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Gravot A, Liégard B, Quadrana L, Veillet F, Aigu Y, Bargain T, Bénéjam J, Lariagon C, Lemoine J, Colot V, Manzanares-Dauleux MJ, Jubault M. Two adjacent NLR genes conferring quantitative resistance to clubroot disease in Arabidopsis are regulated by a stably inherited epiallelic variation. PLANT COMMUNICATIONS 2024; 5:100824. [PMID: 38268192 PMCID: PMC11121752 DOI: 10.1016/j.xplc.2024.100824] [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: 09/05/2023] [Revised: 12/21/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Clubroot caused by the protist Plasmodiophora brassicae is a major disease affecting cultivated Brassicaceae. Using a combination of quantitative trait locus (QTL) fine mapping, CRISPR-Cas9 validation, and extensive analyses of DNA sequence and methylation patterns, we revealed that the two adjacent neighboring NLR (nucleotide-binding and leucine-rich repeat) genes AT5G47260 and AT5G47280 cooperate in controlling broad-spectrum quantitative partial resistance to the root pathogen P. brassicae in Arabidopsis and that they are epigenetically regulated. The variation in DNA methylation is not associated with any nucleotide variation or any transposable element presence/absence variants and is stably inherited. Variations in DNA methylation at the Pb-At5.2 QTL are widespread across Arabidopsis accessions and correlate negatively with variations in expression of the two genes. Our study demonstrates that natural, stable, and transgenerationally inherited epigenetic variations can play an important role in shaping resistance to plant pathogens by modulating the expression of immune receptors.
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Affiliation(s)
- Antoine Gravot
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Benjamin Liégard
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), 75005 Paris, France
| | - Florian Veillet
- IGEPP INRAE, Institut Agro, Université de Rennes, 29260 Ploudaniel, France
| | - Yoann Aigu
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Tristan Bargain
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Juliette Bénéjam
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | | | - Jocelyne Lemoine
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), 75005 Paris, France
| | | | - Mélanie Jubault
- IGEPP Institut Agro, INRAE, Université de Rennes, 35650 Le Rheu, France.
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Zhang N, Dong X, Jain R, Ruan D, de Araujo Junior AT, Li Y, Lipzen A, Martin J, Barry K, Ronald PC. XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent. PeerJ 2024; 12:e17323. [PMID: 38726377 PMCID: PMC11080989 DOI: 10.7717/peerj.17323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/10/2024] [Indexed: 05/12/2024] Open
Abstract
The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21. These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.
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Affiliation(s)
- Nan Zhang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Xiaoou Dong
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, Nanjing Agricultural University, Nanjing, China
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Feedstocks Division, The Joint Bioenergy Institute, Emeryville, CA, USA
| | - Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Deling Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
- Feedstocks Division, The Joint Bioenergy Institute, Emeryville, CA, USA
| | | | - Yan Li
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
- Rice Research Institute and Key Lab for Major Crop Diseases, Sichuan Agricultural University, Chengdu, China
| | - Anna Lipzen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joel Martin
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Feedstocks Division, The Joint Bioenergy Institute, Emeryville, CA, USA
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3
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Gao M, Hao Z, Ning Y, He Z. Revisiting growth-defence trade-offs and breeding strategies in crops. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1198-1205. [PMID: 38410834 PMCID: PMC11022801 DOI: 10.1111/pbi.14258] [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: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 02/28/2024]
Abstract
Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.
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Affiliation(s)
- Mingjun Gao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco‐Chongming, School of Life SciencesFudan UniversityShanghaiChina
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Zuhua He
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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4
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Seni S, Singh RK, Prasad M. Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194966. [PMID: 37532097 DOI: 10.1016/j.bbagrm.2023.194966] [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: 05/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
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Affiliation(s)
- Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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5
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Wen P, He J, Zhang Q, Qi H, Zhang A, Liu D, Sun Q, Wang Y, Li Q, Wang W, Chen Z, Wang Y, Liu Y, Wan J. SET Domain Group 703 Regulates Planthopper Resistance by Suppressing the Expression of Defense-Related Genes. Int J Mol Sci 2023; 24:13003. [PMID: 37629184 PMCID: PMC10455402 DOI: 10.3390/ijms241613003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Plant defense responses against insect pests are intricately regulated by highly complex regulatory networks. Post-translational modifications (PTMs) of histones modulate the expression of genes involved in various biological processes. However, the role of PTMs in conferring insect resistance remains unclear. Through the screening of a T-DNA insertion activation-tagged mutant collection in rice, we identified the mutant planthopper susceptible 1 (phs1), which exhibits heightened expression of SET domain group 703 (SDG703). This overexpression is associated with increased susceptibility to the small brown planthopper (SBPH), an economically significant insect pest affecting rice crops. SDG703 is constitutively expressed in multiple tissues and shows substantial upregulation in response to SBPH feeding. SDG703 demonstrates the activity of histone H3K9 methyltransferase. Transcriptomic analysis revealed the downregulation of genes involved in effector-triggered immunity (ETI) and pattern-triggered immunity (PTI) in plants overexpressing SDG703. Among the downregulated genes, the overexpression of SDG703 in plants resulted in a higher level of histone H3K9 methylation compared to control plants. Collectively, these findings indicate that SDG703 suppresses the expression of defense-related genes through the promotion of histone methylation, consequently leading to reduced resistance against SBPH. The defense-related genes regulated by histone methylation present valuable targets for developing effective pest management strategies in future studies. Furthermore, our study provides novel insight into the epigenetic regulation involved in plant-insect resistance.
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Affiliation(s)
- Peizheng Wen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Jun He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Qiong Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Hongzhi Qi
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Aoran Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Daoming Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Quanguang Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Yongsheng Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Qi Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Wenhui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Zhanghao Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Yunlong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Yuqiang Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Nanjing Rice Germplasm Resources National Field Observation and Research Station, Jiangsu Provincial Research Center of Plant Gene Editing Engineering, Nanjing Agricultural University, Nanjing 210095, China; (P.W.); (J.H.); (Q.Z.); (H.Q.); (A.Z.); (D.L.); (Q.S.); (Y.W.); (Q.L.); (W.W.); (Z.C.); (Y.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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6
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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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7
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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: 5] [Impact Index Per Article: 2.5] [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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8
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Oya S, Takahashi M, Takashima K, Kakutani T, Inagaki S. Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation. Nat Commun 2022; 13:4521. [PMID: 35953471 PMCID: PMC9372134 DOI: 10.1038/s41467-022-32165-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.
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Affiliation(s)
- Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | | | | | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- National Institute of Genetics, Mishima, Japan.
| | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
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9
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Fick A, Swart V, van den Berg N. The Ups and Downs of Plant NLR Expression During Pathogen Infection. FRONTIERS IN PLANT SCIENCE 2022; 13:921148. [PMID: 35720583 PMCID: PMC9201817 DOI: 10.3389/fpls.2022.921148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Plant Nucleotide binding-Leucine rich repeat (NLR) proteins play a significant role in pathogen detection and the activation of effector-triggered immunity. NLR regulation has mainly been studied at a protein level, with large knowledge gaps remaining regarding the transcriptional control of NLR genes. The mis-regulation of NLR gene expression may lead to the inability of plants to recognize pathogen infection, lower levels of immune response activation, and ultimately plant susceptibility. This highlights the importance of understanding all aspects of NLR regulation. Three main mechanisms have been shown to control NLR expression: epigenetic modifications, cis elements which bind transcription factors, and post-transcriptional modifications. In this review, we aim to provide an overview of these mechanisms known to control NLR expression, and those which contribute toward successful immune responses. Furthermore, we discuss how pathogens can interfere with NLR expression to increase pathogen virulence. Understanding how these molecular mechanisms control NLR expression would contribute significantly toward building a complete picture of how plant immune responses are activated during pathogen infection-knowledge which can be applied during crop breeding programs aimed to increase resistance toward numerous plant pathogens.
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Affiliation(s)
- Alicia Fick
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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10
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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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11
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Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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12
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13
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Margaritopoulou T, Kizis D, Kotopoulis D, Papadakis IE, Anagnostopoulos C, Baira E, Termentzi A, Vichou AE, Leifert C, Markellou E. Enriched HeK4me3 marks at Pm-0 resistance-related genes prime courgette against Podosphaera xanthii. PLANT PHYSIOLOGY 2022; 188:576-592. [PMID: 34597395 PMCID: PMC8774738 DOI: 10.1093/plphys/kiab453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew (PM) disease, caused by the obligate biotrophic fungal pathogen Podosphaera xanthii, is the most reported and destructive disease on cultivated Cucurbita species all over the world. Recently, the appearance of highly aggressive P. xanthii isolates has led to PM outbreaks even in resistant crops, making disease management a very difficult task. To challenge this, breeders rely on genetic characteristics for PM control. Analysis of commercially available intermediate resistance courgette (Cucurbita pepo L. var. cylindrica) varieties using cytological, molecular, and biochemical approaches showed that the plants were under a primed state and induced systemic acquired resistance (SAR) responses, exhibiting enhanced callose production, upregulation of salicylic acid (SA) defense signaling pathway genes, and accumulation of SA and defense metabolites. Additionally, the intermediate resistant varieties showed an altered epigenetic landscape in histone marks that affect transcriptional activation. We demonstrated that courgette plants had enriched H3K4me3 marks on SA-BINDING PROTEIN 2 and YODA (YDA) genes of the Pm-0 interval introgression, a genomic region that confers resistant to Cucurbits against P. xanthii. The open chromatin of SA-BINDING PROTEIN 2 and YDA genes was consistent with genes' differential expression, induced SA pathway, altered stomata characteristics, and activated SAR responses. These findings demonstrate that the altered epigenetic landscape of the intermediate resistant varieties modulates the activation of SA-BINDING PROTEIN 2 and YDA genes leading to induced gene transcription that primes courgette plants.
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Affiliation(s)
- Theoni Margaritopoulou
- Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Dimosthenis Kizis
- Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Dimitris Kotopoulis
- Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Ioannis E Papadakis
- Faculty of Crop Science, Agricultural University of Athens, Athens 11855, Greece
| | - Christos Anagnostopoulos
- Scientific Directorate of Pesticides' Assessment & Phytopharmacy, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Eirini Baira
- Scientific Directorate of Pesticides' Assessment & Phytopharmacy, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Aikaterini Termentzi
- Scientific Directorate of Pesticides' Assessment & Phytopharmacy, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Aikaterini-Eleni Vichou
- Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Carlo Leifert
- SCU Plant Science, Southern Cross University, Lismore, Australia
- Department of Nutrition, IMB, University of Oslo, Oslo 0372, Norway
| | - Emilia Markellou
- Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
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14
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Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7927-7941. [PMID: 34387350 DOI: 10.1093/jxb/erab373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
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Affiliation(s)
- Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ram Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nicolas Manosalva Perez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shengbo He
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Xiaoqi Feng
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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15
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Jia M, Shen X, Tang Y, Shi X, Gu Y. A karyopherin constrains nuclear activity of the NLR protein SNC1 and is essential to prevent autoimmunity in Arabidopsis. MOLECULAR PLANT 2021; 14:1733-1744. [PMID: 34153500 DOI: 10.1016/j.molp.2021.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 06/13/2023]
Abstract
The nucleotide-binding and leucine-rich repeat (NLR) proteins comprise a major class of intracellular immune receptors that are capable of detecting pathogen-derived molecules and activating immunity and cell death in plants. The activity of some NLRs, particularly the Toll-like/interleukin-1 receptor (TIR) type, is highly correlated with their nucleocytoplasmic distribution. However, whether and how the nucleocytoplasmic homeostasis of NLRs is coordinated through a bidirectional nuclear shuttling mechanism remains unclear. Here, we identified a nuclear transport receptor, KA120, which is capable of affecting the nucleocytoplasmic distribution of an NLR protein and is essential in preventing its autoactivation. We showed that the ka120 mutant displays an autoimmune phenotype and NLR-induced transcriptome features. Through a targeted genetic screen using an artificial NLR microRNA library, we identified the TIR-NLR gene SNC1 as a genetic interactor of KA120. Loss-of-function snc1 mutations as well as compromising SNC1 protein activities all substantially suppressed ka120-induced autoimmune activation, and the enhanced SNC1 activity upon loss of KA120 functionappeared to occur at the protein level. Overexpression of KA120 efficiently repressed SNC1 activity and led to a nearly complete suppression of the autoimmune phenotype caused by the gain-of-function snc1-1 mutation or SNC1 overexpression in transgenic plants. Further florescence imaging analysis indicated that SNC1 undergoes altered nucleocytoplasmic distribution with significantly reduced nuclear signal when KA120 is constitutively expressed, supporting a role of KA120 in coordinating SNC1 nuclear abundance and activity. Consistently, compromising the SNC1 nuclear level by disrupting the nuclear pore complex could also partially rescue ka120-induced autoimmunity. Collectively, our study demonstrates that KA120 is essential to avoid autoimmune activation in the absence of pathogens and is required to constrain the nuclear activity of SNC1, possibly through coordinating SNC1 nucleocytoplasmic homeostasis as a potential mechanism.
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Affiliation(s)
- Min Jia
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Xueqi Shen
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Xuetao Shi
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
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16
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Huang XX, Wang Y, Lin JS, Chen L, Li YJ, Liu Q, Wang GF, Xu F, Liu L, Hou BK. The novel pathogen-responsive glycosyltransferase UGT73C7 mediates the redirection of phenylpropanoid metabolism and promotes SNC1-dependent Arabidopsis immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:149-165. [PMID: 33866633 DOI: 10.1111/tpj.15280] [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: 09/25/2020] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Recent studies have shown that global metabolic reprogramming is a common event in plant innate immunity; however, the relevant molecular mechanisms remain largely unknown. Here, we identified a pathogen-induced glycosyltransferase, UGT73C7, that plays a critical role in Arabidopsis disease resistance through mediating redirection of the phenylpropanoid pathway. Loss of UGT73C7 function resulted in significantly decreased resistance to Pseudomonas syringae pv. tomato DC3000, whereas constitutive overexpression of UGT73C7 led to an enhanced defense response. UGT73C7-activated immunity was demonstrated to be dependent on the upregulated expression of SNC1, a Toll/interleukin 1 receptor-type NLR gene. Furthermore, in vitro and in vivo assays indicated that UGT73C7 could glycosylate p-coumaric acid and ferulic acid, the upstream metabolites in the phenylpropanoid pathway. Mutations that lead to the loss of UGT73C7 enzyme activities resulted in the failure to induce SNC1 expression. Moreover, glycosylation activity of UGT73C7 resulted in the redirection of phenylpropanoid metabolic flux to biosynthesis of hydroxycinnamic acids and coumarins. The disruption of the phenylpropanoid pathway suppressed UGT73C7-promoted SNC1 expression and the immune response. This study not only identified UGT73C7 as an important regulator that adjusts phenylpropanoid metabolism upon pathogen challenge, but also provided a link between phenylpropanoid metabolism and an NLR gene.
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Affiliation(s)
- Xu-Xu Huang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yong Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Ji-Shan Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lu Chen
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yan-Jie Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Qian Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Guan-Feng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Fang Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Lijing Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bing-Kai Hou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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17
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Ramos-Cruz D, Troyee AN, Becker C. Epigenetics in plant organismic interactions. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102060. [PMID: 34087759 DOI: 10.1016/j.pbi.2021.102060] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 05/26/2023]
Abstract
Plants are hubs of organismic interactions. They constantly engage in beneficial or competitive interactions with fungi, oomycetes, bacteria, insects, nematodes, and other plants. To adjust the molecular processes necessary for the establishment and maintenance of beneficial interactions and for the defense against pathogens and herbivores, plants have evolved intricate regulatory mechanisms. Besides the canonical plant immune system that acts as the primary defense, epigenetic mechanisms have started to emerge as another regulatory entity and as a target of pathogens trying to overcome the plant's defenses. In this review, we highlight recent advances in understanding the contribution of various epigenetic components and of epigenetic diversity to plant-organismic interactions.
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Affiliation(s)
- Daniela Ramos-Cruz
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - A Niloya Troyee
- Department of Evolutionary Ecology, Doñana Biological Station, CSIC, 41092 Sevilla, Spain
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria; Genetics, Faculty of Biology, Ludwig Maximilians University Munich, 82152 Martinsried, Germany.
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18
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Martínez-Aguilar K, Hernández-Chávez JL, Alvarez-Venegas R. Priming of seeds with INA and its transgenerational effect in common bean (Phaseolus vulgaris L.) plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110834. [PMID: 33691968 DOI: 10.1016/j.plantsci.2021.110834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/04/2021] [Accepted: 01/30/2021] [Indexed: 05/14/2023]
Abstract
Priming is a mechanism of defense that prepares the plant's immune system for a faster and/or stronger activation of cellular defenses against future exposure to different types of stress. This enhanced resistance can be achieved by using inorganic and organic compounds which imitate the biological induction of systemic acquired resistance. INA (2,6 dichloro-isonicotinic acid) was the first synthetic compound created as a resistance inducer for plant-pathogen interactions. However, the use of INA to activate primed resistance in common bean, at the seed stage and during germination, remains experimentally unexplored. Here, we test the hypothesis that INA-seed treatment would induce resistance in common bean plants to Pseudomonas syringae pv. phaseolicola, and that the increased resistance is not accompanied by a tradeoff between plant defense and growth. Additionally, it was hypothesized that treating seeds with INA has a transgenerational priming effect. We provide evidence that seed treatment activates a primed state for disease resistance, in which low nucleosome enrichment and reduced histone activation marks during the priming phase, are associated with a defense-resistant phenotype, characterized by symptom appearance, pathogen accumulation, yield, and changes in gene expression. In addition, the priming status for induced resistance can be inherited to its offspring.
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19
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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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20
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Foroozani M, Vandal MP, Smith AP. H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants. PLANTA 2021; 253:4. [PMID: 33387051 DOI: 10.1007/s00425-020-03520-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The H3K4me3 histone mark in plants functions in the regulation of gene expression and transcriptional memory, and influences numerous developmental processes and stress responses. Plants execute developmental programs and respond to changing environmental conditions via adjustments in gene expression, which are modulated in part by chromatin structure dynamics. Histone modifications alter chromatin in precise ways on a global scale, having the potential to influence the expression of numerous genes. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a prominent histone modification that is dogmatically associated with gene activity, but more recently has also been linked to gene repression. As in other eukaryotes, the distribution of H3K4me3 in plant genomes suggests it plays a central role in gene expression regulation, however the underlying mechanisms are not fully understood. Transcript levels of many genes related to flowering, root, and shoot development are affected by dynamic H3K4me3 levels, as are those for a number of stress-responsive and stress memory-related genes. This review examines the current understanding of how H3K4me3 functions in modulating plant responses to developmental and environmental cues.
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Affiliation(s)
- Maryam Foroozani
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matthew P Vandal
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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21
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Nasim Z, Fahim M, Gawarecka K, Susila H, Jin S, Youn G, Ahn JH. Role of AT1G72910, AT1G72940, and ADR1-LIKE 2 in Plant Immunity under Nonsense-Mediated mRNA Decay-Compromised Conditions at Low Temperatures. Int J Mol Sci 2020; 21:E7986. [PMID: 33121126 PMCID: PMC7663611 DOI: 10.3390/ijms21217986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 01/26/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) removes aberrant transcripts to avoid the accumulation of truncated proteins. NMD regulates nucleotide-binding, leucine-rich repeat (NLR) genes to prevent autoimmunity; however, the function of a large number of NLRs still remains poorly understood. Here, we show that three NLR genes (AT1G72910, AT1G72940, and ADR1-LIKE 2) are important for NMD-mediated regulation of defense signaling at lower temperatures. At 16 °C, the NMD-compromised up-frameshift protein1 (upf1) upf3 mutants showed growth arrest that can be rescued by the artificial miRNA-mediated knockdown of the three NLR genes. mRNA levels of these NLRs are induced by Pseudomonas syringae inoculation and exogenous SA treatment. Mutations in AT1G72910, AT1G72940, and ADR1-LIKE 2 genes resulted in increased susceptibility to Pseudomonas syringae, whereas their overexpression resulted in severely stunted growth, which was dependent on basal disease resistance genes. The NMD-deficient upf1 upf3 mutants accumulated higher levels of NMD signature-containing transcripts from these NLR genes at 16 °C. Furthermore, mRNA degradation kinetics showed that these NMD signature-containing transcripts were more stable in upf1 upf3 mutants. Based on these findings, we propose that AT1G72910, AT1G72940, and ADR1-LIKE 2 are directly regulated by NMD in a temperature-dependent manner and play an important role in modulating plant immunity at lower temperatures.
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Affiliation(s)
- Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Muhammad Fahim
- Centre for Omic Sciences, Islamia College University, Peshawar 25120, Pakistan;
| | - Katarzyna Gawarecka
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Suhyun Jin
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Geummin Youn
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
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Leng X, Thomas Q, Rasmussen SH, Marquardt S. A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription. TRENDS IN PLANT SCIENCE 2020; 25:744-764. [PMID: 32673579 DOI: 10.1016/j.tplants.2020.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/24/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.
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Affiliation(s)
- Xueyuan Leng
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Quentin Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Simon Horskjær Rasmussen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark.
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Yang L, Chen X, Wang Z, Sun Q, Hong A, Zhang A, Zhong X, Hua J. HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:507-522. [PMID: 31854111 PMCID: PMC7080574 DOI: 10.1111/nph.16380] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/08/2019] [Indexed: 05/08/2023]
Abstract
Plant immune responses need to be tightly controlled for growth-defense balance. The mechanism underlying this tight control is not fully understood. Here we identify epigenetic regulation of nucleotide-binding leucine rich repeat or Nod-Like Receptor (NLR) genes as an important mechanism for immune responses. Through a sensitized genetic screen and molecular studies, we identified and characterized HOS15 and its associated protein HDA9 as negative regulators of immunity and NLR gene expression. The loss-of-function of HOS15 or HDA9 confers enhanced resistance to pathogen infection accompanied with increased expression of one-third of the 207 NLR genes in Arabidopsis thaliana. HOS15 and HDA9 are physically associated with some of these NLR genes and repress their expression likely through reducing the acetylation of H3K9 at these loci. In addition, these NLR genes are repressed by HOS15 under both pathogenic and nonpathogenic conditions but by HDA9 only under infection condition. Together, this study uncovers a previously uncharacterized histone deacetylase complex in plant immunity and highlights the importance of epigenetic regulation of NLR genes in modulating growth-defense balance.
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Affiliation(s)
- Leiyun Yang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
| | - Zhixue Wang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Qi Sun
- Cornell Computational Biology Service Unit, Cornell University, Ithaca, 14853, USA
| | - Anna Hong
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Aiqin Zhang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
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24
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Zhang X, Ménard R, Li Y, Coruzzi GM, Heitz T, Shen WH, Berr A. Arabidopsis SDG8 Potentiates the Sustainable Transcriptional Induction of the Pathogenesis-Related Genes PR1 and PR2 During Plant Defense Response. FRONTIERS IN PLANT SCIENCE 2020; 11:277. [PMID: 32218796 PMCID: PMC7078350 DOI: 10.3389/fpls.2020.00277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/21/2020] [Indexed: 05/23/2023]
Abstract
Post-translational covalent modifications of histones play important roles in modulating chromatin structure and are involved in the control of multiple developmental processes in plants. Here we provide insight into the contribution of the histone lysine methyltransferase SET DOMAIN GROUP 8 (SDG8), implicated in histone H3 lysine 36 trimethylation (H3K36me3), in connection with RNA polymerase II (RNAPII) to enhance Arabidopsis immunity. We showed that even if the sdg8-1 loss-of-function mutant, defective in H3K36 methylation, displayed a higher sensitivity to different strains of the bacterial pathogen Pseudomonas syringae, effector-triggered immunity (ETI) still operated, but less efficiently than in the wild-type (WT) plants. In sdg8-1, the level of the plant defense hormone salicylic acid (SA) was abnormally high under resting conditions and was accumulated similarly to WT at the early stage of pathogen infection but quickly dropped down at later stages. Concomitantly, the transcription of several defense-related genes along the SA signaling pathway was inefficiently induced in the mutant. Remarkably, albeit the defense genes PATHOGENESIS-RELATED1 (PR1) and PR2 have retained responsiveness to exogenous SA, their inductions fade more rapidly in sdg8-1 than in WT. At chromatin, while global levels of histone methylations were found to be stable, local increases of H3K4 and H3K36 methylations as well as RNAPII loading were observed at some defense genes following SA-treatments in WT. In sdg8-1, the H3K36me3 increase was largely attenuated and also the increases of H3K4me3 and RNAPII were frequently compromised. Lastly, we demonstrated that SDG8 could physically interact with the RNAPII C-terminal Domain, providing a possible link between RNAPII loading and H3K36me3 deposition. Collectively, our results indicate that SDG8, through its histone methyltransferase activity and its physical coupling with RNAPII, participates in the strong transcriptional induction of some defense-related genes, in particular PR1 and PR2, to potentiate sustainable immunity during plant defense response to bacterial pathogen.
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Affiliation(s)
- Xue Zhang
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Rozenn Ménard
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Gloria M. Coruzzi
- Department of Biology, Center for Genomics & Systems Biology, New York University, New York, NY, United States
| | - Thierry Heitz
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
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25
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Li D, Liu R, Singh D, Yuan X, Kachroo P, Raina R. JMJ14 encoded H3K4 demethylase modulates immune responses by regulating defence gene expression and pipecolic acid levels. THE NEW PHYTOLOGIST 2020; 225:2108-2121. [PMID: 31622519 DOI: 10.1111/nph.16270] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Epigenetic modifications have emerged as an important mechanism underlying plant defence against pathogens. We examined the role of JMJ14, a Jumonji (JMJ) domain-containing H3K4 demethylase, in local and systemic plant immune responses in Arabidopsis. The function of JMJ14 in local or systemic defence response was investigated by pathogen growth assays and by analysing expression and H3K4me3 enrichments of key defence genes using qPCR and ChIP-qPCR. Salicylic acid (SA) and pipecolic acid (Pip) levels were quantified and function of JMJ14 in SA- and Pip-mediated defences was analysed in Col-0 and jmj14 plants. jmj14 mutants were compromised in both local and systemic defences. JMJ14 positively regulates pathogen-induced H3K4me3 enrichment and expression of defence genes involved in SA- and Pip-mediated defence pathways. Consequently, loss of JMJ14 results in attenuated defence gene expression and reduced Pip accumulation during establishment of systemic acquired resistance (SAR). Exogenous Pip partially restored SAR in jmj14 plants, suggesting that JMJ14 regulated Pip biosynthesis and other downstream factors regulate SAR in jmj14 plants. JMJ14 positively modulates defence gene expressions and Pip levels in Arabidopsis.
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Affiliation(s)
- Dan Li
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Ruiying Liu
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA
| | - Deepjyoti Singh
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Xinyu Yuan
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, 40546, USA
| | - Ramesh Raina
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
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Tang L, Qiu L, Liu C, Du G, Mo Z, Tang X, Mao Y. Transcriptomic Insights into Innate Immunity Responding to Red Rot Disease in Red Alga Pyropia yezoensis. Int J Mol Sci 2019; 20:E5970. [PMID: 31783543 PMCID: PMC6928737 DOI: 10.3390/ijms20235970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/22/2019] [Accepted: 11/24/2019] [Indexed: 01/17/2023] Open
Abstract
Pyropia yezoensis, one of the most economically important marine algae, suffers from the biotic stress of the oomycete necrotrophic pathogen Pythium porphyrae. However, little is known about the molecular defensive mechanisms employed by Pyr. yezoensis during the infection process. In the present study, we defined three stages of red rot disease based on histopathological features and photosynthetic physiology. Transcriptomic analysis was carried out at different stages of infection to identify the genes related to the innate immune system in Pyr. yezoensis. In total, 2139 up-regulated genes and 1672 down-regulated genes were identified from all the infected groups. Pathogen receptor genes, including three lectin genes (pattern recognition receptors (PRRs)) and five genes encoding typical plant R protein domains (leucine rich repeat (LRR), nucleotide binding site (NBS), or Toll/interleukin-1 receptor (TIR)), were found to be up-regulated after infection. Several defense mechanisms that were typically regarded as PAMP-triggered immunity (PTI) in plants were induced during the infection. These included defensive and protective enzymes, heat shock proteins, secondary metabolites, cellulase, and protease inhibitors. As a part of the effector-triggered immunity (ETI), the expression of genes related to the ubiquitin-proteasome system (UPS) and hypersensitive cell death response (HR) increased significantly during the infection. The current study suggests that, similar to plants, Pyr. yezoensis possesses a conserved innate immune system that counters the invasion of necrotrophic pathogen Pyt. porphyrae. However, the innate immunity genes of Pyr. yezoensis appear to be more ancient in origin compared to those in higher plants.
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Affiliation(s)
- Lei Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.T.); (L.Q.); (C.L.); (G.D.); (X.T.)
| | - Liping Qiu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.T.); (L.Q.); (C.L.); (G.D.); (X.T.)
| | - Cong Liu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.T.); (L.Q.); (C.L.); (G.D.); (X.T.)
| | - Guoying Du
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.T.); (L.Q.); (C.L.); (G.D.); (X.T.)
| | - Zhaolan Mo
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.T.); (L.Q.); (C.L.); (G.D.); (X.T.)
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (L.T.); (L.Q.); (C.L.); (G.D.); (X.T.)
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China
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27
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Zhang C, Chen H, Zhuang RR, Chen YT, Deng Y, Cai TC, Wang SY, Liu QZ, Tang RH, Shan SH, Pan RL, Chen LS, Zhuang WJ. Overexpression of the peanut CLAVATA1-like leucine-rich repeat receptor-like kinase AhRLK1 confers increased resistance to bacterial wilt in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5407-5421. [PMID: 31173088 PMCID: PMC6793444 DOI: 10.1093/jxb/erz274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/31/2019] [Indexed: 06/04/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is a devastating disease affecting hundreds of plant species, yet the host factors remain poorly characterized. The leucine-rich repeat receptor-like kinase gene AhRLK1, characterized as CLAVATA1, was found to be up-regulated in peanut upon inoculation with R. solanacearum. The AhRLK1 protein was localized in the plasma membrane and cell wall. qPCR results showed AhRLK1 was induced in a susceptible variety but little changed in a resistant cultivar after inoculated with R. solanacearum. Hormones such as salicylic acid, abscisic acid, methyl jasmonate, and ethephon induced AhRLK1 expression. In contrast, AhRLK1 expression was down-regulated under cold and drought treatments. Transient overexpression of AhRLK1 led to a hypersensitive response (HR) in Nicotiana benthamiana. Furthermore, AhRLK1 overexpression in tobacco significantly increased the resistance to R. solanacearum. Besides, the transcripts of most representative defense responsive genes in HR and hormone signal pathways were significantly increased in the transgenic lines. EDS1 and PAD4 in the R gene signaling pathway were also up-regulated, but NDR1 was down-regulated. Accordingly, AhRLK1 may increase the defense response to R. solanacearum via HR and hormone defense signaling, in particular through the EDS1 pathway of R gene signaling. These results provide a new understanding of the CLAVATA1 function and will contribute to genetic enhancement of peanut.
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Affiliation(s)
- Chong Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui-Rong Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Ting Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Deng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tie-Cheng Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuai-Yin Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qin-Zheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rong-Hua Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shi-Hua Shan
- Shandong Peanut Research Institute, Qingdao, China
| | - Rong-Long Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin Chu, Taiwan
| | - Li-Song Chen
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Jian Zhuang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou, China
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28
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Lai Y, Cuzick A, Lu XM, Wang J, Katiyar N, Tsuchiya T, Le Roch K, McDowell JM, Holub E, Eulgem T. The Arabidopsis RRM domain protein EDM3 mediates race-specific disease resistance by controlling H3K9me2-dependent alternative polyadenylation of RPP7 immune receptor transcripts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:646-660. [PMID: 30407670 PMCID: PMC7138032 DOI: 10.1111/tpj.14148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/27/2018] [Accepted: 10/26/2018] [Indexed: 05/18/2023]
Abstract
The NLR-receptor RPP7 mediates race-specific immunity in Arabidopsis. Previous screens for enhanced downy mildew (edm) mutants identified the co-chaperone SGT1b (EDM1) and the PHD-finger protein EDM2 as critical regulators of RPP7. Here, we describe a third edm mutant compromised in RPP7 immunity, edm3. EDM3 encodes a nuclear-localized protein featuring an RNA-recognition motif. Like EDM2, EDM3 promotes histone H3 lysine 9 dimethylation (H3K9me2) at RPP7. Global profiling of H3K9me2 showed EDM3 to affect this silencing mark at a large set of loci. Importantly, both EDM3 and EDM2 co-associate in vivo with H3K9me2-marked chromatin and transcripts at a critical proximal polyadenylation site of RPP7, where they suppress proximal transcript polyadeylation/termination. Our results highlight the complexity of plant NLR gene regulation, and establish a functional and physical link between a histone mark and NLR-transcript processing.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
| | - Alayne Cuzick
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Xueqing M Lu
- Department of Molecular, Cell and Systems Biology, Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Jianqiang Wang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Neerja Katiyar
- Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan
| | - Karine Le Roch
- Department of Molecular, Cell and Systems Biology, Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - John M McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24060-0329, USA
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
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29
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Kapos P, Devendrakumar KT, Li X. Plant NLRs: From discovery to application. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:3-18. [PMID: 30709490 DOI: 10.1016/j.plantsci.2018.03.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 05/09/2023]
Abstract
Plants require a complex immune system to defend themselves against a wide range of pathogens which threaten their growth and development. The nucleotide-binding leucine-rich repeat proteins (NLRs) are immune sensors that recognize effectors delivered by pathogens. The first NLR was cloned more than twenty years ago. Since this initial discovery, NLRs have been described as key components of plant immunity responsible for pathogen recognition and triggering defense responses. They have now been described in most of the well-studied mulitcellular plant species, with most having large NLR repertoires. As research has progressed so has the understanding of how NLRs interact with their recognition substrates and how they in turn activate downstream signalling. It has also become apparent that NLR regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels. Even before the first NLR was cloned, breeders were utilising such genes to increase crop performance. Increased understanding of the mechanistic details of the plant immune system enable the generation of plants resistant against devastating pathogens. This review aims to give an updated summary of the NLR field.
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Affiliation(s)
- Paul Kapos
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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30
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Alonso C, Ramos‐Cruz D, Becker C. The role of plant epigenetics in biotic interactions. THE NEW PHYTOLOGIST 2019; 221:731-737. [PMID: 30156271 PMCID: PMC6726468 DOI: 10.1111/nph.15408] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/22/2018] [Indexed: 05/07/2023]
Abstract
Contents Summary 731 I. Biotic interactions in the context of genetic, epigenetic and environmental diversity 731 II. Biotic interactions affect epigenetic configuration 732 III. Plant epigenetic configuration influences biotic interactions 733 IV. Epigenetic memory in the context of biotic interactions 734 V. Conclusions and future research 735 Acknowledgements 735 Author contributions 735 References 735 SUMMARY: Plants are hubs of a wide range of biotic interactions with mutualist and antagonist animals, microbes and neighboring plants. Because the quality and intensity of those relationships can change over time, a fast and reversible response to stress is required. Here, we review recent studies on the role of epigenetic factors such as DNA methylation and histone modifications in modulating plant biotic interactions, and discuss the state of knowledge regarding their potential role in memory and priming. Moreover, we provide an overview of strategies to investigate the contribution of epigenetics to environmentally induced phenotypic changes in an ecological context, highlighting possible transitions from whole-genome high-resolution analyses in plant model organisms to informative reduced representation analyses in genomically less accessible species.
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Affiliation(s)
- Conchita Alonso
- Estación Biológica de DoñanaConsejo Superior de Investigaciones Científicas (CSIC)Av. Américo Vespucio 26Sevilla41092Spain
| | - Daniela Ramos‐Cruz
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr Gasse 3Vienna1030Austria
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna Biocenter (VBC)Dr. Bohr Gasse 3Vienna1030Austria
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31
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Kuźnicki D, Meller B, Arasimowicz-Jelonek M, Braszewska-Zalewska A, Drozda A, Floryszak-Wieczorek J. BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2019; 10:650. [PMID: 31214209 PMCID: PMC6554679 DOI: 10.3389/fpls.2019.00650] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC-mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network.
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Affiliation(s)
- Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Agnieszka Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Andżelika Drozda
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Jolanta Floryszak-Wieczorek
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
- *Correspondence: Jolanta Floryszak-Wieczorek,
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Duan CG, Zhu JK, Cao X. Retrospective and perspective of plant epigenetics in China. J Genet Genomics 2018; 45:621-638. [PMID: 30455036 DOI: 10.1016/j.jgg.2018.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 01/21/2023]
Abstract
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
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Affiliation(s)
- Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Richard MMS, Gratias A, Meyers BC, Geffroy V. Molecular mechanisms that limit the costs of NLR-mediated resistance in plants. MOLECULAR PLANT PATHOLOGY 2018; 19:2516-2523. [PMID: 30011120 PMCID: PMC6638094 DOI: 10.1111/mpp.12723] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 05/25/2023]
Abstract
Crop diseases cause significant yield losses, and the use of resistant cultivars can effectively mitigate these losses and control many plant diseases. Most plant resistance (R) genes encode immune receptors composed of nucleotide-binding and leucine-rich repeat (NLR) domains. These proteins mediate the specific recognition of pathogen avirulence effectors to induce defence responses. However, NLR-triggered immunity can be associated with a reduction in growth and yield, so-called 'fitness costs'. Recent data have shown that plants use an elaborate interplay of different mechanisms to control NLR gene transcript levels, as well as NLR protein abundance and activity, to avoid the associated cost of resistance in the absence of a pathogen. In this review, we discuss the different levels of NLR regulation (transcriptional, post-transcriptional and at the protein level). We address the apparent need for plants to maintain diverse modes of regulation. A recent model suggesting an equilibrium 'ON/OFF state' of NLR proteins, in the absence of a pathogen, provides the context for our discussion.
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Affiliation(s)
- Manon M. S. Richard
- Molecular Plant PathologySILS, University of AmsterdamPO Box 942151090 GEAmsterdamthe Netherlands
| | - Ariane Gratias
- Institute of Plant Sciences Paris‐Saclay IPS2, CNRS, INRA, Université Paris‐Saclay, Université Paris‐Sud, Université Evry, Université Paris‐Diderot, Sorbonne Paris‐CitéBâtiment 63091405OrsayFrance
| | - Blake C. Meyers
- Donald Danforth Plant Science Center975 North Warson RoadSt LouisMO63132USA
- Division of Plant Sciences52 Agriculture LabUniversity of MissouriColumbiaMO65211USA
| | - Valérie Geffroy
- Institute of Plant Sciences Paris‐Saclay IPS2, CNRS, INRA, Université Paris‐Saclay, Université Paris‐Sud, Université Evry, Université Paris‐Diderot, Sorbonne Paris‐CitéBâtiment 63091405OrsayFrance
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Lee CH, Carroll BJ. Evolution and Diversification of Small RNA Pathways in Flowering Plants. PLANT & CELL PHYSIOLOGY 2018; 59:2169-2187. [PMID: 30169685 DOI: 10.1093/pcp/pcy167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Small regulatory RNAs guide gene silencing at the DNA or RNA level through repression of complementary sequences. The two main forms of small RNAs are microRNA (miRNA) and small interfering RNA (siRNAs), which are generated from the processing of different forms of double-stranded RNA (dsRNA) precursors. These two forms of small regulatory RNAs function in distinct but overlapping gene silencing pathways in plants. Gene silencing pathways in eukaryotes evolved from an ancient prokaryotic mechanism involved in genome defense against invasive genetic elements, but has since diversified to also play a crucial role in regulation of endogenous gene expression. Here, we review the biogenesis of the different forms of small RNAs in plants, including miRNAs, phased, secondary siRNAs (phasiRNAs) and heterochromatic siRNAs (hetsiRNAs), with a focus on their functions in genome defense, transcriptional and post-transcriptional gene silencing, RNA-directed DNA methylation, trans-chromosomal methylation and paramutation. We also discuss the important role that gene duplication has played in the functional diversification of gene silencing pathways in plants, and we highlight recently discovered components of gene silencing pathways in plants.
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Affiliation(s)
- Chin Hong Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
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Watkinson JI, Bowerman PA, Crosby KC, Hildreth SB, Helm RF, Winkel BSJ. Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus. PeerJ 2018; 6:e5598. [PMID: 30258711 PMCID: PMC6151112 DOI: 10.7717/peerj.5598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/17/2018] [Indexed: 01/12/2023] Open
Abstract
Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9-CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway.
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Affiliation(s)
- Jonathan I Watkinson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Peter A Bowerman
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,BASF Plant Science LP, Research Triangle Park, NC, USA
| | - Kevin C Crosby
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sherry B Hildreth
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Brenda S J Winkel
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
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Meller B, Kuźnicki D, Arasimowicz-Jelonek M, Deckert J, Floryszak-Wieczorek J. BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2018; 9:1228. [PMID: 30233606 PMCID: PMC6135045 DOI: 10.3389/fpls.2018.01228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 05/23/2023]
Abstract
In this paper we analyzed β-aminobutyric acid (BABA)-primed epigenetic adjustment of potato cv. "Sarpo Mira" to Phytophthora infestans. The first stress-free generation of the potato genotype obtained from BABA-primed parent plants via tubers and seeds showed pronounced resistance to the pathogen, which was tuned with the transcriptional memory of SA-responsive genes. During the early priming phase before the triggering stress, we found robust bistable deposition of histone marks (H3K4me2 and H3K27me3) on the NPR1 (Non-expressor of PR genes) and the SNI1 gene (Suppressor of NPR1, Inducible), in which transcription antagonized silencing. Switchable chromatin states of these adverse systemic acquired resistance (SAR) regulators probably reprogrammed responsiveness of the PR1 and PR2 genes and contributed to stress imprinting. The elevated levels of heritable H3K4me2 tag in the absence of transcription on SA-dependent genes in BABA-primed (F0) and its vegetative and generative progeny (F1) before pathogen challenge provided evidence for the epigenetic mark for intergenerational memory in potato. Moreover, our study revealed that histone acetylation was not critical for maintaining BABA-primed defense information until the plants were triggered with the virulent pathogen when rapid and boosted PRs gene expression probably required histone acetyltransferase (HAT) activity both in F0 and F1 progeny.
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Affiliation(s)
- Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Joanna Deckert
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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Zhang Q, Ma C, Zhang Y, Gu Z, Li W, Duan X, Wang S, Hao L, Wang Y, Wang S, Li T. A Single-Nucleotide Polymorphism in the Promoter of a Hairpin RNA Contributes to Alternaria alternata Leaf Spot Resistance in Apple ( Malus × domestica). THE PLANT CELL 2018; 30:1924-1942. [PMID: 30065047 PMCID: PMC6139694 DOI: 10.1105/tpc.18.00042] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/11/2018] [Accepted: 07/26/2018] [Indexed: 05/04/2023]
Abstract
Apple leaf spot caused by the Alternaria alternata f. sp mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA) named MdhpRNA277 that produces small RNAs and is induced by ALT1 infection in 'Golden Delicious' apple. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five resistance (R) genes that are expressed at high levels in resistant apple variety 'Hanfu' and at low levels in susceptible variety 'Golden Delicious' following ALT1 infection. MdhpRNA277 was strongly induced in 'Golden Delicious' but not 'Hanfu' following ALT1 inoculation. MdhpRNA277 promoter activity was much stronger in inoculated 'Golden Delicious' versus 'Hanfu'. We identified a single-nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between 'Golden Delicious' (pMdhpRNA277-GD) and 'Hanfu' (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF Transgenic 'GL-3' apple expressing pMdhpRNA277-GD:MdhpRNA277 was more susceptible to ALT1 infection than plants expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and reduced expression of the five target R genes. We confirmed that the SNP in pMdhpRNA277 is associated with A. alternata leaf spot resistance by crossing. This SNP could be used as a marker to distinguish between apple varieties that are resistant or susceptible to A. alternata leaf spot.
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Affiliation(s)
- Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chao Ma
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhaoyu Gu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Wei Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuwei Duan
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yuanhua Wang
- Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang, Jiangsu 212400, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
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Lai Y, Eulgem T. Transcript-level expression control of plant NLR genes. MOLECULAR PLANT PATHOLOGY 2018; 19:1267-1281. [PMID: 28834153 PMCID: PMC6638128 DOI: 10.1111/mpp.12607] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Plant NLR genes encode sensitive immune receptors that can mediate the specific recognition of pathogen avirulence effectors and activate a strong defence response, termed effector-triggered immunity. The expression of NLRs requires strict regulation, as their ability to trigger immunity is dependent on their dose, and overexpression of NLRs results in autoimmunity and massive fitness costs. An elaborate interplay of different mechanisms controlling NLR transcript levels allows plants to maximize their defence capacity, whilst limiting negative impact on their fitness. Global suppression of NLR transcripts may be a prerequisite for the fast evolution of new NLR variants and the expansion of this gene family. Here, we summarize recent progress made towards a comprehensive understanding of NLR transcript-level expression control. Multiple mechanistic steps, including transcription as well as co-/post-transcriptional processing and transcript turn-over, contribute to balanced base levels of NLR transcripts and allow for dynamic adjustments to defence situations.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
- College of Life SciencesFujian Agricultural and Forestry UniversityFuzhouFujian 350002China
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
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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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Zou B, Sun Q, Zhang W, Ding Y, Yang DL, Shi Z, Hua J. The Arabidopsis Chromatin-Remodeling Factor CHR5 Regulates Plant Immune Responses and Nucleosome Occupancy. PLANT & CELL PHYSIOLOGY 2017; 58:2202-2216. [PMID: 29048607 DOI: 10.1093/pcp/pcx155] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 10/03/2017] [Indexed: 05/17/2023]
Abstract
ATP-dependent chromatin-remodeling factors use the energy of ATP hydrolysis to alter the structure of chromatin and are important regulators of eukaryotic gene expression. One such factor encoded by CHR5 (Chromatin-Remodeling Factor 5) in Arabidopsis (Arabidopsis thaliana) was previously found to be involved in regulation of growth and development. Here we show that CHR5 is required for the up-regulation of the intracellular immune receptor gene SNC1 (SUPPRESSOR OF npr1-1, CONSTITUTIVE1) and consequently the autoimmunity induced by SNC1 up-regulation. CHR5 functions antagonistically with another chromatin-remodeling gene DDM1 (DECREASED DNA METHYLATION 1) and independently with a histone mono-ubiquitinase HUB1 (HISTONE MONOUBIQUITINATION 1) in SNC1 regulation. In addition, CHR5 is a positive regulator of SNC1-independent plant immunity against the bacterial pathogen Pseudomonas syringae. Furthermore, the chr5 mutant has increased nucleosome occupancy in the promoter region relative to the gene body region at the whole-genome level, suggesting a global role for CHR5 in remodeling nucleosome occupancy. Our study thus establishes CHR5 as a positive regulator of plant immune responses including the expression of SNC1 and reveals a role for CHR5 in nucleosome occupancy which probably impacts gene expression genome wide.
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Affiliation(s)
- Baohong Zou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu 210095, China
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Sun
- Cornell Biocomputing Service Unit, Cornell University, Ithaca, NY 14853, USA
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu 210095, China
| | - Yuan Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu 210095, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu 210095, China
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Zhenying Shi
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Shanghai Institute of Plant Physiology and Ecology, Shanghai, 20032, China
| | - Jian Hua
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu 210095, China
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Gou M, Huang Q, Qian W, Zhang Z, Jia Z, Hua J. Sumoylation E3 Ligase SIZ1 Modulates Plant Immunity Partly through the Immune Receptor Gene SNC1 in Arabidopsis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:334-342. [PMID: 28409535 DOI: 10.1094/mpmi-02-17-0041-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The small ubiqutin-like modifier E3 ligase SIZ1 regulates multiple processes in Arabidopsis, including salicylic-acid-dependent immune responses. However, the targets of SIZ1 in plant immunity are not known. Here, we provide evidence that the plant immune receptor nucleotide-binding leucine-rich repeat gene SNC1 partially mediates the regulation of plant immunity by SIZ1. The siz1 loss-of-function mutant has an autoimmune phenotype that is dependent on SNC1 and temperature. Overexpression of SIZ1 partially rescues autoimmune mutant phenotypes induced by activation or overaccumulation of SNC1, and the SNC1 protein amount is attenuated by SIZ1 overexpression. In addition, overexpression of the F-box protein CPR1 that degrades the SNC1 protein inhibits the growth defects and disease resistance of the siz1 mutant. Furthermore, we found that the SNC1 protein is sumoylated in planta. Although it remains to be determined whether SIZ1 primarily modulates the SNC1 protein via sumoylation or affects SNC1 transcript level, our data indicate that SNC1 is a major mediator of defense response modulated by SIZ1 and that SNC1 is a crucial target for fine-tuning plant defense responses.
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Affiliation(s)
- Mingyue Gou
- 1 Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Quansheng Huang
- 1 Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- 2 Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumuqi 830091, China
| | - Weiqiang Qian
- 1 Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Zemin Zhang
- 1 Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- 3 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China; and
| | - Zhenhua Jia
- 1 Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- 4 Institute of Biology, Hebei Academy of Sciences, Shijiazhuang, Hebei, 050081, China
| | - Jian Hua
- 1 Plant Biology Section, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
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Wu Z, Huang S, Zhang X, Wu D, Xia S, Li X. Regulation of plant immune receptor accumulation through translational repression by a glycine-tyrosine-phenylalanine (GYF) domain protein. eLife 2017; 6:e23684. [PMID: 28362261 PMCID: PMC5403212 DOI: 10.7554/elife.23684] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/14/2017] [Indexed: 01/12/2023] Open
Abstract
Plant immunity is tightly regulated to ensure proper defense against surrounding microbial pathogens without triggering autoimmunity, which negatively impacts plant growth and development. Immune receptor levels are intricately controlled by RNA processing and post-translational modification events, such as ubiquitination. It remains unknown whether, and if yes, how, plant immune receptor homeostasis is regulated at the translational level. From a mutant, snc1-enhancing (muse) forward genetic screen, we identified MUSE11/EXA1, which negatively regulates nucleotide-binding leucine-rich repeat (NLR) receptor mediated defence. EXA1 contains an evolutionarily conserved glycine-tyrosine-phenylalanine (GYF) domain that binds proline-rich sequences. Genetic and biochemical analysis revealed that loss of EXA1 leads to heightened NLR accumulation and enhanced resistance against virulent pathogens. EXA1 also associates with eIF4E initiation factors and the ribosome complex, likely contributing to the proper translation of target proteins. In summary, our study reveals a previously unknown mechanism of regulating NLR homeostasis through translational repression by a GYF protein.
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Affiliation(s)
- Zhongshou Wu
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Shuai Huang
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Xiaobo Zhang
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Agricultural University, Changsha, China
| | - Di Wu
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Agricultural University, Changsha, China
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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Berr A, Zhang X, Shen WH. [Reciprocity between active transcription and histone methylation]. Biol Aujourdhui 2017; 210:269-282. [PMID: 28327284 DOI: 10.1051/jbio/2017004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Indexed: 01/08/2023]
Abstract
In the nucleus of eukaryotic cells, the chromatin states dictated by the different combinations of histone post-translational modifications, such as the methylation of lysine residues, are an integral part of the multitude of epigenomes involved in the fine tuning of all genome functions, and in particular transcription. Over the last decade, an increasing number of factors have been identified as regulators involved in the establishment, reading or erasure of histone methylations. Their characterization in model organisms such as Arabidopsis has thus unraveled their fundamental roles in the control and regulation of essential developmental processes such as the floral transition, cell differentiation, gametogenesis, and/or the response/adaptation of plants to environmental stresses. In this review, we will focus on the methylation of histones functioning as a mark of activate transcription and we will try to highlight, based on recent findings, the more or less direct links between this mark and gene expression. Thus, we will discuss the different mechanisms allowing the dynamics and the integration of the chromatin states resulting from the different histone methylations in connection with the transcriptional machinery of the RNA polymerase II.
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Lee S, Fu F, Xu S, Lee SY, Yun DJ, Mengiste T. Global Regulation of Plant Immunity by Histone Lysine Methyl Transferases. THE PLANT CELL 2016; 28:1640-61. [PMID: 27354553 PMCID: PMC4981126 DOI: 10.1105/tpc.16.00012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/25/2016] [Accepted: 06/24/2016] [Indexed: 05/17/2023]
Abstract
Posttranslational modification of histones modulates gene expression affecting diverse biological functions. We showed that the Arabidopsis thaliana histone methyl transferases SET DOMAIN GROUP8 (SDG8) and SDG25 regulate pep1-, flg22-, and effector-triggered immunity as well as systemic acquired resistance. Genome-wide basal and induced transcriptome changes regulated by SDG8 and/or SDG25 showed that two genes of the SDG-dependent transcriptome, CAROTENOID ISOMERASE2 (CCR2) and ECERIFERUM3 (CER3), were also required for plant immunity, establishing mechanisms in defense functions for SDG8 and SDG25. CCR2 catalyzes the biosynthesis of carotenoids, whereas CER3 is involved in the biosynthesis of cuticular wax. SDG8 and SDG25 affected distinct and overlapping global and locus-specific histone H3 lysine 4 (H3K4) and histone H3 lysine 36 (H3K36) methylations. Loss of immunity in sdg mutants was attributed to altered global and CCR2- and CER3-specific histone lysine methylation (HLM). Loss of immunity in sdg, ccr2, and cer3 mutants was also associated with diminished accumulation of lipids and loss of cuticle integrity. In addition, sdg8 and sdg25 mutants were impaired in H2B ubiquitination (H2Bubn) at CCR2, CER3, and H2Bubn regulated R gene, SNC1, revealing crosstalk between the two types of histone modifications. In summary, SDG8 and SDG25 contribute to plant immunity directly through HLM or indirectly through H2Bubn and by regulating expression of plant immunity genes, accumulation of lipids, biosynthesis of carotenoids, and maintenance of cuticle integrity.
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Affiliation(s)
- Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Siming Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK 21 Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences (BK 21 Program), Gyeongsang National University, Jinju City 660-701, Korea
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
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Zhu QH, Shan WX, Ayliffe MA, Wang MB. Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:187-96. [PMID: 26524162 DOI: 10.1094/mpmi-08-15-0194-fi] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plants have developed diverse molecular and cellular mechanisms to cope with a lifetime of exposure to a variety of pathogens. Host transcriptional reprogramming is a central part of plant defense upon pathogen recognition. Recent studies link DNA methylation and demethylation as well as chromatin remodeling by posttranslational histone modifications, including acetylation, methylation, and ubiquitination, to changes in the expression levels of defense genes upon pathogen challenge. Remarkably these inducible defense mechanisms can be primed prior to pathogen attack by epigenetic modifications and this heightened resistance state can be transmitted to subsequent generations by inheritance of these modification patterns. Beside the plant host, epigenetic mechanisms have also been implicated in virulence development of pathogens. This review highlights recent findings and insights into epigenetic mechanisms associated with interactions between plants and pathogens, in particular bacterial and fungal pathogens, and demonstrates the positive role they can have in promoting plant defense.
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Affiliation(s)
- Qian-Hao Zhu
- 1 CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Wei-Xing Shan
- 2 College of Plant Protection, Northwest Agricultural and Forestry University, Yangling, Shaanxi 712100, China
| | | | - Ming-Bo Wang
- 1 CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601, Australia
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Liu SC, Jin JQ, Ma JQ, Yao MZ, Ma CL, Li CF, Ding ZT, Chen L. Transcriptomic Analysis of Tea Plant Responding to Drought Stress and Recovery. PLoS One 2016; 11:e0147306. [PMID: 26788738 PMCID: PMC4720391 DOI: 10.1371/journal.pone.0147306] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/01/2016] [Indexed: 11/18/2022] Open
Abstract
Tea plant (Camellia sinensis) is an economically important beverage crop. Drought stress (DS) seriously limits the growth and development of tea plant, thus affecting crop yield and quality. To elucidate the molecular mechanisms of tea plant responding to DS, we performed transcriptomic analysis of tea plant during the three stages [control (CK) and during DS, and recovery (RC) after DS] using RNA sequencing (RNA-Seq). Totally 378.08 million high-quality trimmed reads were obtained and assembled into 59,674 unigenes, which were extensively annotated. There were 5,955 differentially expressed genes (DEGs) among the three stages. Among them, 3,948 and 1,673 DEGs were up-regulated under DS and RC, respectively. RNA-Seq data were further confirmed by qRT-PCR analysis. Genes involved in abscisic acid (ABA), ethylene, and jasmonic acid biosynthesis and signaling were generally up-regulated under DS and down-regulated during RC. Tea plant potentially used an exchange pathway for biosynthesis of indole-3-acetic acid (IAA) and salicylic acid under DS. IAA signaling was possibly decreased under DS but increased after RC. Genes encoding enzymes involved in cytokinin synthesis were up-regulated under DS, but down-regulated during RC. It seemed probable that cytokinin signaling was slightly enhanced under DS. In total, 762 and 950 protein kinases belonging to 26 families were differentially expressed during DS and RC, respectively. Overall, 547 and 604 transcription factor (TF) genes belonging to 58 families were induced in the DS vs. CK and RC vs. DS libraries, respectively. Most members of the 12 TF families were up-regulated under DS. Under DS, genes related to starch synthesis were down-regulated, while those related to starch decomposition were up-regulated. Mannitol, trehalose and sucrose synthesis-related genes were up-regulated under DS. Proline was probably mainly biosynthesized from glutamate under DS and RC. The mechanism by which ABA regulated stomatal movement under DS and RC was partly clarified. These results document the global and novel responses of tea plant during DS and RC. These data will serve as a valuable resource for drought-tolerance research and will be useful for breeding drought-resistant tea cultivars.
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Affiliation(s)
- Sheng-Chuan Liu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
- Guizhou Tea Research Institute, Guiyang, Guizhou, China
| | - Ji-Qiang Jin
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Ming-Zhe Yao
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Chun-Lei Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Chun-Fang Li
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
| | - Zhao-Tang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China
- * E-mail: ;
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van Wersch R, Li X, Zhang Y. Mighty Dwarfs: Arabidopsis Autoimmune Mutants and Their Usages in Genetic Dissection of Plant Immunity. FRONTIERS IN PLANT SCIENCE 2016; 7:1717. [PMID: 27909443 PMCID: PMC5112265 DOI: 10.3389/fpls.2016.01717] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/01/2016] [Indexed: 05/17/2023]
Abstract
Plants lack the adaptive immune system possessed by mammals. Instead they rely on innate immunity to defend against pathogen attacks. Genomes of higher plants encode a large number of plant immune receptors belonging to different protein families, which are involved in the detection of pathogens and activation of downstream defense pathways. Plant immunity is tightly controlled to avoid activation of defense responses in the absence of pathogens, as failure to do so can lead to autoimmunity that compromises plant growth and development. Many autoimmune mutants have been reported, most of which are associated with dwarfism and often spontaneous cell death. In this review, we summarize previously reported Arabidopsis autoimmune mutants, categorizing them based on their functional groups. We also discuss how their obvious morphological phenotypes make them ideal tools for epistatic analysis and suppressor screens, and summarize genetic screens that have been carried out in various autoimmune mutant backgrounds.
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Affiliation(s)
- Rowan van Wersch
- Department of Botany, University of British Columbia, VancouverBC, Canada
| | - Xin Li
- Department of Botany, University of British Columbia, VancouverBC, Canada
- The Michael Smith Laboratories, University of British Columbia, VancouverBC, Canada
| | - Yuelin Zhang
- Department of Botany, University of British Columbia, VancouverBC, Canada
- *Correspondence: Yuelin Zhang,
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Paim Pinto DL, Brancadoro L, Dal Santo S, De Lorenzis G, Pezzotti M, Meyers BC, Pè ME, Mica E. The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry. FRONTIERS IN PLANT SCIENCE 2016; 7:1459. [PMID: 27761135 PMCID: PMC5050227 DOI: 10.3389/fpls.2016.01459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 09/13/2016] [Indexed: 05/21/2023]
Abstract
Understanding the molecular mechanisms involved in the interaction between the genetic composition and the environment is crucial for modern viticulture. We approached this issue by focusing on the small RNA transcriptome in grapevine berries of the two varieties Cabernet Sauvignon and Sangiovese, growing in adjacent vineyards in three different environments. Four different developmental stages were studied and a total of 48 libraries of small RNAs were produced and sequenced. Using a proximity-based pipeline, we determined the general landscape of small RNAs accumulation in grapevine berries. We also investigated the presence of known and novel miRNAs and analyzed their accumulation profile. The results showed that the distribution of small RNA-producing loci is variable between the two cultivars, and that the level of variation depends on the vineyard. Differently, the profile of miRNA accumulation mainly depends on the developmental stage. The vineyard in Riccione maximizes the differences between the varieties, promoting the production of more than 1000 specific small RNA loci and modulating their expression depending on the cultivar and the maturation stage. In total, 89 known vvi-miRNAs and 33 novel vvi-miRNA candidates were identified in our samples, many of them showing the accumulation profile modulated by at least one of the factors studied. The in silico prediction of miRNA targets suggests their involvement in berry development and in secondary metabolites accumulation such as anthocyanins and polyphenols.
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Affiliation(s)
| | - Lucio Brancadoro
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanMilan, Italy
| | - Silvia Dal Santo
- Laboratory of Plant Genetics, Department of Biotechnology, University of VeronaVerona, Italy
| | - Gabriella De Lorenzis
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of MilanMilan, Italy
| | - Mario Pezzotti
- Laboratory of Plant Genetics, Department of Biotechnology, University of VeronaVerona, Italy
| | - Blake C. Meyers
- Donald Danforth Plant Science CenterSt. Louis, MO, USA
- Division of Plant Sciences, University of Missouri–ColumbiaColumbia, MO, USA
| | - Mario E. Pè
- Institute of Life Sciences, Sant'Anna School of Advanced StudiesPisa, Italy
| | - Erica Mica
- Institute of Life Sciences, Sant'Anna School of Advanced StudiesPisa, Italy
- Genomics Research Centre, Agricultural Research CouncilFiorenzuola d'Arda, Italy
- *Correspondence: Erica Mica
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Zhang Y, Li D, Zhang H, Hong Y, Huang L, Liu S, Li X, Ouyang Z, Song F. Tomato histone H2B monoubiquitination enzymes SlHUB1 and SlHUB2 contribute to disease resistance against Botrytis cinerea through modulating the balance between SA- and JA/ET-mediated signaling pathways. BMC PLANT BIOLOGY 2015; 15:252. [PMID: 26490733 PMCID: PMC4618151 DOI: 10.1186/s12870-015-0614-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 09/13/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND Histone H2B monoubiquitination pathway has been shown to play critical roles in regulating growth/development and stress response in Arabidopsis. In the present study, we explored the involvement of the tomato histone H2B monoubiquitination pathway in defense response against Botrytis cinerea by functional analysis of SlHUB1 and SlHUB2, orthologues of the Arabidopsis AtHUB1/AtHUB2. METHODS We used the TRV-based gene silencing system to knockdown the expression levels of SlHUB1 or SlHUB2 in tomato plants and compared the phenotype between the silenced and the control plants after infection with B. cinerea and Pseudomonas syringae pv. tomato (Pst) DC3000. Biochemical and interaction properties of proteins were examined using in vitro histone monoubiquitination and yeast two-hybrid assays, respectively. The transcript levels of genes were analyzed by quantitative real time PCR (qRT-PCR). RESULTS The tomato SlHUB1 and SlHUB2 had H2B monoubiquitination E3 ligases activity in vitro and expression of SlHUB1 and SlHUB2 was induced by infection of B. cinerea and Pst DC3000 and by treatment with salicylic acid (SA) and 1-amino cyclopropane-1-carboxylic acid (ACC). Silencing of either SlHUB1 or SlHUB2 in tomato plants showed increased susceptibility to B. cinerea, whereas silencing of SlHUB1 resulted in increased resistance against Pst DC3000. SlMED21, a Mediator complex subunit, interacted with SlHUB1 but silencing of SlMED21 did not affect the disease resistance to B. cinerea and Pst DC3000. The SlHUB1- and SlHUB2-silenced plants had thinner cell wall but increased accumulation of reactive oxygen species (ROS), increased callose deposition and exhibited altered expression of the genes involved in phenylpropanoid pathway and in ROS generation and scavenging system. Expression of genes in the SA-mediated signaling pathway was significantly upregulated, whereas expression of genes in the jasmonic acid (JA)/ethylene (ET)-mediated signaling pathway were markedly decreased in SlHUB1- and SlHUB2-silenced plants after infection of B. cinerea. CONCLUSION VIGS-based functional analyses demonstrate that both SlHUB1 and SlHUB2 contribute to resistance against B. cinerea most likely through modulating the balance between the SA- and JA/ET-mediated signaling pathways.
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Affiliation(s)
- Yafen Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Shixia Liu
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xiaohui Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Zhigang Ouyang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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50
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Johnson KCM, Xia S, Feng X, Li X. The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity. PLANT & CELL PHYSIOLOGY 2015; 56:1616-23. [PMID: 26063389 DOI: 10.1093/pcp/pcv087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/04/2015] [Indexed: 05/17/2023]
Abstract
SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity.
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Affiliation(s)
- Kaeli C M Johnson
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada These authors contributed equally to this work
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China These authors contributed equally to this work
| | - Xiaoqi Feng
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
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