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Atem JEC, Gan L, Yu W, Huang F, Wang Y, Baloch A, Nwafor CC, Barrie AU, Chen P, Zhang C. Bioinformatics and functional analysis of EDS1 genes in Brassica napus in response to Plasmodiophora brassicae infection. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112175. [PMID: 38986913 DOI: 10.1016/j.plantsci.2024.112175] [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: 02/05/2024] [Revised: 06/11/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]
Abstract
Enhanced Disease Susceptibility 1 (EDS1) is a key regulator of plant-pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. In the Brassica napus genome, we identified six novel EDS1 genes, among which four were responsive to clubroot infection, a major rapeseed disease resistant to chemical control. Developing resistant cultivars is a potent and economically viable strategy to control clubroot infection. Bioinformatics analysis revealed conserved domains and structural uniformity in Bna-EDS1 homologs. Bna-EDS1 promoters harbored elements associated with diverse phytohormones and stress responses, highlighting their crucial roles in plant defense. A functional analysis was performed with Bna-EDS1 overexpression and RNAi transgenic lines. Bna-EDS1 overexpression boosted resistance to clubroot and upregulated defense-associated genes (PR1, PR2, ICS1, and CBP60), while Bna-EDS1 RNAi increased plant susceptibility, indicating suppression of the defense signaling pathway downstream of NBS-LRRs. RNA-Seq analysis identified key transcripts associated with clubroot resistance, including phenylpropanoid biosynthesis. Activation of SA regulator NPR1, defense signaling markers PR1 and PR2, and upregulation of MYC-TFs suggested that EDS1-mediated clubroot resistance potentially involves the SA pathway. Our findings underscore the pivotal role of Bna-EDS1-dependent mechanisms in resistance of B. napus to clubroot disease, and provide valuable insights for fortifying resistance against Plasmodiophora brassicae infection in rapeseed.
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Affiliation(s)
- Jalal Eldeen Chol Atem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Longcai Gan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Wenlin Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Fan Huang
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln NE68588, USA; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Yanyan Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Amanullah Baloch
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Chinedu Charles Nwafor
- Guangdong Ocean University, Zhanjiang 524088, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Alpha Umaru Barrie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Peng Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Chunyu Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China; Department of Crop Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria.
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Wu P, Li Y. Prion-like Proteins in Plants: Key Regulators of Development and Environmental Adaptation via Phase Separation. PLANTS (BASEL, SWITZERLAND) 2024; 13:2666. [PMID: 39339640 PMCID: PMC11435361 DOI: 10.3390/plants13182666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]
Abstract
Prion-like domains (PrLDs), a unique type of low-complexity domain (LCD) or intrinsically disordered region (IDR), have been shown to mediate protein liquid-liquid phase separation (LLPS). Recent research has increasingly focused on how prion-like proteins (PrLPs) regulate plant growth, development, and stress responses. This review provides a comprehensive overview of plant PrLPs. We analyze the structural features of PrLPs and the mechanisms by which PrLPs undergo LLPS. Through gene ontology (GO) analysis, we highlight the diverse molecular functions of PrLPs and explore how PrLPs influence plant development and stress responses via phase separation. Finally, we address unresolved questions about PrLP regulatory mechanisms, offering prospects for future research.
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Affiliation(s)
- Peisong Wu
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai 519087, China;
| | - Yihao Li
- Faculty of Arts and Sciences, Beijing Normal University, Zhuhai 519087, China;
- Center for Biological Science and Technology, Guangdong Zhuhai–Macao Joint Biotech Laboratory, Advanced Institute of Natural Science, Beijing Normal University, Zhuhai 519087, China
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3
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Naz M, Zhang D, Liao K, Chen X, Ahmed N, Wang D, Zhou J, Chen Z. The Past, Present, and Future of Plant Activators Targeting the Salicylic Acid Signaling Pathway. Genes (Basel) 2024; 15:1237. [PMID: 39336828 PMCID: PMC11431604 DOI: 10.3390/genes15091237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Plant activators have emerged as promising alternatives to conventional crop protection chemicals for managing crop diseases due to their unique mode of action. By priming the plant's innate immune system, these compounds can induce disease resistance against a broad spectrum of pathogens without directly inhibiting their proliferation. Key advantages of plant activators include prolonged defense activity, lower effective dosages, and negligible risk of pathogen resistance development. Among the various defensive pathways targeted, the salicylic acid (SA) signaling cascade has been extensively explored, leading to the successful development of commercial activators of systemic acquired resistance, such as benzothiadiazole, for widespread application in crop protection. While the action sites of many SA-targeting activators have been preliminarily mapped to different steps along the pathway, a comprehensive understanding of their precise mechanisms remains elusive. This review provides a historical perspective on plant activator development and outlines diverse screening strategies employed, from whole-plant bioassays to molecular and transgenic approaches. We elaborate on the various components, biological significance, and regulatory circuits governing the SA pathway while critically examining the structural features, bioactivities, and proposed modes of action of classical activators such as benzothiadiazole derivatives, salicylic acid analogs, and other small molecules. Insights from field trials assessing the practical applicability of such activators are also discussed. Furthermore, we highlight the current status, challenges, and future prospects in the realm of SA-targeting activator development globally, with a focus on recent endeavors in China. Collectively, this comprehensive review aims to describe existing knowledge and provide a roadmap for future research toward developing more potent plant activators that enhance crop health.
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Affiliation(s)
- Misbah Naz
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
| | - Dongqin Zhang
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
| | - Kangcen Liao
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
| | - Xulong Chen
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
| | - Nazeer Ahmed
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang 550025, China;
| | - Jingjiang Zhou
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
| | - Zhuo Chen
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (M.N.); (K.L.); (X.C.); (J.Z.)
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Pancaldi F, Gulisano A, Severing EI, van Kaauwen M, Finkers R, Kodde L, Trindade LM. The genome of Lupinus mutabilis: Evolution and genetics of an emerging bio-based crop. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39264984 DOI: 10.1111/tpj.17021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/02/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024]
Abstract
Lupinus mutabilis is an under-domesticated legume species from the Andean region of South America. It belongs to the New World lupins clade, which groups several lupin species displaying large genetic variation and adaptability to highly different environments. L. mutabilis is attracting interest as a potential multipurpose crop to diversify the European supply of plant proteins, increase agricultural biodiversity, and fulfill bio-based applications. This study reports the first high-quality L. mutabilis genome assembly, which is also the first sequenced assembly of a New World lupin species. Through comparative genomics and phylogenetics, the evolution of L. mutabilis within legumes and lupins is described, highlighting both genomic similarities and patterns specific to L. mutabilis, potentially linked to environmental adaptations. Furthermore, the assembly was used to study the genetics underlying important traits for the establishment of L. mutabilis as a novel crop, including protein and quinolizidine alkaloids contents in seeds, genomic patterns of classic resistance genes, and genomic properties of L. mutabilis mycorrhiza-related genes. These analyses pointed out copy number variation, differential genomic gene contexts, and gene family expansion through tandem duplications as likely important drivers of the genomic diversity observed for these traits between L. mutabilis and other lupins and legumes. Overall, the L. mutabilis genome assembly will be a valuable resource to conduct genetic research and enable genomic-based breeding approaches to turn L. mutabilis into a multipurpose legume crop.
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Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Agata Gulisano
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Edouard I Severing
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Gennovation B.V, Agro Business Park 10, 6708PW, Wageningen, The Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Gennovation B.V, Agro Business Park 10, 6708PW, Wageningen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Luisa M Trindade
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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5
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Sun B, Huang J, Kong L, Gao C, Zhao F, Shen J, Wang T, Li K, Wang L, Wang Y, Halterman DA, Dong S. Alternative splicing of a potato disease resistance gene maintains homeostasis between growth and immunity. THE PLANT CELL 2024; 36:3729-3750. [PMID: 38941447 PMCID: PMC11371151 DOI: 10.1093/plcell/koae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/31/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Plants possess a robust and sophisticated innate immune system against pathogens and must balance growth with rapid pathogen detection and defense. The intracellular receptors with nucleotide-binding leucine-rich repeat (NLR) motifs recognize pathogen-derived effector proteins and thereby trigger the immune response. The expression of genes encoding NLR receptors is precisely controlled in multifaceted ways. The alternative splicing (AS) of introns in response to infection is recurrently observed but poorly understood. Here we report that the potato (Solanum tuberosum) NLR gene RB undergoes AS of its intron, resulting in 2 transcriptional isoforms, which coordinately regulate plant immunity and growth homeostasis. During normal growth, RB predominantly exists as an intron-retained isoform RB_IR, encoding a truncated protein containing only the N-terminus of the NLR. Upon late blight infection, the pathogen induces intron splicing of RB, increasing the abundance of RB_CDS, which encodes a full-length and active R protein. By deploying the RB splicing isoforms fused with a luciferase reporter system, we identified IPI-O1 (also known as Avrblb1), the RB cognate effector, as a facilitator of RB AS. IPI-O1 directly interacts with potato splicing factor StCWC15, resulting in altered localization of StCWC15 from the nucleoplasm to the nucleolus and nuclear speckles. Mutations in IPI-O1 that eliminate StCWC15 binding also disrupt StCWC15 re-localization and RB intron splicing. Thus, our study reveals that StCWC15 serves as a surveillance facilitator that senses the pathogen-secreted effector and regulates the trade-off between RB-mediated plant immunity and growth, expanding our understanding of molecular plant-microbe interactions.
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Affiliation(s)
- Biying Sun
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Huang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Plant Chemetics Laboratory, Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Liang Kong
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuyun Gao
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Zhao
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayong Shen
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Tian Wang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Kangping Li
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Luyao Wang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen Branch, Shenzhen, Guangdong 518120, China
| | - Yuanchao Wang
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
| | - Dennis A Halterman
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
- US Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706-1514, USA
| | - Suomeng Dong
- Department of Plant Pathology, The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant Immunity, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing 210095, China
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Mo C, Wang H, Wei M, Zeng Q, Zhang X, Fei Z, Zhang Y, Kong Q. Complete genome assembly provides a high-quality skeleton for pan-NLRome construction in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2249-2268. [PMID: 38430487 DOI: 10.1111/tpj.16705] [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: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/03/2024]
Abstract
Melon (Cucumis melo L.), being under intensive domestication and selective breeding, displays an abundant phenotypic diversity. Wild germplasm with tolerance to stress represents an untapped genetic resource for discovery of disease-resistance genes. To comprehensively characterize resistance genes in melon, we generate a telomere-to-telomere (T2T) and gap-free genome of wild melon accession PI511890 (C. melo var. chito) with a total length of 375.0 Mb and a contig N50 of 31.24 Mb. The complete genome allows us to dissect genome architecture and identify resistance gene analogs. We construct a pan-NLRome using seven melon genomes, which include 208 variable and 18 core nucleotide-binding leucine-rich repeat receptors (NLRs). Multiple disease-related transcriptome analyses indicate that most up-regulated NLRs induced by pathogens are shell or cloud NLRs. The T2T gap-free assembly and the pan-NLRome not only serve as essential resources for genomic studies and molecular breeding of melon but also provide insights into the genome architecture and NLR diversity.
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Affiliation(s)
- Changjuan Mo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghua Wei
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingguo Zeng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuejun Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | | | - Yongbing Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
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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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Thomas HR, Gevorgyan A, Hermanson A, Yanders S, Erndwein L, Norman-Ariztía M, Sparks EE, Frank MH. Graft incompatibility between pepper and tomato can be attributed to genetic incompatibility between diverged immune systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587379. [PMID: 38617251 PMCID: PMC11014474 DOI: 10.1101/2024.03.29.587379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Graft compatibility is the capacity of two plants to form cohesive vascular connections. Tomato and pepper are incompatible graft partners; however, the underlying cause of graft rejection between these two species remains unknown.We diagnosed graft incompatibility between tomato and diverse pepper varieties based on weakened biophysical stability, decreased growth, and persistent cell death using trypan blue and TUNEL assays. Transcriptomic analysis of cell death in the junction was performed using RNA-sequencing, and molecular signatures for incompatible graft response were characterized based on meta-transcriptomic comparisons with other biotic processes.We show that tomato is broadly incompatible with diverse pepper cultivars. These incompatible graft partners activate prolonged transcriptional changes that are highly enriched for defense processes. Amongst these processes was broad NLR upregulation and hypersensitive response. Using transcriptomic datasets for a variety of biotic stress treatments, we identified a significant overlap in the genetic profile of incompatible grafting and plant parasitism. In addition, we found over 1000 genes that are uniquely upregulated in incompatible grafts.Based on NLR overactivity, DNA damage, and prolonged cell death we have determined that tomato and pepper graft incompatibility is likely caused by a form of genetic incompatibility, which triggers a hyperimmune-response.
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Affiliation(s)
- Hannah Rae Thomas
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
- John Innes Centre, Department of Cell and Developmental Biology, Norwich UK
| | - Alice Gevorgyan
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - Alexandra Hermanson
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
| | - Samantha Yanders
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
| | - Lindsay Erndwein
- University of Delaware, Department of Plant and Soil Sciences, Newark, DE 19713,USA
- USDA-ARS, Genetic Improvement for Fruits and Vegetables Laboratory, Chatsworth,NJ 08019, USA
| | | | - Erin E. Sparks
- University of Delaware, Department of Plant and Soil Sciences, Newark, DE 19713,USA
| | - Margaret H Frank
- Cornell University, School of Integrative Plant Science, Ithaca, NY 14850, USA
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9
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Normantovich M, Amitzur A, Offri S, Pashkovsky E, Shnaider Y, Nizan S, Yogev O, Jacob A, Taylor CG, Desbiez C, Whitham SA, Bar-Ziv A, Perl-Treves R. The melon Fom-1-Prv resistance gene pair: Correlated spatial expression and interaction with a viral protein. PLANT DIRECT 2024; 8:e565. [PMID: 38389929 PMCID: PMC10883720 DOI: 10.1002/pld3.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
The head-to-head oriented pair of melon resistance genes, Fom-1 and Prv, control resistance to Fusarium oxysporum races 0 and 2 and papaya ringspot virus (PRSV), respectively. They encode, via several RNA splice variants, TIR-NBS-LRR proteins, and Prv has a C-terminal extra domain with a second NBS homologous sequence. In other systems, paired R-proteins were shown to operate by "labor division," with one protein having an extra integrated domain that directly binds the pathogen's Avr factor, and the second protein executing the defense response. We report that the expression of the two genes in two pairs of near-isogenic lines was higher in the resistant isoline and inducible by F. oxysporum race 2 but not by PRSV. The intergenic DNA region separating the coding sequences of the two genes acted as a bi-directional promoter and drove GUS expression in transgenic melon roots and transgenic tobacco plants. Expression of both genes was strong in melon root tips, around the root vascular cylinder, and the phloem and xylem parenchyma of tobacco stems and petioles. The pattern of GUS expression suggests coordinated expression of the two genes. In agreement with the above model, Prv's extra domain was shown to interact with the cylindrical inclusion protein of PRSV both in yeast cells and in planta.
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Affiliation(s)
- Michael Normantovich
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Arie Amitzur
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Sharon Offri
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ekaterina Pashkovsky
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Yula Shnaider
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Shahar Nizan
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ohad Yogev
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Avi Jacob
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | | | | | - Steven A Whitham
- Department of Plant Pathology and Microbiology Iowa State University Ames Iowa USA
| | - Amalia Bar-Ziv
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
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10
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Brabham HJ, Gómez De La Cruz D, Were V, Shimizu M, Saitoh H, Hernández-Pinzón I, Green P, Lorang J, Fujisaki K, Sato K, Molnár I, Šimková H, Doležel J, Russell J, Taylor J, Smoker M, Gupta YK, Wolpert T, Talbot NJ, Terauchi R, Moscou MJ. Barley MLA3 recognizes the host-specificity effector Pwl2 from Magnaporthe oryzae. THE PLANT CELL 2024; 36:447-470. [PMID: 37820736 PMCID: PMC10827324 DOI: 10.1093/plcell/koad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat (NLRs) immune receptors directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley (Hordeum vulgare) NLR gene Mildew locus a (Mla) has undergone functional diversification, and the proteins encoded by different Mla alleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminis f. sp. hordei [Bgh]). Here, we show that Mla3 also confers resistance to the rice blast fungus Magnaporthe oryzae in a dosage-dependent manner. Using a forward genetic screen, we discovered that the recognized effector from M. oryzae is Pathogenicity toward Weeping Lovegrass 2 (Pwl2), a host range determinant factor that prevents M. oryzae from infecting weeping lovegrass (Eragrostis curvula). Mla3 has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.
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Affiliation(s)
- Helen J Brabham
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Diana Gómez De La Cruz
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Motoki Shimizu
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Hiromasa Saitoh
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | | | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jennifer Lorang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Koki Fujisaki
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czech Republic
| | - James Russell
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yogesh Kumar Gupta
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- 2Blades, Evanston, IL 60201, USA
| | - Tom Wolpert
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Centre, Kitakami 024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto 617-0001, Japan
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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11
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Mei S, Song Y, Zhang Z, Cui H, Hou S, Miao W, Rong W. WRR4B contributes to a broad-spectrum disease resistance against powdery mildew in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13415. [PMID: 38279853 PMCID: PMC10777751 DOI: 10.1111/mpp.13415] [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: 09/06/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/29/2024]
Abstract
Oidium heveae HN1106, a powdery mildew (PM) that infects rubber trees, has been found to trigger disease resistance in Arabidopsis thaliana through ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)-, PHYTOALEXIN DEFICIENT 4 (PAD4)- and salicylic acid (SA)-mediated signalling pathways. In this study, a typical TOLL-INTERLEUKIN 1 RECEPTOR, NUCLEOTIDE-BINDING, LEUCINE-RICH REPEAT (TIR-NB-LRR)-encoding gene, WHITE RUST RESISTANCE 4 (WRR4B), was identified to be required for the resistance against O. heveae in Arabidopsis. The expression of WRR4B was upregulated by O. heveae inoculation, and WRR4B positively regulated the expression of genes involved in SA biosynthesis, such as EDS1, PAD4, ICS1 (ISOCHORISMATE SYNTHASE 1), SARD1 (SYSTEMIC-ACQUIRED RESISTANCE DEFICIENT 1) and CBP60g (CALMODULIN-BINDING PROTEIN 60 G). Furthermore, WRR4B triggered self-amplification, suggesting that WRR4B mediated plant resistance through taking part in the SA-based positive feedback loop. In addition, WRR4B induced an EDS1-dependent hypersensitive response in Nicotiana benthamiana and contributed to disease resistance against three other PM species: Podosphaera xanthii, Erysiphe quercicola and Erysiphe neolycopersici, indicating that WRR4B is a broad-spectrum disease resistance gene against PMs.
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Affiliation(s)
- Shuangshuang Mei
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Yuxin Song
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Zuer Zhang
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Haitao Cui
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anShandongChina
| | - Shuguo Hou
- Institute of Advanced Agricultural SciencesPeking UniversityWeifangShandongChina
| | - Weiguo Miao
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Wei Rong
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
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12
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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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13
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Yang S, Cai W, Wu R, Huang Y, Lu Q, Hui Wang, Huang X, Zhang Y, Wu Q, Cheng X, Wan M, Lv J, Liu Q, Zheng X, Mou S, Guan D, He S. Differential CaKAN3-CaHSF8 associations underlie distinct immune and heat responses under high temperature and high humidity conditions. Nat Commun 2023; 14:4477. [PMID: 37491353 PMCID: PMC10368638 DOI: 10.1038/s41467-023-40251-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
High temperature and high humidity (HTHH) conditions increase plant susceptibility to a variety of diseases, including bacterial wilt in solanaceous plants. Some solanaceous plant cultivars have evolved mechanisms to activate HTHH-specific immunity to cope with bacterial wilt disease. However, the underlying mechanisms remain poorly understood. Here we find that CaKAN3 and CaHSF8 upregulate and physically interact with each other in nuclei under HTHH conditions without inoculation or early after inoculation with R. solanacearum in pepper. Consequently, CaKAN3 and CaHSF8 synergistically confer immunity against R. solanacearum via activating a subset of NLRs which initiates immune signaling upon perception of unidentified pathogen effectors. Intriguingly, when HTHH conditions are prolonged without pathogen attack or the temperature goes higher, CaHSF8 no longer interacts with CaKAN3. Instead, it directly upregulates a subset of HSP genes thus activating thermotolerance. Our findings highlight mechanisms controlling context-specific activation of high-temperature-specific pepper immunity and thermotolerance mediated by differential CaKAN3-CaHSF8 associations.
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Affiliation(s)
- Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Weiwei Cai
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- College of Horticultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, Zhejiang, PR China
| | - Ruijie Wu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Yu Huang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Qiaoling Lu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Hui Wang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Xueying Huang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Yapeng Zhang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Qing Wu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Xingge Cheng
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Meiyun Wan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Jingang Lv
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Qian Liu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Xiang Zheng
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Shaoliang Mou
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Deyi Guan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China.
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, PR China.
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14
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Krępski T, Olechowski M, Samborska-Skutnik I, Święcicka M, Grądzielewska A, Rakoczy-Trojanowska M. Identification and characteristics of wheat Lr orthologs in three rye inbred lines. PLoS One 2023; 18:e0288520. [PMID: 37440539 DOI: 10.1371/journal.pone.0288520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The genetic background of the immune response of rye to leaf rust (LR), although extensively studied, is still not well understood. The recent publication of the genome of rye line Lo7 and the development of efficient transcriptomic methods has aided the search for genes that confer resistance to this disease. In this study, we investigated the potential role of rye orthologs of wheat Lr genes (Lr1, Lr10, Lr21, Lr22a, and RGA2/T10rga2-1A) in the LR seedling-stage resistance of inbred rye lines D33, D39, and L318. Bioinformatics analysis uncovered numerous Lr orthologs in the Lo7 genome, namely, 14 ScLr1, 15 ScRga2, and 2 ScLr21 paralogs, and 1 each of ScLr10 and ScLr22a genes. The paralogs of ScLr1, ScRga2, and ScLr21 were structurally different from one another and their wheat counterparts. According to an RNA sequencing analysis, only four wheat Lr gene orthologs identified in the Lo7 genome (ScLr1_3, ScLr1_4, ScLr1_8, and ScRga2_6) were differentially expressed; all four were downregulated after infection with compatible or incompatible isolates of Puccinia recondita f. sp. secalis (Prs). Using a more precise tool, RT-qPCR, we found that two genes were upregulated at 20 h post-infection, namely, ScLr1_4 and ScLr1_8 in lines D33 and D39, respectively, both of which have been found to be resistant to LR under field conditions and after treatment with a semi-compatible Prs strain. We were unable to discern any universal pattern of gene expression after Prs infection; on the contrary, all detected relationships were plant genotype-, Prs isolate-, or time-specific. Nevertheless, at least some Lr orthologs in rye (namely, ScLr1_3 ScLr1_4, ScLr1_8, and ScRga2_6), even though mainly downregulated, may play an important role in the response of rye to LR.
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Affiliation(s)
- Tomasz Krępski
- Department of Plant Genetics, Institute of Biology, Breeding and Biotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Mateusz Olechowski
- Department of Plant Genetics, Institute of Biology, Breeding and Biotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Izabela Samborska-Skutnik
- Department of Plant Genetics, Institute of Biology, Breeding and Biotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Święcicka
- Department of Plant Genetics, Institute of Biology, Breeding and Biotechnology, Warsaw University of Life Sciences, Warsaw, Poland
| | | | - Monika Rakoczy-Trojanowska
- Department of Plant Genetics, Institute of Biology, Breeding and Biotechnology, Warsaw University of Life Sciences, Warsaw, Poland
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15
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Mermigka G, Michalopoulou VA, Amartolou A, Mentzelopoulou A, Astropekaki N, Sarris PF. Assassination tango: an NLR/NLR-ID immune receptors pair of rapeseed co-operates inside the nucleus to activate cell death. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1211-1222. [PMID: 36628462 DOI: 10.1111/tpj.16105] [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: 11/02/2021] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Plant immunity largely relies on intracellular nucleotide-binding domain leucine-rich repeat (NLR) immune receptors. Some plant NLRs carry integrated domains (IDs) that mimic authentic pathogen effector targets. We report here the identification of a genetically linked NLR-ID/NLR pair: BnRPR1 and BnRPR2 in Brassica napus. The NLR-ID carries two ID fusions and the mode of action of the pair conforms to the proposed "integrated sensor/decoy" model. The two NLRs interact and the heterocomplex localizes in the plant-cell nucleus and nucleolus. However, the BnRPRs pair does not operate through a negative regulation as it was previously reported for other NLR-IDs. Cell death is induced only upon co-expression of the two proteins and is dependent on the helper genes, EDS1 and NRG1. The nuclear localization of both proteins seems to be essential for cell death activation, while the IDs of BnRPR1 are dispensable for this purpose. In summary, we describe a new pair of NLR-IDs with interesting features in relation to its regulation and the cell death activation.
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Affiliation(s)
- Glykeria Mermigka
- Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, 70013, Crete, Heraklion, Greece
| | - Vassiliki A Michalopoulou
- Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, 70013, Crete, Heraklion, Greece
| | - Argyro Amartolou
- Department of Biology, University of Crete, Crete, 714 09 Heraklion, Greece
| | | | - Niki Astropekaki
- Department of Biology, University of Crete, Crete, 714 09 Heraklion, Greece
| | - Panagiotis F Sarris
- Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, 70013, Crete, Heraklion, Greece
- Department of Biology, University of Crete, Crete, 714 09 Heraklion, Greece
- Biosciences, University of Exeter, EX4 4QD, Exeter, Geoffrey Pope Building, Stocker Road, UK
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16
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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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17
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Ribeiro C, Xu J, Hendrich C, Pandey SS, Yu Q, Gmitter FG, Wang N. Seasonal Transcriptome Profiling of Susceptible and Tolerant Citrus Cultivars to Citrus Huanglongbing. PHYTOPATHOLOGY 2023; 113:286-298. [PMID: 36001783 DOI: 10.1094/phyto-05-22-0179-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Citrus huanglongbing (HLB) caused by 'Candidatus Liberibacter asiaticus' (CLas) is the most devastating citrus disease worldwide. Most commercial citrus cultivars are susceptible to HLB, with a few more tolerant exceptions such as 'LB8-9' Sugar Belle mandarin. Transcriptomic analyses have been widely used to investigate the potential mechanisms for disease susceptibility, resistance, or tolerance. Previous transcriptomic studies related to HLB mostly focused on single time point data collection. We hypothesize that changes in day length and temperature throughout the seasons have profound effects on citrus-CLas interactions. Here, we conducted RNA-seq analyses on HLB-susceptible Valencia sweet orange and HLB-tolerant mandarin 'LB8-9' in winter, spring, summer, and fall. Significant variations in differentially expressed genes (DEGs) related to HLB were observed among the four seasons. For both cultivars, the highest number of DEGs were found in the spring. CLas infection stimulates the expression of immune-related genes such as NBS-LRR, RLK, RLCK, CDPK, MAPK pathway, reactive oxygen species (ROS), and PR genes in both cultivars, consistent with the model that HLB is a pathogen-triggered immune disease. HLB-positive mandarin 'LB8-9' trees contained higher concentrations of maltose and sucrose, which are known to scavenge ROS. In addition, mandarin 'LB8-9' showed higher expression of genes involved in phloem regeneration, which might contribute to its HLB tolerance. This study shed light on the pathogenicity mechanism of the HLB pathosystem and the tolerance mechanism against HLB, providing valuable insights into HLB management.
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Affiliation(s)
- Camila Ribeiro
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Jin Xu
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Connor Hendrich
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Sheo Shankar Pandey
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Qibin Yu
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Frederick G Gmitter
- Citrus Research & Education Center, Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
| | - Nian Wang
- Citrus Research & Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL 33850
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18
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Wang Y, Tang M, Zhang Y, Huang M, Wei L, Lin Y, Xie J, Cheng J, Fu Y, Jiang D, Li B, Yu X. Coordinated regulation of plant defense and autoimmunity by paired trihelix transcription factors ASR3/AITF1 in Arabidopsis. THE NEW PHYTOLOGIST 2023; 237:914-929. [PMID: 36266950 DOI: 10.1111/nph.18562] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Plants perceive pathogens and induce robust transcriptional reprogramming to rapidly achieve immunity. The mechanisms of how immune-related genes are transcriptionally regulated remain largely unknown. Previously, the trihelix transcriptional factor ARABIDOPSIS SH4-RELATED 3 (ASR3) was shown to negatively regulate pattern-triggered immunity (PTI) in Arabidopsis thaliana. Here, we identified another trihelix family member ASR3-Interacting Transcriptional Factor 1 (AITF1) as an interacting protein of ASR3. ASR3-Interacting Transcriptional Factor 1 and ASR3 form heterogenous and homogenous dimers in planta. Both aitf1 and asr3 single mutants exhibited increased resistance against the bacterial pathogen Pseudomonas syringae, but the double mutant showed reduced resistance, suggesting AITF1 and ASR3 interdependently regulate immune gene expression and resistance. Overexpression of AITF1 triggered autoimmunity dependently on its DNA-binding ability and the presence of ASR3. Notably, autoimmunity caused by overexpression of AITF1 was dependent on a TIR-NBS-LRR (TNL) protein suppressor of AITF1-induced autoimmunity 1 (SAA1), as well as enhanced disease susceptibility 1 (EDS1), the central regulator of TNL signaling. ASR3-Interacting Transcriptional Factor 1 and ASR3 directly activated SAA1 expression through binding to the GT-boxes in SAA1 promoter. Collectively, our results revealed a mechanism of trihelix transcription factor complex in regulating immune gene expression, thereby modulating plant disease resistance and autoimmunity.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Meng Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Ying Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Lan Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
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19
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Guimaraes PM, Quintana AC, Mota APZ, Berbert PS, Ferreira DDS, de Aguiar MN, Pereira BM, de Araújo ACG, Brasileiro ACM. Engineering Resistance against Sclerotinia sclerotiorum Using a Truncated NLR (TNx) and a Defense-Priming Gene. PLANTS (BASEL, SWITZERLAND) 2022; 11:3483. [PMID: 36559595 PMCID: PMC9786959 DOI: 10.3390/plants11243483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The association of both cell-surface PRRs (Pattern Recognition Receptors) and intracellular receptor NLRs (Nucleotide-Binding Leucine-Rich Repeat) in engineered plants have the potential to activate strong defenses against a broad range of pathogens. Here, we describe the identification, characterization, and in planta functional analysis of a novel truncated NLR (TNx) gene from the wild species Arachis stenosperma (AsTIR19), with a protein structure lacking the C-terminal LRR (Leucine Rich Repeat) domain involved in pathogen perception. Overexpression of AsTIR19 in tobacco plants led to a significant reduction in infection caused by Sclerotinia sclerotiorum, with a further reduction in pyramid lines containing an expansin-like B gene (AdEXLB8) potentially involved in defense priming. Transcription analysis of tobacco transgenic lines revealed induction of hormone defense pathways (SA; JA-ET) and PRs (Pathogenesis-Related proteins) production. The strong upregulation of the respiratory burst oxidase homolog D (RbohD) gene in the pyramid lines suggests its central role in mediating immune responses in plants co-expressing the two transgenes, with reactive oxygen species (ROS) production enhanced by AdEXLB8 cues leading to stronger defense response. Here, we demonstrate that the association of potential priming elicitors and truncated NLRs can produce a synergistic effect on fungal resistance, constituting a promising strategy for improved, non-specific resistance to plant pathogens.
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Affiliation(s)
- Patricia Messenberg Guimaraes
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
| | | | - Ana Paula Zotta Mota
- INRAE, Institut Sophia Agrobiotech, CNRS, Université Côte d’Azur, 06903 Sophia Antipolis, France
| | | | | | | | | | | | - Ana Cristina Miranda Brasileiro
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Brasilia 70770-917, Brazil
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20
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Sett S, Prasad A, Prasad M. Resistance genes on the verge of plant-virus interaction. TRENDS IN PLANT SCIENCE 2022; 27:1242-1252. [PMID: 35902346 DOI: 10.1016/j.tplants.2022.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Viruses are acellular pathogens that cause severe infections in plants, resulting in worldwide crop losses every year. The lack of chemical agents to control viral diseases exacerbates the situation. Thus, to devise proper management strategies, it is important that the defense mechanisms of plants against viruses are understood. Resistance (R) genes regulate plant defense against invading pathogens by eliciting a hypersensitive response (HR). Compatible interaction between plant R gene and viral avirulence (Avr) protein activates the necrotic cell death response at the site of infection, resulting in the cessation of disease. Here, we review different aspects of R gene-mediated dominant resistance against plant viruses in dicotyledonous plants and possible ways for developing crops with better disease resistance.
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Affiliation(s)
- Susmita Sett
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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21
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Hunt AG. Review: Mechanisms underlying alternative polyadenylation in plants - looking in the right places. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111430. [PMID: 36007628 DOI: 10.1016/j.plantsci.2022.111430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/01/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Recent years have seen an explosion of interest in the subject of alternative polyadenylation in plants. Connections between the polyadenylation complex and numerous developmental and stress responses are well-established. However, those that link stimuli with the functioning of the polyadenylation complex are less well understood. To this end, it is imperative to clearly delineate the roles of the polyadenylation complex in both plant growth AND alternative polyadenylation. It is also necessary to understand the ways by which other molecular processes may contribute to alternative polyadenylation. This review discusses these issues, with a focus on instances that reveal mechanisms by which mRNA polyadenylation may be regulated. Insights from from characterizations of mutants affected in the polyadenylation complex are discussed, as are the limitations of such characterizations when it comes to teasing out cause and effect. These limitations encourage explorations to other processes that are beyond the core polyadenylation complex. Two such processes that sculpt the plant transcriptome - transcription termination and the epigenetic control of transposon activity - also contribute to regulated poly(A) site choice. These subjects define "the right places" - molecular mechanisms that contribute to the wide-ranging control of gene expression via mRNA polyadenylation.
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Affiliation(s)
- Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, 301A Plant Science Building, 1405 Veterans Road, Lexington, KY 40546-0312, USA.
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22
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Ercolano MR, D’Esposito D, Andolfo G, Frusciante L. Multilevel evolution shapes the function of NB-LRR encoding genes in plant innate immunity. FRONTIERS IN PLANT SCIENCE 2022; 13:1007288. [PMID: 36388554 PMCID: PMC9647133 DOI: 10.3389/fpls.2022.1007288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
A sophisticated innate immune system based on diverse pathogen receptor genes (PRGs) evolved in the history of plant life. To reconstruct the direction and magnitude of evolutionary trajectories of a given gene family, it is critical to detect the ancestral signatures. The rearrangement of functional domains made up the diversification found in PRG repertoires. Structural rearrangement of ancient domains mediated the NB-LRR evolutionary path from an initial set of modular proteins. Events such as domain acquisition, sequence modification and temporary or stable associations are prominent among rapidly evolving innate immune receptors. Over time PRGs are continuously shaped by different forces to find their optimal arrangement along the genome. The immune system is controlled by a robust regulatory system that works at different scales. It is important to understand how the PRG interaction network can be adjusted to meet specific needs. The high plasticity of the innate immune system is based on a sophisticated functional architecture and multi-level control. Due to the complexity of interacting with diverse pathogens, multiple defense lines have been organized into interconnected groups. Genomic architecture, gene expression regulation and functional arrangement of PRGs allow the deployment of an appropriate innate immunity response.
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23
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Chen K, Shi Z, Zhang S, Wang Y, Xia X, Jiang Y, Gull S, Chen L, Guo H, Wu T, Zhang H, Liu J, Kong W. Methylation and Expression of Rice NLR Genes after Low Temperature Stress. Gene 2022; 845:146830. [PMID: 35995119 DOI: 10.1016/j.gene.2022.146830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/17/2022] [Accepted: 08/16/2022] [Indexed: 11/04/2022]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) are included in most plant disease resistance proteins. Some NLR proteins have been revealed to be induced by the invasion of plant pathogens. DNA methylation is required for adaption to adversity and proper regulation of gene expression in plants. Low temperature stress (LTS) is a restriction factor in rice growth, development and production. Here, we report the methylation and expression of NLR genes in two rice cultivars, i.e., 9311 (an indica rice cultivar sensitive to LTS), and P427 (a japonica cultivar, tolerant to LTS), after LTS. We found that the rice NLR genes were heavily methylated within CG sites at room temperature and low temperature in 9311 and P427, and many rice NLR genes showed DNA methylation alteration after LTS. A great number of rice NLR genes were observed to be responsive to LTS at the transcriptional level. Our observation suggests that the alteration of expression of rice NLR genes was similar but their change in DNA methylation was dynamic between the two rice cultivars after LTS. We identified that more P427 NLR genes reacted to LTS than those of 9311 at the methylation and transcriptional level. The results in this study will be useful for further understanding the transcriptional regulation and potential functions of rice NLR genes.
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Affiliation(s)
- Kun Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Zuqi Shi
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shengwei Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yanxin Wang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xue Xia
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yan Jiang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Sadia Gull
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Lin Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hui Guo
- Rice Research Institute, Guizhou Provincial Academy of Agriculture Sciences, Guiyang, 550006, China
| | - Tingkai Wu
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Hongyu Zhang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jinglan Liu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
| | - Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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24
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Sukarta OCA, Zheng Q, Slootweg EJ, Mekken M, Mendel M, Putker V, Bertran A, Brand A, Overmars H, Pomp R, Roosien J, Boeren S, Smant G, Goverse A. GLYCINE-RICH RNA-BINDING PROTEIN 7 potentiates effector-triggered immunity through an RNA recognition motif. PLANT PHYSIOLOGY 2022; 189:972-987. [PMID: 35218353 PMCID: PMC9157115 DOI: 10.1093/plphys/kiac081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The activity of intracellular plant nucleotide-binding leucine-rich repeat (NB-LRR) immune receptors is fine-tuned by interactions between the receptors and their partners. Identifying NB-LRR interacting proteins is therefore crucial to advance our understanding of how these receptors function. A co-immunoprecipitation/mass spectrometry screening was performed in Nicotiana benthamiana to identify host proteins associated with the resistance protein Gpa2, a CC-NB-LRR immune receptor conferring resistance against the potato cyst nematode Globodera pallida. A combination of biochemical, cellular, and functional assays was used to assess the role of a candidate interactor in defense. A N. benthamiana homolog of the GLYCINE-RICH RNA-BINDING PROTEIN7 (NbGRP7) protein was prioritized as a Gpa2-interacting protein for further investigations. NbGRP7 also associates in planta with the homologous Rx1 receptor, which confers immunity to Potato Virus X. We show that NbGRP7 positively regulates extreme resistance by Rx1 and cell death by Gpa2. Mutating the NbGRP7 RNA recognition motif (RRM) compromises its role in Rx1-mediated defense. Strikingly, ectopic NbGRP7 expression is likely to impact the steady-state levels of Rx1, which relies on an intact RRM. Our findings illustrate that NbGRP7 is a pro-immune component in effector-triggered immunity by regulating Gpa2/Rx1 function at a posttranscriptional level.
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Affiliation(s)
- Octavina C A Sukarta
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Qi Zheng
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erik J Slootweg
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Mark Mekken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Melanie Mendel
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Vera Putker
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - André Bertran
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Anouk Brand
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Rikus Pomp
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Jan Roosien
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
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25
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Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: Zig-zag through the plant immune system. THE PLANT CELL 2022; 34:1447-1478. [PMID: 35167697 PMCID: PMC9048904 DOI: 10.1093/plcell/koac041] [Citation(s) in RCA: 295] [Impact Index Per Article: 147.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, UK
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26
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Freh M, Gao J, Petersen M, Panstruga R. Plant autoimmunity-fresh insights into an old phenomenon. PLANT PHYSIOLOGY 2022; 188:1419-1434. [PMID: 34958371 PMCID: PMC8896616 DOI: 10.1093/plphys/kiab590] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
The plant immune system is well equipped to ward off the attacks of different types of phytopathogens. It primarily relies on two types of immune sensors-plasma membrane-resident receptor-like kinases and intracellular nucleotide-binding domain leucine-rich repeat (NLRs) receptors that engage preferentially in pattern- and effector-triggered immunity, respectively. Delicate fine-tuning, in particular of the NLR-governed branch of immunity, is key to prevent inappropriate and deleterious activation of plant immune responses. Inadequate NLR allele constellations, such as in the case of hybrid incompatibility, and the mis-activation of NLRs or the absence or modification of proteins guarded by these NLRs can result in the spontaneous initiation of plant defense responses and cell death-a phenomenon referred to as plant autoimmunity. Here, we review recent insights augmenting our mechanistic comprehension of plant autoimmunity. The recent findings broaden our understanding regarding hybrid incompatibility, unravel candidates for proteins likely guarded by NLRs and underline the necessity for the fine-tuning of NLR expression at various levels to avoid autoimmunity. We further present recently emerged tools to study plant autoimmunity and draw a cross-kingdom comparison to the role of NLRs in animal autoimmune conditions.
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Affiliation(s)
- Matthias Freh
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen 52056, Germany
| | - Jinlan Gao
- Institute of Biology, Functional Genomics, Copenhagen University, Copenhagen 2200, Denmark
| | - Morten Petersen
- Institute of Biology, Functional Genomics, Copenhagen University, Copenhagen 2200, Denmark
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen 52056, Germany
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27
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Transcriptome and Small RNA Profiling of Potato Virus Y Infected Potato Cultivars, Including Systemically Infected Russet Burbank. Viruses 2022; 14:v14030523. [PMID: 35336930 PMCID: PMC8952017 DOI: 10.3390/v14030523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/06/2023] Open
Abstract
Potatoes are the world’s most produced non-grain crops and an important food source for billions of people. Potatoes are susceptible to numerous pathogens that reduce yield, including Potato virus Y (PVY). Genetic resistance to PVY is a sustainable way to limit yield and quality losses due to PVY infection. Potato cultivars vary in their susceptibility to PVY and include susceptible varieties such as Russet Burbank, and resistant varieties such as Payette Russet. Although the loci and genes associated with PVY-resistance have been identified, the genes and mechanisms involved in limiting PVY during the development of systemic infections have yet to be fully elucidated. To increase our understanding of PVY infection, potato antiviral responses, and resistance, we utilized RNA sequencing to characterize the transcriptomes of two potato cultivars. Since transcriptional responses associated with the extreme resistance response occur soon after PVY contact, we analyzed the transcriptome and small RNA profile of both the PVY-resistant Payette Russet cultivar and PVY-susceptible Russet Burbank cultivar 24 h post-inoculation. While hundreds of genes, including terpene synthase and protein kinase encoding genes, exhibited increased expression, the majority, including numerous genes involved in plant pathogen interactions, were downregulated. To gain greater understanding of the transcriptional changes that occur during the development of systemic PVY-infection, we analyzed Russet Burbank leaf samples one week and four weeks post-inoculation and identified similarities and differences, including higher expression of genes involved in chloroplast function, photosynthesis, and secondary metabolite production, and lower expression of defense response genes at those time points. Small RNA sequencing identified different populations of 21- and 24-nucleotide RNAs and revealed that the miRNA profiles in PVY-infected Russet Burbank plants were similar to those observed in other PVY-tolerant cultivars and that during systemic infection ~32% of the NLR-type disease resistance genes were targeted by 21-nt small RNAs. Analysis of alternative splicing in PVY-infected potato plants identified splice variants of several hundred genes, including isoforms that were more dominant in PVY-infected plants. The description of the PVYN-Wi-associated transcriptome and small RNA profiles of two potato cultivars described herein adds to the body of knowledge regarding differential outcomes of infection for specific PVY strain and host cultivar pairs, which will help further understanding of the mechanisms governing genetic resistance and/or virus-limiting responses in potato plants.
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Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H. De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. THE NEW PHYTOLOGIST 2022; 233:2094-2110. [PMID: 34532854 PMCID: PMC9293310 DOI: 10.1111/nph.17738] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 09/02/2021] [Indexed: 05/27/2023]
Abstract
Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. The 309 Mb of the genome is predicted to encode 34 403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Ferdinand Marlétaz
- Department of Genetics, Evolution and Environment (GEE)University College LondonDarwin Building, Gower StreetLondonWC1E 6BTUK
| | - Daria Gavriouchkina
- Molecular Genetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
| | - Hidetoshi Saze
- Plant Epigenetics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawa904‐0495Japan
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Yan T, Zhou Z, Wang R, Bao D, Li S, Li A, Yu R, Wuriyanghan H. A cluster of atypical resistance genes in soybean confers broad-spectrum antiviral activity. PLANT PHYSIOLOGY 2022; 188:1277-1293. [PMID: 34730802 PMCID: PMC8825445 DOI: 10.1093/plphys/kiab507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/02/2021] [Indexed: 06/12/2023]
Abstract
Soybean mosaic virus (SMV) is a severe soybean (Glycine max) pathogen. Here we characterize a soybean SMV resistance cluster (SRC) that comprises five resistance (R) genes. SRC1 encodes a Toll/interleukin-1 receptor and nucleotide-binding site (TIR-NBS [TN]) protein, SRC4 and SRC6 encode TIR proteins with a short EF-hand domain, while SRC7 and SRC8 encode TNX proteins with a noncanonical basic secretory protein (BSP) domain at their C-termini. We mainly studied SRC7, which contains a noncanonical BSP domain and gave full resistance to SMV. SRC7 possessed broad-spectrum antiviral activity toward several plant viruses including SMV, plum pox virus, potato virus Y, and tobacco mosaic virus. The TIR domain alone was both necessary and sufficient for SRC7 immune signaling, while the NBS domain enhanced its activity. Nuclear oligomerization via the interactions of both TIR and NBS domains was essential for SRC7 function. SRC7 expression was transcriptionally inducible by SMV infection and salicylic acid (SA) treatment, and SA was required for SRC7 triggered virus resistance. SRC7 expression was posttranscriptionally regulated by miR1510a and miR2109, and the SRC7-miR1510a/miR2109 regulatory network appeared to contribute to SMV-soybean interactions in both resistant and susceptible soybean cultivars. In summary, we report a soybean R gene cluster centered by SRC7 that is regulated at both transcriptional and posttranscriptional levels, possesses a yet uncharacterized BSP domain, and has broad-spectrum antiviral activities. The SRC cluster is special as it harbors several functional R genes encoding atypical TIR-NBS-LRR (TNL) type R proteins, highlighting its importance in SMV-soybean interaction and plant immunity.
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Affiliation(s)
- Ting Yan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Zikai Zhou
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ru Wang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Duran Bao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Shanshan Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Aoga Li
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
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Huang CY, Jin H. Coordinated Epigenetic Regulation in Plants: A Potent Managerial Tool to Conquer Biotic Stress. FRONTIERS IN PLANT SCIENCE 2022; 12:795274. [PMID: 35046981 PMCID: PMC8762163 DOI: 10.3389/fpls.2021.795274] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Plants have evolved variable phenotypic plasticity to counteract different pathogens and pests during immobile life. Microbial infection invokes multiple layers of host immune responses, and plant gene expression is swiftly and precisely reprogramed at both the transcriptional level and post-transcriptional level. Recently, the importance of epigenetic regulation in response to biotic stresses has been recognized. Changes in DNA methylation, histone modification, and chromatin structures have been observed after microbial infection. In addition, epigenetic modifications may be preserved as transgenerational memories to allow the progeny to better adapt to similar environments. Epigenetic regulation involves various regulatory components, including non-coding small RNAs, DNA methylation, histone modification, and chromatin remodelers. The crosstalk between these components allows precise fine-tuning of gene expression, giving plants the capability to fight infections and tolerant drastic environmental changes in nature. Fully unraveling epigenetic regulatory mechanisms could aid in the development of more efficient and eco-friendly strategies for crop protection in agricultural systems. In this review, we discuss the recent advances on the roles of epigenetic regulation in plant biotic stress responses.
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Affiliation(s)
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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Identification of the Capsicum baccatum NLR Protein CbAR9 Conferring Disease Resistance to Anthracnose. Int J Mol Sci 2021; 22:ijms222212612. [PMID: 34830493 PMCID: PMC8620258 DOI: 10.3390/ijms222212612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022] Open
Abstract
Anthracnose is caused by Colletotrichum species and is one of the most virulent fungal diseases affecting chili pepper (Capsicum) yield globally. However, the noble genes conferring resistance to Colletotrichum species remain largely elusive. In this study, we identified CbAR9 as the causal locus underlying the large effect quantitative trait locus CcR9 from the anthracnose-resistant chili pepper variety PBC80. CbAR9 encodes a nucleotide-binding and leucine-rich repeat (NLR) protein related to defense-associated NLRs in several other plant species. CbAR9 transcript levels were induced dramatically after Colletotrichum capsici infection. To explore the biological function, we generated transgenic Nicotiana benthamiana lines overexpressing CbAR9, which showed enhanced resistance to C. capsici relative to wild-type plants. Transcript levels of pathogenesis-related (PR) genes increased markedly in CbAR9-overexpressing N. benthamiana plants. Moreover, resistance to anthracnose and transcript levels of PR1 and PR2 were markedly reduced in CbAR9-silenced chili pepper fruits after C. capsici infection. Our results revealed that CbAR9 contributes to innate immunity against C. capsici.
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Wang W, Chen L, Fengler K, Bolar J, Llaca V, Wang X, Clark CB, Fleury TJ, Myrvold J, Oneal D, van Dyk MM, Hudson A, Munkvold J, Baumgarten A, Thompson J, Cai G, Crasta O, Aggarwal R, Ma J. A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean. Nat Commun 2021; 12:6263. [PMID: 34741017 PMCID: PMC8571336 DOI: 10.1038/s41467-021-26554-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Phytophthora root and stem rot caused by P. sojae is a destructive soybean soil-borne disease found worldwide. Discovery of genes conferring broad-spectrum resistance to the pathogen is a need to prevent the outbreak of the disease. Here, we show that soybean Rps11 is a 27.7-kb nucleotide-binding site-leucine-rich repeat (NBS-LRR or NLR) gene conferring broad-spectrum resistance to the pathogen. Rps11 is located in a genomic region harboring a cluster of large NLR genes of a single origin in soybean, and is derived from rounds of unequal recombination. Such events result in promoter fusion and LRR expansion that may contribute to the broad resistance spectrum. The NLR gene cluster exhibits drastic structural diversification among phylogenetically representative varieties, including gene copy number variation ranging from five to 23 copies, and absence of allelic copies of Rps11 in any of the non-Rps11-donor varieties examined, exemplifying innovative evolution of NLR genes and NLR gene clusters.
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Affiliation(s)
- Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Kevin Fengler
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Joy Bolar
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Victor Llaca
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Tomara J Fleury
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Crop Production and Pest Control Research Unit, USDA, ARS, West Lafayette, IN, 47907, USA
| | - Jon Myrvold
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - David Oneal
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | | | - Ashley Hudson
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Jesse Munkvold
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Andy Baumgarten
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Jeff Thompson
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
| | - Guohong Cai
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Crop Production and Pest Control Research Unit, USDA, ARS, West Lafayette, IN, 47907, USA
| | - Oswald Crasta
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA
- R&D, Equinom, Inc., Indianapolis, IN, 46268, USA
| | - Rajat Aggarwal
- Research and Development, Corteva Agriscience™, Johnston, IA, 50131, USA.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA.
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Diao P, Sun H, Bao Z, Li W, Niu N, Li W, Wuriyanghan H. Expression of an Antiviral Gene GmRUN1 from Soybean Is Regulated via Intron-Mediated Enhancement (IME). Viruses 2021; 13:2032. [PMID: 34696462 PMCID: PMC8539222 DOI: 10.3390/v13102032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/18/2022] Open
Abstract
Most of R (resistance) genes encode the protein containing NBS-LRR (nucleotide binding site and leucine-rich repeat) domains. Here, N. benthamiana plants were used for transient expression assays at 3-4 weeks of age. We identified a TNL (TIR-NBS-LRR) encoding gene GmRUN1 that was resistant to both soybean mosaic virus (SMV) and tobacco mosaic virus (TMV). Truncation analysis indicated the importance of all three canonical domains for GmRUN1-mediated antiviral activity. Promoter-GUS analysis showed that GmRUN1 expression is inducible by both salicylic acid (SA) and a transcription factor GmDREB3 via the cis-elements as-1 and ERE (ethylene response element), which are present in its promoter region. Interestingly, GmRUN1 gDNA (genomic DNA) shows higher viral resistance than its cDNA (complementary DNA), indicating the existence of intron-mediated enhancement (IME) for GmRUN1 regulation. We provided evidence that intron2 of GmRUN1 increased the mRNA level of native gene GmRUN1, a soybean antiviral gene SRC7 and also a reporter gene Luciferase, indicating the general transcriptional enhancement of intron2 in different genes. In summary, we identified an antiviral TNL type soybean gene GmRUN1, expression of which was regulated at different layers. The investigation of GmRUN1 gene regulatory network would help to explore the mechanism underlying soybean-SMV interactions.
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Affiliation(s)
- Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Hongyu Sun
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Zhuo Bao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Wenxia Li
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Niu Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
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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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Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
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Son S, Kim S, Lee KS, Oh J, Choi I, Do JW, Yoon JB, Han J, Park SR. The Capsicum baccatum-Specific Truncated NLR Protein CbCN Enhances the Innate Immunity against Colletotrichum acutatum. Int J Mol Sci 2021; 22:ijms22147672. [PMID: 34299290 PMCID: PMC8306327 DOI: 10.3390/ijms22147672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022] Open
Abstract
Chili pepper (Capsicumannuum) is an important fruit and spice used globally, but its yield is seriously threatened by anthracnose. Capsicum baccatum is particularly valuable as it carries advantageous disease resistance genes. However, most of the genes remain to be identified. In this study, we identified the C. baccatum-specific gene CbCN, which encodes a truncated nucleotide-binding and leucine-rich repeat protein in the anthracnose resistant chili pepper variety PBC80. The transcription of CbCN was greater in PBC80 than it was in the susceptible variety An-S after Colletotrichum acutatum inoculation. In order to investigate the biological function of CbCN, we generated transgenic tobacco lines constitutively expressing CbCN. Notably, CbCN-overexpressing transgenic plants exhibited enhanced resistance to C. acutatum compared to wild-type plants. Moreover, the expression of pathogenesis-related (PR) genes was remarkably increased in a CbCN-overexpressing tobacco plants. In order to confirm these results in chili pepper, we silenced the CbCN gene using the virus-induced gene silencing system. The anthracnose resistance and expressions of PR1, PR2, and NPR1 were significantly reduced in CbCN-silenced chili peppers after C. acutatum inoculations. These results indicate that CbCN enhances the innate immunity against anthracnose caused by C. acutatum by regulating defense response genes.
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Affiliation(s)
- Seungmin Son
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
| | - Soohong Kim
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
| | - Kyong Sil Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
| | - Jun Oh
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
| | - Inchan Choi
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
| | - Jae Wahng Do
- Pepper and Breeding Institute, K-Seed Valley, Gimje 54324, Korea; (J.W.D.); (J.B.Y.)
| | - Jae Bok Yoon
- Pepper and Breeding Institute, K-Seed Valley, Gimje 54324, Korea; (J.W.D.); (J.B.Y.)
| | - Jungheon Han
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.S.); (S.K.); (K.S.L.); (J.O.); (I.C.); (J.H.)
- Correspondence: ; Tel.: +82-63-238-4582
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Wetzel V, Willlems G, Darracq A, Galein Y, Liebe S, Varrelmann M. The Beta vulgaris-derived resistance gene Rz2 confers broad-spectrum resistance against soilborne sugar beet-infecting viruses from different families by recognizing triple gene block protein 1. MOLECULAR PLANT PATHOLOGY 2021; 22:829-842. [PMID: 33951264 PMCID: PMC8232027 DOI: 10.1111/mpp.13066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 05/03/2023]
Abstract
Sugar beet cultivation is dependent on an effective control of beet necrotic yellow vein virus (BNYVV, family Benyviridae), which causes tremendous economic losses in sugar production. As the virus is transmitted by a soilborne protist, the use of resistant cultivars is currently the only way to control the disease. The Rz2 gene product belongs to a family of proteins conferring resistance towards diverse pathogens in plants. These proteins contain coiled-coil and leucine-rich repeat domains. After artificial inoculation of homozygous Rz2 resistant sugar beet lines, BNYVV and beet soilborne mosaic virus (BSBMV, family Benyviridae) were not detected. Analysis of the expression of Rz2 in naturally infected plants indicated constitutive expression in the root system. In a transient assay, coexpression of Rz2 and the individual BNYVV-encoded proteins revealed that only the combination of Rz2 and triple gene block protein 1 (TGB1) resulted in a hypersensitive reaction (HR)-like response. Furthermore, HR was also triggered by the TGB1 homologues from BSBMV as well as from the more distantly related beet soilborne virus (family Virgaviridae). This is the first report of an R gene providing resistance across different plant virus families.
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38
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Schmittmann L, Franzenburg S, Pita L. Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea. Front Immunol 2021; 12:689051. [PMID: 34220847 PMCID: PMC8242945 DOI: 10.3389/fimmu.2021.689051] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
The animal immune system mediates host-microbe interactions from the host perspective. Pattern recognition receptors (PRRs) and the downstream signaling cascades they induce are a central part of animal innate immunity. These molecular immune mechanisms are still not fully understood, particularly in terms of baseline immunity vs induced specific responses regulated upon microbial signals. Early-divergent phyla like sponges (Porifera) can help to identify the evolutionarily conserved mechanisms of immune signaling. We characterized both the expressed immune gene repertoire and the induced response to lipopolysaccharides (LPS) in Halichondria panicea, a promising model for sponge symbioses. We exposed sponges under controlled experimental conditions to bacterial LPS and performed RNA-seq on samples taken 1h and 6h after exposure. H. panicea possesses a diverse array of putative PRRs. While part of those PRRs was constitutively expressed in all analyzed sponges, the majority was expressed individual-specific and regardless of LPS treatment or timepoint. The induced immune response by LPS involved differential regulation of genes related to signaling and recognition, more specifically GTPases and post-translational regulation mechanisms like ubiquitination and phosphorylation. We have discovered individuality in both the immune receptor repertoire and the response to LPS, which may translate into holobiont fitness and susceptibility to stress. The three different layers of immune gene control observed in this study, - namely constitutive expression, individual-specific expression, and induced genes -, draw a complex picture of the innate immune gene regulation in H. panicea. Most likely this reflects synergistic interactions among the different components of immunity in their role to control and respond to a stable microbiome, seawater bacteria, and potential pathogens.
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Affiliation(s)
- Lara Schmittmann
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sören Franzenburg
- Research Group Genetics&Bioinformatics/Systems Immunology, Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Lucía Pita
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. THE PLANT CELL 2021; 33:814-831. [PMID: 33793812 PMCID: PMC8226294 DOI: 10.1093/plcell/koaa002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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Parker MT, Knop K, Zacharaki V, Sherwood AV, Tomé D, Yu X, Martin PGP, Beynon J, Michaels SD, Barton GJ, Simpson GG. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife 2021; 10:e65537. [PMID: 33904405 PMCID: PMC8116057 DOI: 10.7554/elife.65537] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Daniel Tomé
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Xuhong Yu
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Pascal GP Martin
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Jim Beynon
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Scott D Michaels
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | | | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- The James Hutton InstituteInvergowrieUnited Kingdom
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Sánchez-Martín J, Widrig V, Herren G, Wicker T, Zbinden H, Gronnier J, Spörri L, Praz CR, Heuberger M, Kolodziej MC, Isaksson J, Steuernagel B, Karafiátová M, Doležel J, Zipfel C, Keller B. Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins. NATURE PLANTS 2021; 7:327-341. [PMID: 33707738 PMCID: PMC7610370 DOI: 10.1038/s41477-021-00869-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/01/2021] [Indexed: 05/07/2023]
Abstract
Crop breeding for resistance to pathogens largely relies on genes encoding receptors that confer race-specific immunity. Here, we report the identification of the wheat Pm4 race-specific resistance gene to powdery mildew. Pm4 encodes a putative chimeric protein of a serine/threonine kinase and multiple C2 domains and transmembrane regions, a unique domain architecture among known resistance proteins. Pm4 undergoes constitutive alternative splicing, generating two isoforms with different protein domain topologies that are both essential for resistance function. Both isoforms interact and localize to the endoplasmatic reticulum when co-expressed. Pm4 reveals additional diversity of immune receptor architecture to be explored for breeding and suggests an endoplasmatic reticulum-based molecular mechanism of Pm4-mediated race-specific resistance.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
| | - Victoria Widrig
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Julien Gronnier
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Laurin Spörri
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Coraline R Praz
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Unité de Recherche Résistance Induite et BioProtection des Plantes, UFR Sciences Exactes et Naturelles, Université de Reims-Champagne-Ardenne, Reims, France
| | - Matthias Heuberger
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Markus C Kolodziej
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | | | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Cyril Zipfel
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Beat Keller
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
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Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
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Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
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Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
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Cambiagno DA, Torres JR, Alvarez ME. Convergent Epigenetic Mechanisms Avoid Constitutive Expression of Immune Receptor Gene Subsets. FRONTIERS IN PLANT SCIENCE 2021; 12:703667. [PMID: 34557212 PMCID: PMC8452986 DOI: 10.3389/fpls.2021.703667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 05/14/2023]
Abstract
The gene pool encoding PRR and NLR immune receptors determines the ability of a plant to resist microbial infections. Basal expression of these genes is prevented by diverse mechanisms since their hyperactivity can be harmful. To approach the study of epigenetic control of PRR/NLR genes we here analyzed their expression in mutants carrying abnormal repressive 5-methyl cytosine (5-mC) and histone 3 lysine 9 dimethylation (H3K9me2) marks, due to lack of MET1, CMT3, MOM1, SUVH4/5/6, or DDM1. At optimal growth conditions, none of the mutants showed basal expression of the defense gene marker PR1, but all of them had greater resistance to Pseudomonas syringae pv. tomato than wild type plants, suggesting they are primed to stimulate immune cascades. Consistently, analysis of available transcriptomes indicated that all mutants showed activation of particular PRR/NLR genes under some growth conditions. Under low defense activation, 37 PRR/NLR genes were expressed in these plants, but 29 of them were exclusively activated in specific mutants, indicating that MET1, CMT3, MOM1, SUVH4/5/6, and DDM1 mediate basal repression of different subsets of genes. Some epigenetic marks present at promoters, but not gene bodies, could explain the activation of these genes in the mutants. As expected, suvh4/5/6 and ddm1 activated genes carrying 5-mC and H3K9me2 marks in wild type plants. Surprisingly, all mutants expressed genes harboring promoter H2A.Z/H3K27me3 marks likely affected by the chromatin remodeler PIE1 and the histone demethylase REF6, respectively. Therefore, MET1, CMT3, MOM1, SUVH4/5/6, and DDM1, together with REF6, seemingly contribute to the establishment of chromatin states that prevent constitutive PRR/NLR gene activation, but facilitate their priming by modulating epigenetic marks at their promoters.
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Affiliation(s)
- Damián Alejandro Cambiagno
- Unidad de Estudios Agropecuarios (UDEA), INTA-CONICET, Córdoba, Argentina
- *Correspondence: Damián Alejandro Cambiagno,
| | - José Roberto Torres
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Elena Alvarez
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
- María Elena Alvarez,
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45
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Deng Y, Ning Y, Yang DL, Zhai K, Wang GL, He Z. Molecular Basis of Disease Resistance and Perspectives on Breeding Strategies for Resistance Improvement in Crops. MOLECULAR PLANT 2020; 13:1402-1419. [PMID: 32979566 DOI: 10.1016/j.molp.2020.09.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/31/2020] [Accepted: 09/19/2020] [Indexed: 05/24/2023]
Abstract
Crop diseases are major factors responsible for substantial yield losses worldwide, which affects global food security. The use of resistance (R) genes is an effective and sustainable approach to controlling crop diseases. Here, we review recent advances on R gene studies in the major crops and related wild species. Current understanding of the molecular mechanisms underlying R gene activation and signaling, and susceptibility (S) gene-mediated resistance in crops are summarized and discussed. Furthermore, we propose some new strategies for R gene discovery, how to balance resistance and yield, and how to generate crops with broad-spectrum disease resistance. With the rapid development of new genome-editing technologies and the availability of increasing crop genome sequences, the goal of breeding next-generation crops with durable resistance to pathogens is achievable, and will be a key step toward increasing crop production in a sustainable way.
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Affiliation(s)
- Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Keran Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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46
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Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet 2020; 16:e1008993. [PMID: 32925902 PMCID: PMC7529245 DOI: 10.1371/journal.pgen.1008993] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic “arms race” with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7-associated H3K9me2 is required for optimal expression of RPP7. By profiling of genome-wide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the “raw material” for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase. We previously found the Arabidopsis thaliana PHD-finger protein EDM2 to serve as a chromatin-associated factor controlling expression of the NLR-type immune receptor gene RPP7. EDM2 binds to the transposon-silencing signal H3K9me2 and affects levels of this epigenetic mark at various loci. By genome-wide profiling of transcript- and H3K9me2-levels we now found EDM2 to have a broader role in controlling NLR gene expression. In order to mitigate fitness costs caused by its promoting effects on RPP7 expression and that of several other NLR genes, EDM2 seems to suppress expression of many additional members of this gene family. This observation is in line with multiple reports demonstrating the need for balanced expression of NLRs, which can substantially reduce overall plant fitness, but need to be present at certain minimal levels to confer sufficient immune protection. Our previous results demonstrated that the influence of EDM2 on RPP7 expression was co-opted to this immune receptor gene by the insertion of an EDM2-controlled transposon. Here, we are providing additional examples for transposon-associated effects on NLR gene expression, suggesting that these mobile elements play an important role for NLR genes by equipping members of this rapidly evolving gene family with regulatory mechanisms needed for balanced expression.
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Affiliation(s)
- Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Xueqing Maggie Lu
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Songqin Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Jianqiang Wang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Wei Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne campus, United Kingdom
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Karine G. Le Roch
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
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Raxwal VK, Simpson CG, Gloggnitzer J, Entinze JC, Guo W, Zhang R, Brown JWS, Riha K. Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis. THE PLANT CELL 2020; 32:2725-2741. [PMID: 32665305 PMCID: PMC7474300 DOI: 10.1105/tpc.20.00244] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 05/19/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is an RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not yet been fully assessed, partially because NMD inactivation is lethal in many organisms. Here, we performed an in-depth comparative analysis of Arabidopsis (Arabidopsis thaliana) mutants lacking the NMD-related proteins UPF3, UPF1, and SMG7. We found different impacts of these proteins on NMD and the Arabidopsis transcriptome, with UPF1 having the biggest effect. Transcriptome assembly in UPF1-null plants revealed genome-wide changes in alternative splicing, suggesting that UPF1 functions in splicing. The inactivation of UPF1 led to translational repression, as manifested by a global shift in mRNAs from polysomes to monosomes and the downregulation of genes involved in translation and ribosome biogenesis. Despite these global changes, NMD targets and mRNAs expressed at low levels with short half-lives were enriched in the polysomes of upf1 mutants, indicating that UPF1/NMD suppresses the translation of aberrant RNAs. Particularly striking was an increase in the translation of TIR domain-containing, nucleotide binding, leucine-rich repeat (TNL) immune receptors. The regulation of TNLs via UPF1/NMD-mediated mRNA stability and translational derepression offers a dynamic mechanism for the rapid activation of TNLs in response to pathogen attack.
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Affiliation(s)
- Vivek K Raxwal
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Craig G Simpson
- Cell and Molecular Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | | | - Juan Carlos Entinze
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Cell and Molecular Sciences, James Hutton Institute, Dundee DD2 5DA, United Kingdom
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Karel Riha
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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48
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Chantarachot T, Sorenson RS, Hummel M, Ke H, Kettenburg AT, Chen D, Aiyetiwa K, Dehesh K, Eulgem T, Sieburth LE, Bailey-Serres J. DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs. NATURE PLANTS 2020; 6:675-685. [PMID: 32483330 DOI: 10.1038/s41477-020-0681-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/29/2020] [Indexed: 05/21/2023]
Abstract
Gene transcription is counterbalanced by messenger RNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA hellicases of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. They function to limit the precocious accumulation and ribosome association of stress-responsive mRNAs involved in auto-immunity and growth inhibition under non-stress conditions. Given the conservation of this RNA helicase subfamily, they may control basal levels of conditionally regulated mRNAs in diverse eukaryotes, accelerating responses without penalty.
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Affiliation(s)
- Thanin Chantarachot
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Reed S Sorenson
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Maureen Hummel
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Haiyan Ke
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Alek T Kettenburg
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Daniel Chen
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Karen Aiyetiwa
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Katayoon Dehesh
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Thomas Eulgem
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
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49
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Dunker F, Trutzenberg A, Rothenpieler JS, Kuhn S, Pröls R, Schreiber T, Tissier A, Kemen A, Kemen E, Hückelhoven R, Weiberg A. Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. eLife 2020; 9:56096. [PMID: 32441255 PMCID: PMC7297541 DOI: 10.7554/elife.56096] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
The exchange of small RNAs (sRNAs) between hosts and pathogens can lead to gene silencing in the recipient organism, a mechanism termed cross-kingdom RNAi (ck-RNAi). While fungal sRNAs promoting virulence are established, the significance of ck-RNAi in distinct plant pathogens is not clear. Here, we describe that sRNAs of the pathogen Hyaloperonospora arabidopsidis, which represents the kingdom of oomycetes and is phylogenetically distant from fungi, employ the host plant’s Argonaute (AGO)/RNA-induced silencing complex for virulence. To demonstrate H. arabidopsidis sRNA (HpasRNA) functionality in ck-RNAi, we designed a novel CRISPR endoribonuclease Csy4/GUS reporter that enabled in situ visualization of HpasRNA-induced target suppression in Arabidopsis. The significant role of HpasRNAs together with AtAGO1 in virulence was revealed in plant atago1 mutants and by transgenic Arabidopsis expressing a short-tandem-target-mimic to block HpasRNAs, that both exhibited enhanced resistance. HpasRNA-targeted plant genes contributed to host immunity, as Arabidopsis gene knockout mutants displayed quantitatively enhanced susceptibility.
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Affiliation(s)
- Florian Dunker
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Adriana Trutzenberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Jan S Rothenpieler
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Sarah Kuhn
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
| | - Reinhard Pröls
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tom Schreiber
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Ariane Kemen
- Center for Plant Molecular Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Eric Kemen
- Center for Plant Molecular Biology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany
| | - Ralph Hückelhoven
- Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Martinsried, Germany
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50
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Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis. PLoS Pathog 2020; 16:e1008401. [PMID: 32302366 PMCID: PMC7164602 DOI: 10.1371/journal.ppat.1008401] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1950 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants in the absence of PAMP treatment showed no major splicing changes. However, in contrast to MPK3 and MPK6, MPK4 was found to be a key regulator of PAMP-induced DAS events as the AS of a number of splicing factors and immunity-related protein kinases is affected, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, supporting the notion that PAMP-triggered MPK4 activation mediates regulation of alternative splicing. Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied PAMP-induced alternative splicing in Arabidopsis and identified several hundred differentially alternatively spliced (DAS) genes. Importantly, of these PAMP-induced DAS genes, only 18% overlap with the set of PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of MAPK mutants identified MPK4 as a key regulator of PAMP-induced DAS events. Although MPK4 is guarded by SUMM2 and consequently, the mpk4 dwarf and DEG phenotypes are suppressed in mpk4 summ2 mutants, MPK4-dependent DAS is not suppressed by SUMM2, showing that PAMP-triggered MPK4 activation mediates regulation of alternative splicing.
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