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Xie JQ, Zhou X, Jia ZC, Su CF, Zhang Y, Fernie AR, Zhang J, Du ZY, Chen MX. Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37916838 DOI: 10.1021/acs.jafc.3c04163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Disease represents a major problem in sustainable agricultural development. Plants interact closely with various microorganisms during their development and in response to the prevailing environment. In particular, pathogenic microorganisms can cause plant diseases, affecting the fertility, yield, and longevity of plants. During the long coevolution of plants and their pathogens, plants have evolved both molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) signaling networks in order to regulate host cells in response to pathogen infestation. Additionally, in the postgenomic era, alternative splicing (AS) has become uncovered as one of the major drivers of proteome diversity, and abnormal RNA splicing is closely associated with bacterial infections. Currently, the complexity of host-bacteria interactions is a much studied area of research that has shown steady progress over the past decade. Although the development of high-throughput sequencing technologies and their application in transcriptomes have revolutionized our understanding of AS, many mechanisms related to host-bacteria interactions remain still unclear. To this end, this review summarizes the changes observed in AS during host-bacteria interactions and outlines potential therapeutics for bacterial diseases based on existing studies. In doing so, we hope to provide guidelines for plant disease management in agriculture.
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Affiliation(s)
- Ji-Qin Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Chang-Feng Su
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhi-Yan Du
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Mo-Xian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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2
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Fu W, Yu Y, Shu J, Yu Z, Zhong Y, Zhu T, Zhang Z, Liang Z, Cui Y, Chen C, Li C. Organization, genomic targeting, and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis. THE PLANT CELL 2023; 35:2464-2483. [PMID: 37062961 PMCID: PMC10291025 DOI: 10.1093/plcell/koad111] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
Switch defective/sucrose nonfermentable (SWI/SNF) complexes are evolutionarily conserved multisubunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes are poorly understood. Here, we report the organization, genomic targeting, and assembly of 3 distinct SWI/SNF complexes in Arabidopsis thaliana: BRAHMA-Associated SWI/SNF complexes (BAS), SPLAYED-Associated SWI/SNF complexes (SAS), and MINUSCULE-Associated SWI/SNF complexes (MAS). We show that BAS complexes are equivalent to human ncBAF, whereas SAS and MAS complexes evolve in multiple subunits unique to plants, suggesting plant-specific functional evolution of SWI/SNF complexes. We further show overlapping and specific genomic targeting of the 3 plant SWI/SNF complexes on chromatin and reveal that SAS complexes are necessary for the correct genomic localization of the BAS complexes. Finally, we define the role of the core module subunit in the assembly of plant SWI/SNF complexes and highlight that ATPase module subunit is required for global complex stability and the interaction of core module subunits in Arabidopsis SAS and BAS complexes. Together, our work highlights the divergence of SWI/SNF chromatin remodelers during eukaryote evolution and provides a comprehensive landscape for understanding plant SWI/SNF complex organization, assembly, genomic targeting, and function.
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Affiliation(s)
- Wei Fu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Shu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zewang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yixiong Zhong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhihao Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada N5V 4T3
| | - Chen Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Yang L, Wang Z, Hua J. Multiple chromatin-associated modules regulate expression of an intracellular immune receptor gene in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:2284-2297. [PMID: 36509711 DOI: 10.1111/nph.18672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The expression of an intracellular immune receptor gene SNC1 (SUPPRESSOR OF npr1, CONSTITUTIVE 1) is regulated by multiple chromatin-associated proteins for tuning immunity and growth in Arabidopsis. Whether and how these regulators coordinate to regulate SNC1 expression under varying environmental conditions is not clear. Here, we identified two activation and one repression regulatory modules based on genetic and molecular characterizations of five chromatin-associated regulators of SNC1. Modifier of snc1 (MOS1) constitutes the first module and is required for the interdependent functions of ARABIDOPSIS TRITHORAX-RELATED 7 (ATXR7) and HISTONE MONOUBIQUITINATION 1 (HUB1) to deposit H3K4me3 and H2Bub1 at the SNC1 locus. CHROMATIN REMODELING 5 (CHR5) constitutes a second module and works independently of ATXR7 and HUB1 in the MOS1 module. HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15) constitutes a third module responsible for removing H3K9ac to repress SNC1 expression under nonpathogenic conditions. The upregulation of SNC1 resulting from removing the HOS15 repression module is partially dependent on the function of the CHR5 module and the MOS1 module. Together, this study reveals both the distinct and interdependent regulatory mechanisms at the chromatin level for SNC1 expression regulation and highlights the intricacy of regulatory mechanisms of NLR expression under different environment.
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Affiliation(s)
- Leiyun Yang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Department of Plant Pathology, College of Plant Protection, Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhixue Wang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Wang L, Xu F, Yu F. Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation. PLANT, CELL & ENVIRONMENT 2023; 46:718-732. [PMID: 36609800 DOI: 10.1111/pce.14537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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5
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Xie Y, Wang Y, Yu X, Lin Y, Zhu Y, Chen J, Xie H, Zhang Q, Wang L, Wei Y, Xiao Y, Cai Q, Zheng Y, Wang M, Xie H, Zhang J. SH3P2, an SH3 domain-containing protein that interacts with both Pib and AvrPib, suppresses effector-triggered, Pib-mediated immunity in rice. MOLECULAR PLANT 2022; 15:1931-1946. [PMID: 36321201 DOI: 10.1016/j.molp.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 09/03/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Plants usually keep resistance (R) proteins in a static state under normal conditions to avoid autoimmunity and save energy for growth, but R proteins can be rapidly activated upon perceiving pathogen invasion. Pib, the first cloned blast disease R gene in rice, encoding a nucleotide-binding leucine-rich repeat (NLR) protein, mediates resistance to the blast fungal (Magnaporthe oryzae) isolates carrying the avirulence gene AvrPib. However, the molecular mechanisms about how Pib recognizes AvrPib and how it is inactivated and activated remain largely unclear. In this study, through map-based cloning and CRISPR-Cas9 gene editing, we proved that Pib contributes to the blast disease resistance of rice cultivar Yunyin (YY). Furthermore, an SH3 domain-containing protein, SH3P2, was found to associate with Pib mainly at clathrin-coated vesicles in rice cells, via direct binding with the coiled-coil (CC) domain of Pib. Interestingly, overexpression of SH3P2 in YY compromised Pib-mediated resistance to M. oryzae isolates carrying AvrPib and Pib-AvrPib recognition-induced cell death. SH3P2 competitively inhibits the self-association of the Pib CC domain in vitro, suggesting that binding of SH3P2 with Pib undermines its homodimerization. Moreover, SH3P2 can also interact with AvrPib and displays higher affinity to AvrPib than to Pib, which leads to dissociation of SH3P2 from Pib in the presence of AvrPib. Taken together, our results suggest that SH3P2 functions as a "protector" to keep Pib in a static state by direct interaction during normal growth but could be triggered off by the invasion of AvrPib-carrying M. oryzae isolates. Our study reveals a new mechanism about how an NLR protein is inactivated under normal conditions but is activated upon pathogen infection.
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Affiliation(s)
- Yunjie Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yupeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Xiangzhen Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yuelong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yongsheng Zhu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Jinwen Chen
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Hongguang Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Qingqing Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lanning Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yidong Wei
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yanjia Xiao
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Qiuhua Cai
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Yanmei Zheng
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China
| | - Mo Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huaan Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China.
| | - Jianfu Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs, Fuzhou, P.R. China; Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology, Fuzhou, China; Fuzhou Branch, National Rice Improvement Center of China, Fuzhou, China; Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China; Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou 350003, China.
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6
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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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Kufel J, Diachenko N, Golisz A. Alternative splicing as a key player in the fine-tuning of the immunity response in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2022; 23:1226-1238. [PMID: 35567423 PMCID: PMC9276941 DOI: 10.1111/mpp.13228] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/01/2023]
Abstract
Plants, like animals, are constantly exposed to abiotic and biotic stresses, which often inhibit plant growth and development, and cause tissue damage, disease, and even plant death. Efficient and timely response to stress requires appropriate co- and posttranscriptional reprogramming of gene expression. Alternative pre-mRNA splicing provides an important layer of this regulation by controlling the level of factors involved in stress response and generating additional protein isoforms with specific features. Recent high-throughput studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection. Despite extensive work, the exact mechanisms underlying these relationships are still unclear, but the contribution of alternative protein isoforms to the defence response and the role of regulatory factors, including components of the splicing machinery, have been established. Modulation of gene expression in response to stress includes alternative splicing, chromatin remodelling, histone modifications, and nucleosome occupancy. How these processes affect plant immunity is mostly unknown, but these facets open new regulatory possibilities. Here we provide an overview of the current state of knowledge and recent findings regarding the growing importance of alternative splicing in plant response to biotic stress.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Nataliia Diachenko
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Anna Golisz
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
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8
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Transcriptional regulation of plant innate immunity. Essays Biochem 2022; 66:607-620. [PMID: 35726519 PMCID: PMC9528082 DOI: 10.1042/ebc20210100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022]
Abstract
Transcriptional reprogramming is an integral part of plant immunity. Tight regulation of the immune transcriptome is essential for a proper response of plants to different types of pathogens. Consequently, transcriptional regulators are proven targets of pathogens to enhance their virulence. The plant immune transcriptome is regulated by many different, interconnected mechanisms that can determine the rate at which genes are transcribed. These include intracellular calcium signaling, modulation of the redox state, post-translational modifications of transcriptional regulators, histone modifications, DNA methylation, modulation of RNA polymerases, alternative transcription inititation, the Mediator complex and regulation by non-coding RNAs. In addition, on their journey from transcription to translation, mRNAs are further modulated through mechanisms such as nuclear RNA retention, storage of mRNA in stress granules and P-bodies, and post-transcriptional gene silencing. In this review, we highlight the latest insights into these mechanisms. Furthermore, we discuss some emerging technologies that promise to greatly enhance our understanding of the regulation of the plant immune transcriptome in the future.
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9
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Lapin D, Johanndrees O, Wu Z, Li X, Parker JE. Molecular innovations in plant TIR-based immunity signaling. THE PLANT CELL 2022; 34:1479-1496. [PMID: 35143666 PMCID: PMC9153377 DOI: 10.1093/plcell/koac035] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 05/19/2023]
Abstract
A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.
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Affiliation(s)
- Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
- Author for correspondence: (D.L.), (J.E.P.)
| | - Oliver Johanndrees
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Zhongshou Wu
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Duesseldorf 40225, Germany
- Author for correspondence: (D.L.), (J.E.P.)
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10
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Zhang X, Dong X. Life-or-death decisions in plant immunity. Curr Opin Immunol 2022; 75:102169. [PMID: 35168119 PMCID: PMC9081146 DOI: 10.1016/j.coi.2022.102169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/17/2022] [Accepted: 01/25/2022] [Indexed: 11/19/2022]
Abstract
Upon pathogen challenge, plant cells can mount defense not only by triggering programmed cell death (PCD) to limit pathogen growth, but also by secreting immune signals to activate subsequent organism-scale defense responses. Recent advances in the study of plant immune mechanisms have found that pathogen-induced oligomerization of immune receptors is a common 'on' switch for the normally self-inhibitory proteins. The resulting 'resistosome' triggers PCD through the formation of a calcium channel or a NADase. Synergy between different receptor-mediated signaling pathways appears to be required for sustained immune induction to trigger PCD of infected cells. In the neighboring cells, PCD is inhibited through the production of immune signal salicylic acid (SA) which mediates degradation of PCD-inducing immune components in biomolecular condensates. Future work is required to connect the resistosome-mediated channel formation and the NADase activity to the downstream regulation of immune execution.
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Affiliation(s)
- Xing Zhang
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Xinnian Dong
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA.
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11
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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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12
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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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13
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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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14
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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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15
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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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