay between chromatin remodeling and transcription dynamics upon activation of plant immunity remain poorly understood. Here, we present evidence that activation of plant immunity by bacteria leads to nucleosome repositioning, which correlates with altered transcription. Nucleosome remodeling follows distinct patterns of nucleosome repositioning at different loci. Using a reverse genetic screen, we identify multiple chromatin remodeling ATPases with previously undescribed roles in immunity, including EMBRYO SAC DEVELOPMENT ARREST 16, EDA16. Functional characterization of the immune-inducible chromatin remodeling ATPase EDA16 revealed a mechanism to negatively regulate immunity activation and limit changes in redox homeostasis. Our transcriptomic data combined with MNase-seq data for EDA16 functional knock-out and over-expressor mutants show that EDA16 selectively regulates a defined subset of genes involved in redox signaling through nucleosome repositioning. Thus, collectively, chromatin remodeling ATPases fine-tune immune responses and provide a previously uncharacterized mechanism of immune regulation.
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Affiliation(s)
- Alonso J. Pardal
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sophie J. M. Piquerez
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | | | - Lucas Frungillo
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Emma Reilly
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Selena Gimenez-Ibanez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, Spain
| | - Steven H. Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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17
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Song ZT, Liu JX, Han JJ. Chromatin remodeling factors regulate environmental stress responses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:438-450. [PMID: 33421288 DOI: 10.1111/jipb.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality. As sessile organisms, plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes. In eukaryotes, nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation. To enable dynamic access to packaged DNA, eukaryotes have evolved Snf2 (sucrose nonfermenting 2) family proteins as chromatin remodeling factors (CHRs) that modulate the position of nucleosomes on chromatin. During plant stress responses, CHRs are recruited to specific genomic loci, where they regulate the distribution or composition of nucleosomes, which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery. Moreover, CHRs interplay with other epigenetic mechanisms, including DNA methylation, histone modifications, and deposition of histone variants. CHRs are also involved in RNA processing at the post-transcriptional level. In this review, we discuss major advances in our understanding of the mechanisms by which CHRs function during plants' response to environmental stress.
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Affiliation(s)
- Ze-Ting Song
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500, China
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18
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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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19
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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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20
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Marsh DJ, Ma Y, Dickson KA. Histone Monoubiquitination in Chromatin Remodelling: Focus on the Histone H2B Interactome and Cancer. Cancers (Basel) 2020; 12:E3462. [PMID: 33233707 PMCID: PMC7699835 DOI: 10.3390/cancers12113462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin remodelling is a major mechanism by which cells control fundamental processes including gene expression, the DNA damage response (DDR) and ensuring the genomic plasticity required by stem cells to enable differentiation. The post-translational modification of histone H2B resulting in addition of a single ubiquitin, in humans at lysine 120 (K120; H2Bub1) and in yeast at K123, has key roles in transcriptional elongation associated with the RNA polymerase II-associated factor 1 complex (PAF1C) and in the DDR. H2Bub1 itself has been described as having tumour suppressive roles and a number of cancer-related proteins and/or complexes are recognised as part of the H2Bub1 interactome. These include the RING finger E3 ubiquitin ligases RNF20, RNF40 and BRCA1, the guardian of the genome p53, the PAF1C member CDC73, subunits of the switch/sucrose non-fermenting (SWI/SNF) chromatin remodelling complex and histone methyltransferase complexes DOT1L and COMPASS, as well as multiple deubiquitinases including USP22 and USP44. While globally depleted in many primary human malignancies, including breast, lung and colorectal cancer, H2Bub1 is selectively enriched at the coding region of certain highly expressed genes, including at p53 target genes in response to DNA damage, functioning to exercise transcriptional control of these loci. This review draws together extensive literature to cement a significant role for H2Bub1 in a range of human malignancies and discusses the interplay between key cancer-related proteins and H2Bub1-associated chromatin remodelling.
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Affiliation(s)
- Deborah J. Marsh
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
- Kolling Institute, Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Camperdown, NSW 2006, Australia
| | - Yue Ma
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
| | - Kristie-Ann Dickson
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
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21
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Khadka J, Pesok A, Grafi G. Plant Histone HTB (H2B) Variants in Regulating Chromatin Structure and Function. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1435. [PMID: 33113795 PMCID: PMC7694166 DOI: 10.3390/plants9111435] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/09/2020] [Accepted: 10/23/2020] [Indexed: 02/07/2023]
Abstract
Besides chemical modification of histone proteins, chromatin dynamics can be modulated by histone variants. Most organisms possess multiple genes encoding for core histone proteins, which are highly similar in amino acid sequence. The Arabidopsis thaliana genome contains 11 genes encoding for histone H2B (HTBs), 13 for H2A (HTAs), 15 for H3 (HTRs), and 8 genes encoding for histone H4 (HFOs). The finding that histone variants may be expressed in specific tissues and/or during specific developmental stages, often displaying specific nuclear localization and involvement in specific nuclear processes suggests that histone variants have evolved to carry out specific functions in regulating chromatin structure and function and might be important for better understanding of growth and development and particularly the response to stress. In this review, we will elaborate on a group of core histone proteins in Arabidopsis, namely histone H2B, summarize existing data, and illuminate the potential function of H2B variants in regulating chromatin structure and function in Arabidopsis thaliana.
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Affiliation(s)
| | | | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel; (J.K.); (A.P.)
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22
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Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties. Int J Genomics 2019; 2019:4168045. [PMID: 31687375 PMCID: PMC6811786 DOI: 10.1155/2019/4168045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 01/30/2023] Open
Abstract
Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.
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23
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Yang X, Lu Y, Zhao X, Jiang L, Xu S, Peng J, Zheng H, Lin L, Wu Y, MacFarlane S, Chen J, Yan F. Downregulation of Nuclear Protein H2B Induces Salicylic Acid Mediated Defense Against PVX Infection in Nicotiana benthamiana. Front Microbiol 2019; 10:1000. [PMID: 31134032 PMCID: PMC6517552 DOI: 10.3389/fmicb.2019.01000] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022] Open
Abstract
Histone H2B protein is not only structurally important for chromosomal DNA packaging but is also involved in the regulation of gene expression, including the immune response of plants against pathogens. In this study, we show that the potato virus X (PVX) infection resulted in the reduced expression of H2B at both the mRNA and protein level in Nicotiana benthamiana. Tobacco rattle virus (TRV)-based virus-induced gene silencing (VIGS) was then used to down-regulate the expression of H2B in N. benthamiana and tests showed that the titre of TRV was similar in these plants to that in control treated plants. When these H2B-silenced plants were inoculated with PVX, the virus spread more slowly through the plant and there was a lower titre of PVX compared to non-silenced plants. Abnormal leaf development and stem necrosis were observed in the H2B-silenced plants, which were alleviated in H2B-silenced NahG transgenic plants suggesting the involvement of salicylic acid (SA) in the production of these symptoms. Indeed, quantitative reverse transcription (qRT)-PCR and liquid chromatography tandem mass spectroscopy (LC-MS) results showed that endogenous SA is increased in H2B-silenced N. benthamiana. Thus, downregulation of H2B induced the accumulation of endogenous SA, which was correlated with stem necrosis and a decreased accumulation of PVX in N. benthamiana.
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Affiliation(s)
- Xue Yang
- Department of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuwen Lu
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xing Zhao
- Department of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Liangliang Jiang
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease - Key Laboratory of Biotechnology in Plant Protection, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Shengchun Xu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiejun Peng
- Institute of Plant Virology, Ningbo University, Ningbo, China.,State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease - Key Laboratory of Biotechnology in Plant Protection, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongying Zheng
- Institute of Plant Virology, Ningbo University, Ningbo, China.,State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease - Key Laboratory of Biotechnology in Plant Protection, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lin Lin
- Institute of Plant Virology, Ningbo University, Ningbo, China.,State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease - Key Laboratory of Biotechnology in Plant Protection, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuanhua Wu
- Department of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Stuart MacFarlane
- Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, United Kingdom
| | - Jianping Chen
- Institute of Plant Virology, Ningbo University, Ningbo, China.,State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease - Key Laboratory of Biotechnology in Plant Protection, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fei Yan
- Institute of Plant Virology, Ningbo University, Ningbo, China
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24
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Sharma C, Kumar S, Saripalli G, Jain N, Raghuvanshi S, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. H3K4/K9 acetylation and Lr28-mediated expression of six leaf rust responsive genes in wheat (Triticum aestivum). Mol Genet Genomics 2018; 294:227-241. [PMID: 30298213 DOI: 10.1007/s00438-018-1500-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
Abstract
Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose. The proximal and distal promoters of these genes contained a number of motifs that are known to respond to biotic stresses. The enrichment of two acetylation marks changed with passage of time; changes in expression of two of the six genes (N-acetyltransferase and peroxidase12), largely matched with changes in H3K4/H3K9 acetylation patterns of the two promoter regions. For example, enrichment of both the marks matched with higher expression of N-acetyltransferase gene in susceptible NIL and the deacetylation (H3K4ac) largely matched with reduced gene expression in resistant NIL. In peroxidase12, enrichment of H3K4ac and H3K9ac largely matched with higher expression in both the NILs. In the remaining four genes, changes in H3 acetylation did not always match with gene expression levels. This indicated complexity in the regulation of the expression of these remaining four genes, which may be controlled by other epigenetic/genetic regulatory mechanisms that need further analysis.
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Affiliation(s)
- Chanchal Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.,Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan, Gyeongbuk, 38453, South Korea
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - J B Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - K V Prabhu
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
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Ramirez-Prado JS, Piquerez SJM, Bendahmane A, Hirt H, Raynaud C, Benhamed M. Modify the Histone to Win the Battle: Chromatin Dynamics in Plant-Pathogen Interactions. FRONTIERS IN PLANT SCIENCE 2018; 9:355. [PMID: 29616066 PMCID: PMC5868138 DOI: 10.3389/fpls.2018.00355] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/02/2018] [Indexed: 05/02/2023]
Abstract
Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses. Herein, we review the state of the art in the epigenomic aspects of plant immunity, focusing on chromatin modifications, chromatin modifiers, and their physiological consequences. In addition, we explore the exciting field of understanding how plant pathogens have adapted to manipulate the plant epigenomic regulation in order to weaken their immune system and thrive in their host, as well as how histone modifications in eukaryotic pathogens are involved in the regulation of their virulence.
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Affiliation(s)
- Juan S. Ramirez-Prado
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Sophie J. M. Piquerez
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Abdelhafid Bendahmane
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Heribert Hirt
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Cécile Raynaud
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
| | - Moussa Benhamed
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, University Paris-Sud, University of Évry Val d’Essonne, University Paris Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, UMR9213 Institut des Sciences des Plantes de Paris Saclay, Essonne, France
- *Correspondence: Moussa Benhamed,
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26
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Hadwiger LA, Tanaka K. Non-host Resistance: DNA Damage Is Associated with SA Signaling for Induction of PR Genes and Contributes to the Growth Suppression of a Pea Pathogen on Pea Endocarp Tissue. FRONTIERS IN PLANT SCIENCE 2017; 8:446. [PMID: 28421088 PMCID: PMC5379135 DOI: 10.3389/fpls.2017.00446] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/14/2017] [Indexed: 05/06/2023]
Abstract
Salicylic acid (SA) has been reported to induce plant defense responses. The transcriptions of defense genes that are responsible for a given plant's resistance to an array of plant pathogens are activated in a process called non-host resistance. Biotic signals capable of carrying out the activation of pathogenesis-related (PR) genes in pea tissue include fungal DNase and chitosan, two components released from Fusarium solani spores that are known to target host DNA. Recent reports indicate that SA also has a physical affinity for DNA. Here, we report that SA-induced reactive oxygen species release results in fragment alterations in pea nuclear DNA and cytologically detectable diameter and structural changes in the pea host nuclei. Additionally, we examine the subsequent SA-related increase of resistance to the true pea pathogen F. solani f.sp. pisi and the accumulation of the phytoalexin pisatin. This is the first report showing that SA-induced PR gene activation may be attributed to the host pea genomic DNA damage and that at certain concentrations, SA can be temporally associated with subsequent increases in the defense response of this legume.
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27
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Chen W, Zhu Q, Liu Y, Zhang Q. Chromatin Remodeling and Plant Immunity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 106:243-260. [PMID: 28057214 DOI: 10.1016/bs.apcsb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense. So what are the links between Snf2-mediated ATP-dependent chromosome remodeling and plant immunity, and what mechanisms might support its involvement in disease resistance?
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Affiliation(s)
- W Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Y Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Q Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, College of Life Sciences, South China Agricultural University, Guangzhou, China.
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