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Li Y, Wang Q, Jia H, Ishikawa K, Kosami KI, Ueba T, Tsujimoto A, Yamanaka M, Yabumoto Y, Miki D, Sasaki E, Fukao Y, Fujiwara M, Kaneko-Kawano T, Tan L, Kojima C, Wing RA, Sebastian A, Nishimura H, Fukada F, Niu Q, Shimizu M, Yoshida K, Terauchi R, Shimamoto K, Kawano Y. An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function. Nat Commun 2024; 15:4610. [PMID: 38816417 PMCID: PMC11139913 DOI: 10.1038/s41467-024-48943-5] [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: 04/27/2020] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
NLR family proteins act as intracellular receptors. Gene duplication amplifies the number of NLR genes, and subsequent mutations occasionally provide modifications to the second gene that benefits immunity. However, evolutionary processes after gene duplication and functional relationships between duplicated NLRs remain largely unclear. Here, we report that the rice NLR protein Pit1 is associated with its paralogue Pit2. The two are required for the resistance to rice blast fungus but have different functions: Pit1 induces cell death, while Pit2 competitively suppresses Pit1-mediated cell death. During evolution, the suppression of Pit1 by Pit2 was probably generated through positive selection on two fate-determining residues in the NB-ARC domain of Pit2, which account for functional differences between Pit1 and Pit2. Consequently, Pit2 lost its plasma membrane localization but acquired a new function to interfere with Pit1 in the cytosol. These findings illuminate the evolutionary trajectory of tandemly duplicated NLR genes after gene duplication.
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Affiliation(s)
- Yuying Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qiong Wang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- College of Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Huimin Jia
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Kazuya Ishikawa
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Ken-Ichi Kosami
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Fruit Tree Research Center, Ehime Research Institute of Agriculture, Forestry and Fisheries, Ehime, 791-0112, Japan
| | - Takahiro Ueba
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Nara, 630-0101, Japan
| | - Atsumi Tsujimoto
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Nara, 630-0101, Japan
| | - Miki Yamanaka
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Nara, 630-0101, Japan
| | - Yasuyuki Yabumoto
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Nara, 630-0101, Japan
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Eriko Sasaki
- Faculty of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Yoichiro Fukao
- Department of Bioinformatics, Ritsumeikan University, Shiga, 525-8577, Japan
| | | | - Takako Kaneko-Kawano
- College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Li Tan
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Chojiro Kojima
- Graduate School of Engineering Science, Yokohama National University, Yokohama, Kanagawa, 240-8501, Japan
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Alfino Sebastian
- Institute of Plant Science and Resources, Okayama University, Okayama, 710-0046, Japan
| | - Hideki Nishimura
- Institute of Plant Science and Resources, Okayama University, Okayama, 710-0046, Japan
| | - Fumi Fukada
- Institute of Plant Science and Resources, Okayama University, Okayama, 710-0046, Japan
| | - Qingfeng Niu
- Advanced Academy, Anhui Agricultural University, Research Centre for Biological Breeding Technology, Hefei, Anhui, 230036, China
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Iwate, 024-0003, Japan
| | - Kentaro Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, 617-0001, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Iwate, 024-0003, Japan
- Graduate School of Agriculture, Kyoto University, Kyoto, 617-0001, Japan
| | - Ko Shimamoto
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Nara, 630-0101, Japan
| | - Yoji Kawano
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
- Institute of Plant Science and Resources, Okayama University, Okayama, 710-0046, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan.
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Bernasconi Z, Stirnemann U, Heuberger M, Sotiropoulos AG, Graf J, Wicker T, Keller B, Sánchez-Martín J. Mutagenesis of Wheat Powdery Mildew Reveals a Single Gene Controlling Both NLR and Tandem Kinase-Mediated Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:264-276. [PMID: 37934013 DOI: 10.1094/mpmi-09-23-0136-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal wheat pathogen. Some wheat genotypes contain powdery mildew resistance (Pm) genes encoding immune receptors that recognize specific fungal-secreted effector proteins, defined as avirulence (Avr) factors. Identifying Avr factors is vital for understanding the mechanisms, functioning, and durability of wheat resistance. Here, we present AvrXpose, an approach to identify Avr genes in Bgt by generating gain-of-virulence mutants on Pm genes. We first identified six Bgt mutants with gain of virulence on Pm3b and Pm3c. They all had point mutations, deletions or insertions of transposable elements within the corresponding AvrPm3b2/c2 gene or its promoter region. We further selected six mutants on Pm3a, aiming to identify the yet unknown AvrPm3a3 recognized by Pm3a, in addition to the previously described AvrPm3a2/f2. Surprisingly, Pm3a virulence in the obtained mutants was always accompanied by an additional gain of virulence on the unrelated tandem kinase resistance gene WTK4. No virulence toward 11 additional R genes tested was observed, indicating that the gain of virulence was specific for Pm3a and WTK4. Several independently obtained Pm3a-WTK4 mutants have mutations in Bgt-646, a gene encoding a putative, nonsecreted ankyrin repeat-containing protein. Gene expression analysis suggests that Bgt-646 regulates a subset of effector genes. We conclude that Bgt-646 is a common factor required for avirulence on both a specific nucleotide-binding leucine-rich repeat and a WTK immune receptor. Our findings suggest that, beyond effectors, another type of pathogen protein can control the race-specific interaction between powdery mildew and wheat. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zoe Bernasconi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Ursin Stirnemann
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alexandros G Sotiropoulos
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Centre for Crop Health, University of Southern Queensland, Darling Heights, Queensland, Australia
| | - Johannes Graf
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Microbiology and Genetics, Spanish-Portuguese Agricultural Research Centre (CIALE), University of Salamanca, Salamanca, Spain
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3
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Sirangelo TM. NLR- and mlo-Based Resistance Mechanisms against Powdery Mildew in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2023; 13:105. [PMID: 38202413 PMCID: PMC10780410 DOI: 10.3390/plants13010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Powdery mildew (PM) is one of the most common Cannabis sativa diseases. In spite of this, very few documented studies have characterized the resistance genes involved in PM defense mechanisms, or sources of natural genetic resistance in cannabis. The focus of the present work is on the two primary mechanisms for qualitative resistance against PM. The first is based on resistance (R) genes characterized by conserved nucleotide-binding site and/or leucine-rich repeat domains (NLRs). The second one involves susceptibility (S) genes, and particularly mildew resistance locus o (MLO) genes, whose loss-of-function mutations seem to be a reliable way to protect plants from PM infection. Cannabis defenses against PM are thus discussed, mainly detailing the strategies based on these two mechanisms. Emerging studies about this research topic are also reported and, based on the most significant results, a potential PM resistance model in cannabis plant-pathogen interactions is proposed. Finally, innovative approaches, based on the pyramiding of multiple R genes, as well as on genetic engineering and genome editing methods knocking out S genes, are discussed, to obtain durable PM-resistant cannabis cultivars with a broad-spectrum resistance range.
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Affiliation(s)
- Tiziana M Sirangelo
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development-Division Biotechnologies and Agroindustry, 00123 Rome, Italy
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4
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Huang Z, Liu J, Lu X, Guo Y, Li Y, Liu Y, Zhang R, Xing L, Cao A. Identification and transfer of a new Pm21 haplotype with high genetic diversity and a special molecular resistance mechanism. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:10. [PMID: 36658294 PMCID: PMC9852157 DOI: 10.1007/s00122-023-04251-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
A new functional Pm21 haplotype, Pm21(8#), was cloned from the new wheat-H. villosa translocation line T6VS(8#)·6DL, which confers the same strong resistance to powdery mildew through a different resistance mechanism. Broad-spectrum disease resistance genes are desirable in crop breeding for conferring stable, durable resistance in field production. Pm21(4#) is a gene introduced from wild Haynaldia villosa into wheat that confers broad-spectrum resistance to wheat powdery mildew and has been widely used in wheat production for approximately 30 years. The discovery and transfer of new functional haplotypes of Pm21 into wheat will expand its genetic diversity in production and avoid the breakdown of resistance conferred by a single gene on a large scale. Pm21(4#) previously found from T6VS(4#)·6AL has been cloned. In this study, a new wheat-H. villosa translocation, T6VS(8#)·6DL, was identified. A new functional Pm21 haplotype, designated Pm21(8#), was cloned and characterized. The genomic structures and the splicing patterns of Pm21(4#) and Pm21(8#) were different, and widespread sequence diversity was observed in the gene coding region and the promoter region. In the field, Pm21(8#) conferred resistance to Blumeria graminis f. sp. tritici (Bgt), similar to Pm21(4#), indicating that Pm21(8#) was also a resistance gene. However, Bgt development during the infection stage was obviously different between Pm21(4#)- and Pm21(8#)-containing materials under the microscopic observation. Pm21(4#) inhibited the formation of haustoria and the development of hyphae in the initial infection stage, while Pm21(8#) limited the growth of hyphae and inhibited the formation of conidiophores in the late infection stage. Therefore, Pm21(8#) is a new functional Pm21 haplotype that provides a new gene resource for wheat breeding.
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Affiliation(s)
- Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315000 China
| | - Xiangqian Lu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yifei Guo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yueying Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yangqi Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
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5
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Ma L, Yu Y, Li C, Wang P, Liu K, Ma W, Wang W, Fan Y, Xiong Z, Jiang T, Zhang J, Wang Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene Pb3 Encoding NLR Protein. Int J Mol Sci 2022; 23:ijms232214032. [PMID: 36430507 PMCID: PMC9698523 DOI: 10.3390/ijms232214032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rice blast is a worldwide fungal disease that seriously affects the yield and quality of rice. Identification of resistance genes against rice blast disease is one of the effective ways to control this disease. However, panicle blast resistance genes, which are useful in the fields, have rarely been studied due to the difficulty in phenotypic identification and the environmental influences. Here, panicle blast resistance-3 (Pb3) was identified by a genome-wide association study (GWAS) based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel I (RDP-I) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A total of 16 panicle blast resistance loci (PBRLs) within three years including one repeated locus PBRL3 located in chromosome 11 were identified. In addition, 7 genes in PBRL3 were identified as candidate genes by haplotype analysis, which showed significant differences between resistant and susceptible varieties. Among them, one nucleotide-binding domain and Leucine-rich Repeat (NLR) gene Pb3 was highly conserved in multiple resistant rice cultivars, and its expression was significantly induced after rice blast inoculation. Evolutionary analysis showed that Pb3 was a typical disease resistance gene containing coiled-coil, NB-ARC, and LRR domains. T-DNA insertion mutants and CRISPR lines of Pb3 showed significantly reduced panicle blast resistance. These results indicate that Pb3 is a panicle blast resistance gene and GWAS is a rapid method for identifying panicle blast resistance in rice.
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Affiliation(s)
- Lu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changqing Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Panting Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kunquan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunxin Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziwei Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingran Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhixue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Cesari S, Xi Y, Declerck N, Chalvon V, Mammri L, Pugnière M, Henriquet C, de Guillen K, Chochois V, Padilla A, Kroj T. New recognition specificity in a plant immune receptor by molecular engineering of its integrated domain. Nat Commun 2022; 13:1524. [PMID: 35314704 PMCID: PMC8938504 DOI: 10.1038/s41467-022-29196-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPlant nucleotide-binding and leucine-rich repeat domain proteins (NLRs) are immune sensors that recognize pathogen effectors. Here, we show that molecular engineering of the integrated decoy domain (ID) of an NLR can extend its recognition spectrum to a new effector. We relied for this on detailed knowledge on the recognition of the Magnaporthe oryzae effectors AVR-PikD, AVR-Pia, and AVR1-CO39 by, respectively, the rice NLRs Pikp-1 and RGA5. Both receptors detect their effectors through physical binding to their HMA (Heavy Metal-Associated) IDs. By introducing into RGA5_HMA the AVR-PikD binding residues of Pikp-1_HMA, we create a high-affinity binding surface for this effector. RGA5 variants carrying this engineered binding surface perceive the new ligand, AVR-PikD, and still recognize AVR-Pia and AVR1-CO39 in the model plant N. benthamiana. However, they do not confer extended disease resistance specificity against M. oryzae in transgenic rice plants. Altogether, our study provides a proof of concept for the design of new effector recognition specificities in NLRs through molecular engineering of IDs.
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Duxbury Z, Wu CH, Ding P. A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:155-184. [PMID: 33689400 DOI: 10.1146/annurev-arplant-080620-104948] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection.
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Affiliation(s)
- Zane Duxbury
- Jealott's Hill International Research Centre, Syngenta, Bracknell RG42 6EY, United Kingdom;
| | - Chih-Hang Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- Current affiliation: Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands;
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8
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Manser B, Koller T, Praz CR, Roulin AC, Zbinden H, Arora S, Steuernagel B, Wulff BBH, Keller B, Sánchez-Martín J. Identification of specificity-defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:993-1007. [PMID: 33629439 DOI: 10.1111/tpj.15214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 05/23/2023]
Abstract
Plant nucleotide-binding leucine-rich repeat receptors (NLRs) act as intracellular sensors for pathogen-derived effector proteins and trigger an immune response, frequently resulting in the hypersensitive cell death response (HR) of the infected host cell. The wheat (Triticum aestivum) NLR Pm2 confers resistance against the fungal pathogen Blumeria graminis f. sp. tritici (Bgt) if the isolate contains the specific RNase-like effector AvrPm2. We identified and isolated seven new Pm2 alleles (Pm2e-i) in the wheat D-genome ancestor Aegilops tauschii and two new natural AvrPm2 haplotypes from Bgt. Upon transient co-expression in Nicotiana benthamiana, we observed a variant-specific HR of the Pm2 variants Pm2a and Pm2i towards AvrPm2 or its homolog from the AvrPm2 effector family, BgtE-5843, respectively. Through the introduction of naturally occurring non-synonymous single nucleotide polymorphisms and structure-guided mutations, we identified single amino acids in both the wheat NLR Pm2 and the fungal effector proteins AvrPm2 and BgtE-5843 responsible for the variant-specific HR of the Pm2 variants. Exchanging these amino acids led to a modified HR of the Pm2-AvrPm2 interaction and allowed the identification of the effector head epitope, a 20-amino-acid long unit of AvrPm2 involved in the HR. Swapping of the AvrPm2 head epitope to the non-HR-triggering AvrPm2 family member BgtE-5846 led to gain of a HR by Pm2a. Our study presents a molecular approach to identify crucial effector surface structures involved in the HR and demonstrates that natural and induced diversity in an immune receptor and its corresponding effectors can provide the basis for understanding and modifying NLR-effector specificity.
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Affiliation(s)
- Beatrice Manser
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Teresa Koller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland
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Santos SA, Vidigal PMP, Guimarães LMS, Mafia RG, Templeton MD, Alfenas AC. Transcriptome analysis of Eucalyptus grandis genotypes reveals constitutive overexpression of genes related to rust (Austropuccinia psidii) resistance. PLANT MOLECULAR BIOLOGY 2020; 104:339-357. [PMID: 32638297 DOI: 10.1007/s11103-020-01030-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/29/2020] [Indexed: 05/02/2023]
Abstract
Key Message A resistant E. grandis genotype showed a constitutive overexpression of genes related to resistance to myrtle rust caused by A. psidii. Abstract Myrtle rust caused by Austropuccinia psidii is considered one of the most important fungal diseases affecting Eucalyptus spp. plantations in Brazil. Although the selection and planting of resistant eucalypt genotypes have been the major strategies to manage the disease in Brazil, the molecular mechanisms involved in resistance are still unclear. In this study, we evaluated the gene expression profile of two contrasting Eucalyptus grandis genotypes in resistance level to rust by RNA-Seq. The two genotypes showed a very different background gene expression level even without A. psidii infection. The resistant genotype had a constitutive overexpression of a large number of protein-coding genes compared to the susceptible genotype. These genes were mainly associated with signal transduction, photosynthesis, regulation and response to salicylic acid (SA), and protein kinase leucine-rich receptors (PK-LRR). PK-LRR and SA mediated disease resistance are well known to be effective against obligate biotroph pathogens, such as A. psidii. In addition, at 24 h after infection, the susceptible genotype was able to activate some response, however, several resistance-related proteins had their expression level reduced with A. psidii infection. Here, we present the first analysis of E. grandis genotypes transcriptomes infected by A. psidii and it reveals a constitutive overexpression of several resistance-related genes in the resistant genotype compared to the susceptible one. Our findings have the potential to be used as candidate molecular markers for resistance to myrtle rust.
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Affiliation(s)
- Samuel A Santos
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
- The New Zealand Institute for Plant and Food Research Limited, Auckland, 1142, New Zealand
| | - Pedro M P Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Centro de Ciências Biológicas, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lúcio M S Guimarães
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | | | - Matthew D Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, 1142, New Zealand
| | - Acelino C Alfenas
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
- Department of Plant Pathology, Instituto de Biotecnologia Aplicada à agropecuária-BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs s/n, Campus Universitário, Viçosa, MG, 36570-900, Brazil.
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10
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Identification and Analysis of NBS-LRR Genes in Actinidia chinensis Genome. PLANTS 2020; 9:plants9101350. [PMID: 33065969 PMCID: PMC7601643 DOI: 10.3390/plants9101350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 11/17/2022]
Abstract
Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes represent the most important disease resistance genes in plants. The genome sequence of kiwifruit (Actinidia chinensis) provides resources for the characterization of NBS-LRR genes and identification of new R-genes in kiwifruit. In the present study, we identified 100 NBS-LRR genes in the kiwifruit genome and they were grouped into six distinct classes based on their domain architecture. Of the 100 genes, 79 are truncated non-regular NBS-LRR genes. Except for 37 NBS-LRR genes with no location information, the remaining 63 genes are distributed unevenly across 18 kiwifruit chromosomes and 38.01% of them are present in clusters. Seventeen families of cis-acting elements were identified in the promoters of the NBS-LRR genes, including AP2, NAC, ERF and MYB. Pseudomonas syringae pv. actinidiae (pathogen of the kiwifruit bacterial canker) infection induced differential expressions of 16 detected NBS-LRR genes and three of them are involved in plant immunity responses. Our study provides insight of the NBS-LRR genes in kiwifruit and a resource for the identification of new R-genes in the fruit.
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11
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Schenke D, Cai D. Applications of CRISPR/Cas to Improve Crop Disease Resistance: Beyond Inactivation of Susceptibility Factors. iScience 2020; 23:101478. [PMID: 32891884 PMCID: PMC7479627 DOI: 10.1016/j.isci.2020.101478] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Current crop production systems are prone to increasing pathogen pressure. Fundamental understanding of molecular plant-pathogen interactions, the availability of crop and pathogen genomic information, as well as emerging genome editing permits a novel approach for breeding of crop disease resistance. We describe here strategies to identify new targets for resistance breeding with focus on interruption of the compatible plant-pathogen interaction by CRISPR/Cas-mediated genome editing. Basically, crop genome editing can be applied in several ways to achieve this goal. The most common approach focuses on the "simple" knockout by non-homologous end joining repair of plant susceptibility factors required for efficient host colonization. However, genome re-writing via homology-directed repair or base editing can also prevent host manipulation by changing the targets of pathogen-derived effectors or molecules beyond recognition, which also decreases plant susceptibility. We conclude that genome editing by CRISPR/Cas will become increasingly indispensable to generate in relatively short time beneficial resistance traits in crops to meet upcoming challenges.
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Affiliation(s)
- Dirk Schenke
- Institute of Phytopathology, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, 24118 Kiel, Germany
| | - Daguang Cai
- Institute of Phytopathology, Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, Hermann Rodewald Str. 9, 24118 Kiel, Germany
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12
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Lindner S, Keller B, Singh SP, Hasenkamp Z, Jung E, Müller MC, Bourras S, Keller B. Single residues in the LRR domain of the wheat PM3A immune receptor can control the strength and the spectrum of the immune response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:200-214. [PMID: 32645755 DOI: 10.1111/tpj.14917] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/13/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
The development of improved plant nucleotide-binding, leucine-rich repeat (LRR) immune receptors (NLRs) has mostly been based on random mutagenesis or on structural information available for specific receptors complexed with the recognized pathogen effector. Here, we use a targeted mutagenesis approach based on the natural diversity of the Pm3 powdery mildew resistance alleles present in different wheat (Triticum aestivum) genotypes. In order to understand the functional importance of the amino acid polymorphisms between the active immune receptor PM3A and the inactive ancestral variant PM3CS, we exchanged polymorphic regions and residues in the LRR domain of PM3A with the corresponding segments of PM3CS. These novel variants were functionally tested for recognition of the corresponding AVRPM3A2/F2 avirulence protein in Nicotiana benthamiana. We identified polymorphic residues in four regions of PM3A that enhance the immune response, but also residues that reduce it or result in complete loss of function. We found that the identified critical residues in PM3A modify its activation threshold towards different protein variants of AVRPM3A2/F2 . PM3A variants with a lowered threshold gave a stronger overall response and gained an extended recognition spectrum. One of these variant proteins with a single amino acid change was stably transformed into wheat, where it conferred race-specific resistance to mildew. This is a proof of concept that improved PM3A variants with an enlarged recognition spectrum can be engineered based on natural diversity by exchanging single or multiple residues that modulate resistance function.
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Affiliation(s)
- Stefan Lindner
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Bettina Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Simrat P Singh
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Zsuzsanna Hasenkamp
- Institute of Pharmacology and Toxicology, University of Zurich, Zürich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Marion C Müller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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13
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Gao A, Hu M, Gong Y, Dong R, Jiang Y, Zhu S, Ji J, Zhang D, Li S, He H. Pm21 CC domain activity modulated by intramolecular interactions is implicated in cell death and disease resistance. MOLECULAR PLANT PATHOLOGY 2020; 21:975-984. [PMID: 32421925 PMCID: PMC7279971 DOI: 10.1111/mpp.12943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 05/14/2023]
Abstract
Nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs) provide resistance against several plant pathogens. We previously cloned the wheat powdery mildew resistance gene Pm21, which encodes a coiled-coil (CC) NLR that confers broad-spectrum resistance against Blumeria graminis f. sp. tritici. Here, we report comprehensive biochemical and functional analyses of Pm21 CC domain in Nicotiana benthamiana. Transient overexpression assay suggested that only the extended CC (eCC, amino acid residues 1-159) domain has cell-death-inducing activity, whereas the CC-containing truncations, including CC-NB and CC-NB-LRR, do not induce cell-death responses. Coimmunoprecipitation (Co-IP) assay showed that the eCC domain self-associates and interacts with the NB and LRR domains in planta. These results imply that the activity of the eCC domain is inhibited by the intramolecular interactions of different domains in the absence of pathogens. We found that the LRR domain plays a crucial role in D491V-mediated full-length (FL) Pm21 autoactivation. Some mutations in the CC domain leading to the loss of Pm21 resistance to powdery mildew impaired the CC activity of cell-death induction. Two mutations (R73Q and E80K) interfered with D491V-mediated Pm21 autoactivation without affecting the cell-death-inducing activity of the eCC domain. Notably, some susceptible mutants harbouring mutations in the CC domain still exhibited cell-death-inducing activity. Taken together, these results implicate the CC domain of Pm21 in cell-death signalling and disease-resistance signalling, which are potentially independent of each other.
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Affiliation(s)
- Anli Gao
- School of Life SciencesHenan UniversityKaifengChina
| | - Minjie Hu
- School of Life SciencesHenan UniversityKaifengChina
| | - Yifei Gong
- School of Life SciencesHenan UniversityKaifengChina
| | | | - Yuan Jiang
- School of Life SciencesHenan UniversityKaifengChina
| | - Shanying Zhu
- School of Food and Biological EngineeringJiangsu UniversityZhenjiangChina
| | - Jian Ji
- School of Food and Biological EngineeringJiangsu UniversityZhenjiangChina
| | - Dale Zhang
- School of Life SciencesHenan UniversityKaifengChina
| | - Suoping Li
- School of Life SciencesHenan UniversityKaifengChina
| | - Huagang He
- School of Food and Biological EngineeringJiangsu UniversityZhenjiangChina
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14
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Li W, Deng Y, Ning Y, He Z, Wang GL. Exploiting Broad-Spectrum Disease Resistance in Crops: From Molecular Dissection to Breeding. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:575-603. [PMID: 32197052 DOI: 10.1146/annurev-arplant-010720-022215] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant diseases reduce crop yields and threaten global food security, making the selection of disease-resistant cultivars a major goal of crop breeding. Broad-spectrum resistance (BSR) is a desirable trait because it confers resistance against more than one pathogen species or against the majority of races or strains of the same pathogen. Many BSR genes have been cloned in plants and have been found to encode pattern recognition receptors, nucleotide-binding and leucine-rich repeat receptors, and defense-signaling and pathogenesis-related proteins. In addition, the BSR genes that underlie quantitative trait loci, loss of susceptibility and nonhost resistance have been characterized. Here, we comprehensively review the advances made in the identification and characterization of BSR genes in various species and examine their application in crop breeding. We also discuss the challenges and their solutions for the use of BSR genes in the breeding of disease-resistant crops.
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Affiliation(s)
- Wei Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and 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
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio 43210, USA;
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15
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Schaefer LK, Parlange F, Buchmann G, Jung E, Wehrli A, Herren G, Müller MC, Stehlin J, Schmid R, Wicker T, Keller B, Bourras S. Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:253. [PMID: 32211008 PMCID: PMC7076181 DOI: 10.3389/fpls.2020.00253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Cross-kingdom RNA interference (RNAi) is a biological process allowing plants to transfer small regulatory RNAs to invading pathogens to trigger the silencing of target virulence genes. Transient assays in cereal powdery mildews suggest that silencing of one or two effectors could lead to near loss of virulence, but evidence from stable RNAi lines is lacking. We established transient host-induced gene silencing (HIGS) in wheat, and demonstrate that targeting an essential housekeeping gene in the wheat powdery mildew pathogen (Blumeria graminis f. sp. tritici) results in significant reduction of virulence at an early stage of infection. We generated stable transgenic RNAi wheat lines encoding a HIGS construct simultaneously silencing three B.g. tritici effectors including SvrPm3 a1/f1 , a virulence factor involved in the suppression of the Pm3 powdery mildew resistance gene. We show that all targeted effectors are effectively downregulated by HIGS, resulting in reduced fungal virulence on adult wheat plants. Our findings demonstrate that stable HIGS of effector genes can lead to quantitative gain of resistance without major pleiotropic effects in wheat.
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Affiliation(s)
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriele Buchmann
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Andreas Wehrli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jonas Stehlin
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Roman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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16
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Helm M, Qi M, Sarkar S, Yu H, Whitham SA, Innes RW. Engineering a Decoy Substrate in Soybean to Enable Recognition of the Soybean Mosaic Virus NIa Protease. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:760-769. [PMID: 30676230 DOI: 10.1094/mpmi-12-18-0324-r] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Arabidopsis, recognition of the AvrPphB effector protease from Pseudomonas syringae is mediated by the disease resistance (R) protein RPS5, which is activated by AvrPphB-induced cleavage of the Arabidopsis protein kinase PBS1. The recognition specificity of RPS5 can be altered by substituting the AvrPphB cleavage site within PBS1 with cleavage sequences for other proteases, including proteases from viruses. AvrPphB also activates defense responses in soybean (Glycine max), suggesting that soybean may contain an R protein analogous to RPS5. It was unknown, however, whether this response is mediated by cleavage of a soybean PBS1-like protein. Here, we show that soybean contains three PBS1 orthologs and that their products are cleaved by AvrPphB. Further, transient expression of soybean PBS1 derivatives containing a five-alanine insertion at their AvrPphB cleavage sites activated cell death in soybean protoplasts, demonstrating that soybean likely contains an AvrPphB-specific resistance protein that is activated by a conformational change in soybean PBS1 proteins. Significantly, we show that a soybean PBS1 decoy protein modified to contain a cleavage site for the soybean mosaic virus (SMV) NIa protease triggers cell death in soybean protoplasts when cleaved by this protease, indicating that the PBS1 decoy approach will work in soybean, using endogenous PBS1 genes. Lastly, we show that activation of the AvrPphB-dependent cell death response effectively inhibits systemic spread of SMV in soybean. These data also indicate that decoy engineering may be feasible in other crop plant species that recognize AvrPphB protease activity.
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Affiliation(s)
- Matthew Helm
- 1 Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
| | - Mingsheng Qi
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Shayan Sarkar
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Haiyue Yu
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Steven A Whitham
- 2 Department of Pant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Roger W Innes
- 1 Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
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17
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Carter ME, Helm M, Chapman AVE, Wan E, Restrepo Sierra AM, Innes RW, Bogdanove AJ, Wise RP. Convergent Evolution of Effector Protease Recognition by Arabidopsis and Barley. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:550-565. [PMID: 30480480 DOI: 10.1094/mpmi-07-18-0202-fi] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Pseudomonas syringae cysteine protease AvrPphB activates the Arabidopsis resistance protein RPS5 by cleaving a second host protein, PBS1. AvrPphB induces defense responses in other plant species, but the genes and mechanisms mediating AvrPphB recognition in those species have not been defined. Here, we show that AvrPphB induces defense responses in diverse barley cultivars. We also show that barley contains two PBS1 orthologs, that their products are cleaved by AvrPphB, and that the barley AvrPphB response maps to a single locus containing a nucleotide-binding leucine-rich repeat (NLR) gene, which we termed AvrPphB Response 1 (Pbr1). Transient coexpression of PBR1 with wild-type AvrPphB but not with a protease inactive mutant triggered defense responses, indicating that PBR1 detects AvrPphB protease activity. Additionally, PBR1 coimmunoprecipitated with barley and Nicotiana benthamiana PBS1 proteins, suggesting mechanistic similarity to detection by RPS5. Lastly, we determined that wheat cultivars also recognize AvrPphB protease activity and contain two putative Pbr1 orthologs. Phylogenetic analyses showed, however, that Pbr1 is not orthologous to RPS5. Our results indicate that the ability to recognize AvrPphB evolved convergently and imply that selection to guard PBS1-like proteins occurs across species. Also, these results suggest that PBS1-based decoys may be used to engineer protease effector recognition-based resistance in barley and wheat.
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Affiliation(s)
- Morgan E Carter
- 1 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Matthew Helm
- 2 Department of Biology, Indiana University, Bloomington, IN, U.S.A
| | - Antony V E Chapman
- 3 Interdepartmental Genetics & Genomics Graduate Program and
- 4 Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA, U.S.A
| | - Emily Wan
- 1 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Ana Maria Restrepo Sierra
- 1 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
- 5 Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Medellín, Colombia; and
| | - Roger W Innes
- 2 Department of Biology, Indiana University, Bloomington, IN, U.S.A
| | - Adam J Bogdanove
- 1 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Roger P Wise
- 3 Interdepartmental Genetics & Genomics Graduate Program and
- 4 Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA, U.S.A
- 6 Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA, U.S.A
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18
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Yin K, Qiu JL. Genome editing for plant disease resistance: applications and perspectives. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180322. [PMID: 30967029 PMCID: PMC6367152 DOI: 10.1098/rstb.2018.0322] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant disease resistance is essential for sustainable agriculture. Genome editing has been revolutionizing plant biology and biotechnology by enabling precise, targeted genome modifications. Editing provides new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. Here, we first summarize the challenges for breeding resistant crops. Next, we focus on applications of genome editing technology in generating plants with resistance to bacterial, fungal and viral diseases. Finally, we discuss the potential of genome editing for breeding crops that present novel disease resistance in the future. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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19
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Sánchez-Martín J, Keller B. Contribution of recent technological advances to future resistance breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:713-732. [PMID: 30756126 DOI: 10.1007/s00122-019-03297-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/02/2019] [Indexed: 05/23/2023]
Abstract
The development of durable host resistance strategies to control crop diseases is a primary need for sustainable agricultural production in the future. This article highlights the potential of recent progress in the understanding of host resistance for future cereal breeding. Much of the novel work is based on advancements in large-scale sequencing and genomics, rapid gene isolation techniques and high-throughput molecular marker technologies. Moreover, emerging applications on the pathogen side like effector identification or field pathogenomics are discussed. The combination of knowledge from both sides of cereal pathosystems will result in new approaches for resistance breeding. We describe future applications and innovative strategies to implement effective and durable strategies to combat diseases of major cereal crops while reducing pesticide dependency.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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20
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Vaid N, Laitinen RAE. Diverse paths to hybrid incompatibility in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:199-213. [PMID: 30098060 DOI: 10.1111/tpj.14061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/02/2018] [Accepted: 08/08/2018] [Indexed: 05/28/2023]
Abstract
One of the most essential questions of biology is to understand how different species have evolved. Hybrid incompatibility, a phenomenon in which hybrids show reduced fitness in comparison with their parents, can result in reproductive isolation and speciation. Therefore, studying hybrid incompatibility provides an entry point in understanding speciation. Hybrid incompatibilities are known throughout taxa, and the underlying mechanisms have mystified scientists since the theory of evolution by means of natural selection was introduced. In plants, it is only in recent years that the high-throughput genetic and molecular tools have become available for the Arabidopsis genus, thus helping to shed light on the different genes and molecular and evolutionary mechanisms that underlie hybrid incompatibilities. In this review, we highlight the current knowledge of diverse mechanisms that are known to contribute to hybrid incompatibility.
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Affiliation(s)
- Neha Vaid
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Roosa A E Laitinen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
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21
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Langner T, Kamoun S, Belhaj K. CRISPR Crops: Plant Genome Editing Toward Disease Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:479-512. [PMID: 29975607 DOI: 10.1146/annurev-phyto-080417-050158] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.
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Affiliation(s)
- Thorsten Langner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
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22
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Monteiro F, Nishimura MT. Structural, Functional, and Genomic Diversity of Plant NLR Proteins: An Evolved Resource for Rational Engineering of Plant Immunity. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:243-267. [PMID: 29949721 DOI: 10.1146/annurev-phyto-080417-045817] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants employ a diverse intracellular system of NLR (nucleotide binding-leucine-rich repeat) innate immune receptors to detect pathogens of all types. These receptors represent valuable agronomic traits that plant breeders rely on to maximize yield in the face of devastating pathogens. Despite their importance, the mechanistic underpinnings of NLR-based disease resistance remain obscure. The rapidly increasing numbers of plant genomes are revealing a diverse array of NLR-type immune receptors. In parallel, mechanistic studies are describing diverse functions for NLR immune receptors. In this review, we intend to broadly describe how the structural, functional, and genomic diversity of plant immune receptors can provide a valuable resource for rational engineering of plant immunity.
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Affiliation(s)
- Freddy Monteiro
- Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280, USA
| | - Marc T Nishimura
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870;
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23
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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24
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Cesari S. Multiple strategies for pathogen perception by plant immune receptors. THE NEW PHYTOLOGIST 2018; 219:17-24. [PMID: 29131341 DOI: 10.1111/nph.14877] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/15/2017] [Indexed: 05/20/2023]
Abstract
Contents Summary 17 I. Introduction 17 II. Pathogen perception by NLRs: from direct recognition to integrated decoys 18 III. Multiple activation and signaling pathways for NLRs 18 IV. How to engineer NLR-mediated disease resistance? 21 V. Conclusion 23 Acknowledgements 23 References 23 SUMMARY: Plants have evolved a complex immune system to protect themselves against phytopathogens. A major class of plant immune receptors called nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) is ubiquitous in plants and is widely used for crop disease protection, making these proteins critical contributors to global food security. Until recently, NLRs were thought to be conserved in their modular architecture and functional features. Investigation of their biochemical, functional and structural properties has revealed fascinating mechanisms that enable these proteins to perceive a wide range of pathogens. Here, I review recent insights demonstrating that NLRs are more mechanistically and structurally diverse than previously thought. I also discuss how these findings provide exciting future prospects to improve plant disease resistance.
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Affiliation(s)
- Stella Cesari
- Institut National de la Recherche Agronomique, UMR de Biologie et Génétique des Interactions Plante-Pathogènes, TA A-54/K Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
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25
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McNally KE, Menardo F, Lüthi L, Praz CR, Müller MC, Kunz L, Ben‐David R, Chandrasekhar K, Dinoor A, Cowger C, Meyers E, Xue M, Zeng F, Gong S, Yu D, Bourras S, Keller B. Distinct domains of the AVRPM3 A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. THE NEW PHYTOLOGIST 2018; 218:681-695. [PMID: 29453934 PMCID: PMC6175116 DOI: 10.1111/nph.15026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/05/2018] [Indexed: 05/22/2023]
Abstract
Recognition of the AVRPM3A2/F2 avirulence protein from powdery mildew by the wheat PM3A/F immune receptor induces a hypersensitive response after co-expression in Nicotiana benthamiana. The molecular determinants of this interaction and how they shape natural AvrPm3a2/f2 allelic diversity are unknown. We sequenced the AvrPm3a2/f2 gene in a worldwide collection of 272 mildew isolates. Using the natural polymorphisms of AvrPm3a2/f2 as well as sequence information from related gene family members, we tested 85 single-residue-altered AVRPM3A2/F2 variants with PM3A, PM3F and PM3FL456P/Y458H (modified for improved signaling) in Nicotiana benthamiana for effects on recognition. An intact AvrPm3a2/f2 gene was found in all analyzed isolates and the protein variant recognized by PM3A/F occurred globally at high frequencies. Single-residue alterations in AVRPM3A2/F2 mostly disrupted, but occasionally enhanced, the recognition response by PM3A, PM3F and PM3FL456P/Y458H . Residues enhancing hypersensitive responses constituted a protein domain separate from both naturally occurring polymorphisms and positively selected residues of the gene family. These results demonstrate the utility of using gene family sequence diversity to screen residues for their role in recognition. This approach identified a putative interaction surface in AVRPM3A2/F2 not polymorphic in natural alleles. We conclude that molecular mechanisms besides recognition drive AvrPm3a2/f2 diversification.
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Affiliation(s)
- Kaitlin Elyse McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Linda Lüthi
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Coraline Rosalie Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Lukas Kunz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani Center50250Bet DaganIsrael
| | - Kottakota Chandrasekhar
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Amos Dinoor
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Christina Cowger
- United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)North Carolina State UniversityRaleighNC27695USA
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Emily Meyers
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Mingfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Fangsong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Shuangjun Gong
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
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26
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Die JV, Román B, Qi X, Rowland LJ. Genome-scale examination of NBS-encoding genes in blueberry. Sci Rep 2018; 8:3429. [PMID: 29467425 PMCID: PMC5821885 DOI: 10.1038/s41598-018-21738-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/08/2018] [Indexed: 01/07/2023] Open
Abstract
Blueberry is an important crop worldwide. It is, however, susceptible to a variety of diseases, which can lead to losses in yield and fruit quality. Although screening studies have identified resistant germplasm for some important diseases, still little is known about the molecular basis underlying that resistance. The most predominant type of resistance (R) genes contains nucleotide binding site and leucine rich repeat (NBS-LRR) domains. The identification and characterization of such a gene family in blueberry would enhance the foundation of knowledge needed for its genetic improvement. In this study, we searched for and found a total of 106 NBS-encoding genes (including 97 NBS-LRR) in the current blueberry genome. The NBS genes were grouped into eleven distinct classes based on their domain architecture. More than 22% of the NBS genes are present in clusters. Ten genes were mapped onto seven linkage groups. Phylogenetic analysis grouped these genes into two major clusters based on their structural variation, the first cluster having toll and interleukin-1 like receptor (TIR) domains and most of the second cluster containing a coiled-coil domain. Our study provides new insight into the NBS gene family in blueberry and is an important resource for the identification of functional R-genes.
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Affiliation(s)
- Jose V Die
- Genetic Improvement Fruits and Vegetables Lab. U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA.
| | - Belén Román
- Crop Breeding and Biotechnology Department, IFAPA Research Centre Alameda del Obispo, Córdoba, Spain
| | - Xinpeng Qi
- Genetic Improvement Fruits and Vegetables Lab. U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Lisa J Rowland
- Genetic Improvement Fruits and Vegetables Lab. U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
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27
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Białas A, Zess EK, De la Concepcion JC, Franceschetti M, Pennington HG, Yoshida K, Upson JL, Chanclud E, Wu CH, Langner T, Maqbool A, Varden FA, Derevnina L, Belhaj K, Fujisaki K, Saitoh H, Terauchi R, Banfield MJ, Kamoun S. Lessons in Effector and NLR Biology of Plant-Microbe Systems. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:34-45. [PMID: 29144205 DOI: 10.1101/171223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A diversity of plant-associated organisms secrete effectors-proteins and metabolites that modulate plant physiology to favor host infection and colonization. However, effectors can also activate plant immune receptors, notably nucleotide-binding domain and leucine-rich repeat region (NLR)-containing proteins, enabling plants to fight off invading organisms. This interplay between effectors, their host targets, and the matching immune receptors is shaped by intricate molecular mechanisms and exceptionally dynamic coevolution. In this article, we focus on three effectors, AVR-Pik, AVR-Pia, and AVR-Pii, from the rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae), and their corresponding rice NLR immune receptors, Pik, Pia, and Pii, to highlight general concepts of plant-microbe interactions. We draw 12 lessons in effector and NLR biology that have emerged from studying these three little effectors and are broadly applicable to other plant-microbe systems.
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Affiliation(s)
- Aleksandra Białas
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Erin K Zess
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Marina Franceschetti
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Helen G Pennington
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Kentaro Yoshida
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Jessica L Upson
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Emilie Chanclud
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Hang Wu
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Freya A Varden
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Lida Derevnina
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Khaoula Belhaj
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Koki Fujisaki
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Hiromasa Saitoh
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
- 5 Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryohei Terauchi
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Mark J Banfield
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Sophien Kamoun
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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28
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Białas A, Zess EK, De la Concepcion JC, Franceschetti M, Pennington HG, Yoshida K, Upson JL, Chanclud E, Wu CH, Langner T, Maqbool A, Varden FA, Derevnina L, Belhaj K, Fujisaki K, Saitoh H, Terauchi R, Banfield MJ, Kamoun S. Lessons in Effector and NLR Biology of Plant-Microbe Systems. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:34-45. [PMID: 29144205 DOI: 10.1094/mpmi-08-17-0196-fi] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A diversity of plant-associated organisms secrete effectors-proteins and metabolites that modulate plant physiology to favor host infection and colonization. However, effectors can also activate plant immune receptors, notably nucleotide-binding domain and leucine-rich repeat region (NLR)-containing proteins, enabling plants to fight off invading organisms. This interplay between effectors, their host targets, and the matching immune receptors is shaped by intricate molecular mechanisms and exceptionally dynamic coevolution. In this article, we focus on three effectors, AVR-Pik, AVR-Pia, and AVR-Pii, from the rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae), and their corresponding rice NLR immune receptors, Pik, Pia, and Pii, to highlight general concepts of plant-microbe interactions. We draw 12 lessons in effector and NLR biology that have emerged from studying these three little effectors and are broadly applicable to other plant-microbe systems.
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Affiliation(s)
- Aleksandra Białas
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Erin K Zess
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Marina Franceschetti
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Helen G Pennington
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Kentaro Yoshida
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Jessica L Upson
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Emilie Chanclud
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Hang Wu
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Freya A Varden
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Lida Derevnina
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Khaoula Belhaj
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Koki Fujisaki
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Hiromasa Saitoh
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
- 5 Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryohei Terauchi
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Mark J Banfield
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Sophien Kamoun
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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29
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Abstract
The first plant disease resistance (R) genes were identified and cloned more than two decades ago. Since then, many more R genes have been identified and characterized in numerous plant pathosystems. Most of these encode members of the large family of intracellular NLRs (NOD-like receptors), which also includes animal immune receptors. New discoveries in this expanding field of research provide new elements for our understanding of plant NLR function. But what do we know about plant NLR function today? Genetic, structural, and functional analyses have uncovered a number of commonalities and differences in pathogen recognition strategies as well as how NLRs are regulated and activate defense signaling, but many unknowns remain. This review gives an update on the latest discoveries and breakthroughs in this field, with an emphasis on structural findings and some comparison to animal NLRs, which can provide additional insights and paradigms in plant NLR function.
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Affiliation(s)
- Xiaoxiao Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
| | - Maud Bernoux
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia;
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30
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Tran DTN, Chung EH, Habring-Müller A, Demar M, Schwab R, Dangl JL, Weigel D, Chae E. Activation of a Plant NLR Complex through Heteromeric Association with an Autoimmune Risk Variant of Another NLR. Curr Biol 2017; 27:1148-1160. [PMID: 28416116 PMCID: PMC5405217 DOI: 10.1016/j.cub.2017.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/09/2017] [Accepted: 03/09/2017] [Indexed: 12/18/2022]
Abstract
When independently evolved immune receptor variants meet in hybrid plants, they can activate immune signaling in the absence of non-self recognition. Such autoimmune risk alleles have recurrently evolved at the DANGEROUS MIX2 (DM2) nucleotide-binding domain and leucine-rich repeat (NLR)-encoding locus in A. thaliana. One of these activates signaling in the presence of a particular variant encoded at another NLR locus, DM1. We show that the risk variants of DM1 and DM2d NLRs signal through the same pathway that is activated when plant NLRs recognize non-self elicitors. This requires the P loops of each protein and Toll/interleukin-1 receptor (TIR)-domain-mediated heteromeric association of DM1 and DM2d. DM1 and DM2d each resides in a multimeric complex in the absence of signaling, with the DM1 complex shifting to higher molecular weight when heteromerizing DM2 variants are present. The activation of the DM1 complex appears to be sensitive to the conformation of the heteromerizing DM2 variant. Autoimmunity triggered by interaction of this NLR pair thus suggests that activity of heteromeric NLR signaling complexes depends on the sum of activation potentials of partner NLRs. Two unlinked plant NLRs physically interact to trigger autoimmunity The N-terminal TIR domains mediate heteromeric NLR association NLR multimerization is not sufficient for signaling
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Affiliation(s)
- Diep T N Tran
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Eui-Hwan Chung
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anette Habring-Müller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Monika Demar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, Chapel Hill, NC 27599, USA; Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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31
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Praz CR, Bourras S, Zeng F, Sánchez‐Martín J, Menardo F, Xue M, Yang L, Roffler S, Böni R, Herren G, McNally KE, Ben‐David R, Parlange F, Oberhaensli S, Flückiger S, Schäfer LK, Wicker T, Yu D, Keller B. AvrPm2 encodes an RNase-like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. THE NEW PHYTOLOGIST 2017; 213:1301-1314. [PMID: 27935041 PMCID: PMC5347869 DOI: 10.1111/nph.14372] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/02/2016] [Indexed: 05/20/2023]
Abstract
There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race-specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3a2/f2 that is recognized by Pm3a/f was known molecularly. We performed map-based cloning and genome-wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2. The virulent AvrPm2 allele arose from a conserved 12 kb deletion, while there is no protein sequence diversity in the gene pool of avirulent B. g. tritici isolates. We found one polymorphic AvrPm2 allele in B. g. triticale and one orthologue in B. g. secalis and both are recognized by Pm2. AvrPm2 belongs to a small gene family encoding structurally conserved RNase-like effectors, including Avra13 from B. g. hordei, the cognate Avr of the barley resistance gene Mla13. These results demonstrate the conservation of functional avirulence genes in two cereal powdery mildews specialized on different hosts, thus providing a possible explanation for successful introgression of resistance genes from rye or other grass relatives to wheat.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Fansong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | | | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Lijun Yang
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Stefan Roffler
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Rainer Böni
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Gerard Herren
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Kaitlin E. McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani CenterBet Dagan50250Israel
| | - Francis Parlange
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Luisa K. Schäfer
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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32
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Andolfo G, Iovieno P, Frusciante L, Ercolano MR. Genome-Editing Technologies for Enhancing Plant Disease Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1813. [PMID: 27990151 PMCID: PMC5130979 DOI: 10.3389/fpls.2016.01813] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/16/2016] [Indexed: 05/23/2023]
Abstract
One of the greatest challenges for agricultural science in the 21st century is to improve yield stability through the progressive development of superior cultivars. The increasing numbers of infectious plant diseases that are caused by plant-pathogens make it ever more necessary to develop new strategies for plant disease resistance breeding. Targeted genome engineering allows the introduction of precise modifications directly into a commercial variety, offering a viable alternative to traditional breeding methods. Genome editing is a powerful tool for modifying crucial players in the plant immunity system. In this work, we propose and discuss genome-editing strategies and targets for improving resistance to phytopathogens. First of all, we present the opportunities to rewrite the effector-target sequence for avoiding effector-target molecular interaction and also to modify effector-target promoters for increasing the expression of target genes involved in the resistance process. In addition, we describe potential approaches for obtaining synthetic R-genes through genome-editing technologies (GETs). Finally, we illustrate a genome editing flowchart to modify the pathogen recognition sites and engineer an R-gene that mounts resistance to some phylogenetically divergent pathogens. GETs potentially mark the beginning of a new era, in which synthetic biology affords a basis for obtaining a reinforced plant defense system. Nowadays it is conceivable that by modulating the function of the major plant immunity players, we will be able to improve crop performance for a sustainable agriculture.
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Affiliation(s)
| | | | | | - Maria R. Ercolano
- Department of Agricultural Sciences, University of Naples ‘Federico II’Portici, Italy
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Structural insights into plant NLR immune receptor function. Proc Natl Acad Sci U S A 2016; 113:12619-12621. [PMID: 27803318 DOI: 10.1073/pnas.1615933113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Whole-Genome Resequencing of a Cucumber Chromosome Segment Substitution Line and Its Recurrent Parent to Identify Candidate Genes Governing Powdery Mildew Resistance. PLoS One 2016; 11:e0164469. [PMID: 27764118 PMCID: PMC5072683 DOI: 10.1371/journal.pone.0164469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels). When compared against the reference genome of the inbred cucumber line 9930, a total of 468,616 SNPs and 67,259 indels were identified in SSL508-28, and 537,352 SNPs and 91,698 indels were identified in D8. Of these, 3,014 non-synonymous SNPs and 226 frameshift indels in SSL508-28, and 3,104 non-synonymous SNPs and 251 frameshift indels in D8, were identified. Bioinformatics analysis of these variations revealed a total of 15,682 SNPs and 6,262 indels between SSL508-28 and D8, among which 120 non-synonymous SNPs and 30 frameshift indels in 94 genes were detected between SSL508-28 and D8. Finally, out of these 94 genes, five resistance genes with nucleotide-binding sites and leucine-rich repeat domains were selected for qRT-PCR analysis. This revealed an upregulation of two transcripts, Csa2M435460.1 and Csa5M579560.1, in SSL508-28. Furthermore, the results of qRT-PCR analysis of these two genes in ten PM resistant and ten PM susceptible cucumber lines showed that when exposed to PM, Csa2M435460.1 and Csa5M579560.1 exhibited a higher expression level of resistant lines than susceptible lines. This indicates that Csa2M435460.1 and Csa5M579560.1 are candidate genes for PM resistance in cucumber. In addition, the non-synonymous SNPs in Csa2M435460.1 and Csa5M579560.1, identified in SSL508-28 and D8, might be the key to high PM-resistance in SSL508-28.
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Schreiber KJ, Bentham A, Williams SJ, Kobe B, Staskawicz BJ. Multiple Domain Associations within the Arabidopsis Immune Receptor RPP1 Regulate the Activation of Programmed Cell Death. PLoS Pathog 2016; 12:e1005769. [PMID: 27427964 PMCID: PMC4948778 DOI: 10.1371/journal.ppat.1005769] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/24/2016] [Indexed: 11/18/2022] Open
Abstract
Upon recognition of pathogen virulence effectors, plant nucleotide-binding leucine-rich repeat (NLR) proteins induce defense responses including localized host cell death. In an effort to understand the molecular mechanisms leading to this response, we examined the Arabidopsis thaliana NLR protein RECOGNITION OF PERONOSPORA PARASITICA1 (RPP1), which recognizes the Hyaloperonospora arabidopsidis effector ARABIDOPSIS THALIANA RECOGNIZED1 (ATR1). Expression of the N-terminus of RPP1, including the Toll/interleukin-1 receptor (TIR) domain (“N-TIR”), elicited an effector-independent cell death response, and we used allelic variation in TIR domain sequences to define the key residues that contribute to this phenotype. Further biochemical characterization indicated that cell death induction was correlated with N-TIR domain self-association. In addition, we demonstrated that the nucleotide-binding (NB)-ARC1 region of RPP1 self-associates and plays a critical role in cell death activation, likely by facilitating TIR:TIR interactions. Structural homology modeling of the NB subdomain allowed us to identify a putative oligomerization interface that was shown to influence NB-ARC1 self-association. Significantly, full-length RPP1 exhibited effector-dependent oligomerization and, although mutations at the NB-ARC1 oligomerization interface eliminated cell death induction, RPP1 self-association was unaffected, suggesting that additional regions contribute to oligomerization. Indeed, the leucine-rich repeat domain of RPP1 also self-associates, indicating that multiple interaction interfaces exist within activated RPP1 oligomers. Finally, we observed numerous intramolecular interactions that likely function to negatively regulate RPP1, and present a model describing the transition to an active NLR protein. Many plant pathogens inject proteins known as effectors into the cells of their hosts in order to suppress host immune responses and promote pathogen growth. Over time, plants have evolved receptors, described as nucleotide-binding leucine-rich repeat (NLR) proteins, which recognize the activity of pathogen effectors and stimulate defense responses. Plant NLRs contain several domains that exhibit striking functional conservation with NLRs from other eukaryotes. Despite their important contribution to plant immunity, the molecular mechanisms that underlie effector recognition and subsequent immune activation by NLRs remain to be fully elucidated. Here, we focus on RPP1, an NLR from Arabidopsis that recognizes the oomycete effector ATR1. Using transient co-expression of proteins in plants, we demonstrate that recognition of ATR1 stimulates RPP1 oligomerization. This interaction involves multiple domains of RPP1 and is critical for immune activation. In the absence of ATR1, we documented interactions between domains within an individual RPP1 protein, likely occurring to prevent inappropriate immune activation. Finally, we examined differences between RPP1 alleles as well as structural data from animal NLRs to help identify specific amino acids that mediate interactions within and between RPP1 molecules. Collectively, these data allow us to propose a model for the activation of RPP1 following ATR1 recognition.
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Affiliation(s)
- Karl J. Schreiber
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Adam Bentham
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
- School of Biological Sciences, Faculty of Science and Engineering, Flinders University, Adelaide, Australia
| | - Simon J. Williams
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Brian J. Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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Helft L, Thompson M, Bent AF. Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition. PLoS One 2016; 11:e0157155. [PMID: 27270917 PMCID: PMC4894583 DOI: 10.1371/journal.pone.0157155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/25/2016] [Indexed: 12/20/2022] Open
Abstract
Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wild-type Arabidopsis FLS2 confers little or no response. A targeted approach generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. These studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.
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Affiliation(s)
- Laura Helft
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Cellular and Molecular Biology Program, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mikayla Thompson
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Andrew F. Bent
- Department of Plant Pathology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Sukarta OCA, Slootweg EJ, Goverse A. Structure-informed insights for NLR functioning in plant immunity. Semin Cell Dev Biol 2016; 56:134-149. [PMID: 27208725 DOI: 10.1016/j.semcdb.2016.05.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
Abstract
To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning.
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Affiliation(s)
- Octavina C A Sukarta
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Erik J Slootweg
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Aska Goverse
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Giannakopoulou A, Bialas A, Kamoun S, Vleeshouwers VGAA. Plant immunity switched from bacteria to virus. Nat Biotechnol 2016; 34:391-2. [DOI: 10.1038/nbt.3538] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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The battle for survival between viruses and their host plants. Curr Opin Virol 2016; 17:32-38. [PMID: 26800310 DOI: 10.1016/j.coviro.2015.12.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022]
Abstract
Evolution has equipped plants with defense mechanisms to counterattack virus infections. However, some viruses have acquired the capacity to escape these defense barriers. In their combats, plants use mechanisms such as antiviral RNA silencing that viruses fight against using silencing-repressors. Plants could also resist by mutating a host factor required by the virus to complete a particular step of its infectious cycle. Another successful mechanism of resistance is the hypersensitive response, where plants engineer R genes that recognize specifically their assailants. The recognition is followed by the triggering of a broad spectrum resistance. New understanding of such resistance mechanisms will probably helps to propose new means to enhance plant resistance against viruses.
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Bourras S, McNally KE, Müller MC, Wicker T, Keller B. Avirulence Genes in Cereal Powdery Mildews: The Gene-for-Gene Hypothesis 2.0. FRONTIERS IN PLANT SCIENCE 2016; 7:241. [PMID: 26973683 PMCID: PMC4771761 DOI: 10.3389/fpls.2016.00241] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/12/2016] [Indexed: 05/22/2023]
Abstract
The gene-for-gene hypothesis states that for each gene controlling resistance in the host, there is a corresponding, specific gene controlling avirulence in the pathogen. Allelic series of the cereal mildew resistance genes Pm3 and Mla provide an excellent system for genetic and molecular analysis of resistance specificity. Despite this opportunity for molecular research, avirulence genes in mildews remain underexplored. Earlier work in barley powdery mildew (B.g. hordei) has shown that the reaction to some Mla resistance alleles is controlled by multiple genes. Similarly, several genes are involved in the specific interaction of wheat mildew (B.g. tritici) with the Pm3 allelic series. We found that two mildew genes control avirulence on Pm3f: one gene is involved in recognition by the resistance protein as demonstrated by functional studies in wheat and the heterologous host Nicotiana benthamiana. A second gene is a suppressor, and resistance is only observed in mildew genotypes combining the inactive suppressor and the recognized Avr. We propose that such suppressor/avirulence gene combinations provide the basis of specificity in mildews. Depending on the particular gene combinations in a mildew race, different genes will be genetically identified as the "avirulence" gene. Additionally, the observation of two LINE retrotransposon-encoded avirulence genes in B.g. hordei further suggests that the control of avirulence in mildew is more complex than a canonical gene-for-gene interaction. To fully understand the mildew-cereal interactions, more knowledge on avirulence determinants is needed and we propose ways how this can be achieved based on recent advances in the field.
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Guo C, Sun X, Chen X, Yang S, Li J, Wang L, Zhang X. Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice. PLANT MOLECULAR BIOLOGY 2016; 90:95-105. [PMID: 26530637 DOI: 10.1007/s11103-015-0398-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/24/2015] [Indexed: 05/28/2023]
Abstract
Most rice blast resistance genes (R-genes) encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. Our previous study has shown that more rice blast R-genes can be cloned in rapidly evolving NBS-LRR gene families. In the present study, two rapidly evolving R-gene families in rice were selected for cloning a subset of genes from their paralogs in three resistant rice lines. A total of eight functional blast R-genes were identified among nine NBS-LRR genes, and some of these showed resistance to three or more blast strains. Evolutionary analysis indicated that high nucleotide diversity of coding regions served as important parameters in the determination of gene resistance. We also observed that amino-acid variants (nonsynonymous mutations, insertions, or deletions) in essential motifs of the NBS domain contribute to the blast resistance capacity of NBS-LRR genes. These results suggested that the NBS regions might also play an important role in resistance specificity determination. On the other hand, different splicing patterns of introns were commonly observed in R-genes. The results of the present study contribute to improving the effectiveness of R-gene identification by using evolutionary analysis method and acquisition of novel blast resistance genes.
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Affiliation(s)
- Changjiang Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaoguang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiao Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Li
- Institute for Research on Cancer and Ageing, Nice (IRCAN), University of Nice, Nice, France
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Giannakopoulou A, Steele JFC, Segretin ME, Bozkurt TO, Zhou J, Robatzek S, Banfield MJ, Pais M, Kamoun S. Tomato I2 Immune Receptor Can Be Engineered to Confer Partial Resistance to the Oomycete Phytophthora infestans in Addition to the Fungus Fusarium oxysporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1316-29. [PMID: 26367241 DOI: 10.1094/mpmi-07-15-0147-r] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plants and animals rely on immune receptors, known as nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins, to defend against invading pathogens and activate immune responses. How NLR receptors respond to pathogens is inadequately understood. We previously reported single-residue mutations that expand the response of the potato immune receptor R3a to AVR3a(EM), a stealthy effector from the late blight oomycete pathogen Phytophthora infestans. I2, another NLR that mediates resistance to the will-causing fungus Fusarium oxysporum f. sp. lycopersici, is the tomato ortholog of R3a. We transferred previously identified R3a mutations to I2 to assess the degree to which the resulting I2 mutants have an altered response. We discovered that wild-type I2 protein responds weakly to AVR3a. One mutant in the N-terminal coiled-coil domain, I2(I141N), appeared sensitized and displayed markedly increased response to AVR3a. Remarkably, I2(I141N) conferred partial resistance to P. infestans. Further, I2(I141N) has an expanded response spectrum to F. oxysporum f. sp. lycopersici effectors compared with the wild-type I2 protein. Our results suggest that synthetic immune receptors can be engineered to confer resistance to phylogenetically divergent pathogens and indicate that knowledge gathered for one NLR could be exploited to improve NLR from other plant species.
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Affiliation(s)
| | - John F C Steele
- 2 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | | | - Tolga O Bozkurt
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, United Kingdom
- 4 Imperial College, Faculty of Natural Sciences, Department of Life Sciences, South Kensington Campus, London SW7 2AZ, United Kingdom; and
| | - Ji Zhou
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, United Kingdom
- 5 The Genome Analysis Centre, Norwich Research Park, NR4 7UH Norwich, United Kingdom
| | - Silke Robatzek
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, United Kingdom
| | - Mark J Banfield
- 2 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Marina Pais
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, United Kingdom
| | - Sophien Kamoun
- 1 The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, United Kingdom
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Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles. Fungal Genet Biol 2015; 82:181-92. [DOI: 10.1016/j.fgb.2015.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/10/2015] [Accepted: 06/09/2015] [Indexed: 01/26/2023]
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Chavan S, Gray J, Smith SM. Diversity and evolution of Rp1 rust resistance genes in four maize lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:985-98. [PMID: 25805314 DOI: 10.1007/s00122-015-2484-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 02/13/2015] [Indexed: 05/24/2023]
Abstract
This manuscript provides genome-level analysis of disease resistance genes in four maize lines, including studies of haplotype and resistance gene number as well as selection and recombination. The Rp1 locus of maize is a complex resistance gene (R-gene) cluster that confers race-specific resistance to Puccinia sorghi, the causal agent of common leaf rust. Rp1 NB-LRR disease resistance genes were isolated from two Rp1 haplotypes (HRp1-B and HRp1-M) and two maize inbred lines (B73 and H95). Sixty-one Rp1 genes were isolated from Rp1-B, Rp1-M, B73 and H95 with a PCR-based approach. The four maize lines carried from 12 to 19 Rp1 genes. From 4 to 9 of the identified Rp1 genes were transcribed in the four maize lines. The Rp1 gene nucleotide diversity was higher in HRp1-B and HRp1-M than in B73 and H95. Phylogenic analysis of 69 Rp1 genes revealed that the Rp1 genes maintained in HRp1-B, HRp1-M and H95 are evolving independently of each other, while Rp1 genes in B73 and HRp1-D appear more like each other than they do genes in the other lines. The results also revealed that the analysed Rp1 R-genes were under positive selection in HRp1-M and B73. Intragenic recombination was detected in Rp1 genes maintained in the four maize lines. This demonstrates that a genetic process that has the potential to generate new resistance genes with new specificities is active at the Rp1 locus in the four analysed maize lines and that the new resistance genes may act against newly arising pathogen races that become prevalent in the pathogen population.
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Affiliation(s)
- Suchitra Chavan
- Department of Plant Pathology, The University of Georgia, 120 Carlton St., Miller Plant Science, Room 4309, 30602, Athens, Georgia
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Zhang J, Liu W, Han H, Song L, Bai L, Gao Z, Zhang Y, Yang X, Li X, Gao A, Li L. De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat. Genomics 2015; 106:129-36. [PMID: 25889708 DOI: 10.1016/j.ygeno.2015.04.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 01/08/2023]
Abstract
Agropyron cristatum is a wild grass of the tribe Triticeae that is widely grown in harsh environments. As a wild relative of wheat, A. cristatum carries many resistance genes that could be used to broaden the genetic diversity of wheat. Here, we report the transcriptome sequencing of the flag leaf and young spike tissues of a representative tetraploid A. cristatum. More than 90 million reads from the two tissues were assembled into 73,664 unigenes. All unigenes were functionally annotated against the KEGG, COG, and Gene Ontology databases and predicted long non-coding RNAs. Pfam prediction demonstrates that A. cristatum carries an abundance of stress resistance genes. The extent of specific genes and rare alleles make A. cristatum a vital genetic reservoir for the improvement of wheat. Altogether, the available gene resources in A. cristatum facilitate efforts to harness the genetic diversity of wild relatives to enhance wheat.
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Affiliation(s)
- Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiming Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liqiang Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Bai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhihui Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ainong Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wang GF, Ji J, EI-Kasmi F, Dangl JL, Johal G, Balint-Kurti PJ. Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity. PLoS Pathog 2015; 11:e1004674. [PMID: 25719542 PMCID: PMC4342346 DOI: 10.1371/journal.ppat.1004674] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/09/2015] [Indexed: 12/22/2022] Open
Abstract
Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR). Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC), a nucleotide binding (NB-ARC) and a leucine rich repeat (LRR) domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance.
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Affiliation(s)
- Guan-Feng Wang
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail: (GFW); (PJBK)
| | - Jiabing Ji
- Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Farid EI-Kasmi
- Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery L. Dangl
- Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics and Molecular Biology, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Guri Johal
- Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Peter J. Balint-Kurti
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
- USDA-ARS Plant Science Research Unit, Raleigh, North Carolina, United States of America
- * E-mail: (GFW); (PJBK)
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47
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Recognition and activation domains contribute to allele-specific responses of an Arabidopsis NLR receptor to an oomycete effector protein. PLoS Pathog 2015; 11:e1004665. [PMID: 25671309 PMCID: PMC4335498 DOI: 10.1371/journal.ppat.1004665] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 01/06/2015] [Indexed: 11/19/2022] Open
Abstract
In plants, specific recognition of pathogen effector proteins by nucleotide-binding leucine-rich repeat (NLR) receptors leads to activation of immune responses. RPP1, an NLR from Arabidopsis thaliana, recognizes the effector ATR1, from the oomycete pathogen Hyaloperonospora arabidopsidis, by direct association via C-terminal leucine-rich repeats (LRRs). Two RPP1 alleles, RPP1-NdA and RPP1-WsB, have narrow and broad recognition spectra, respectively, with RPP1-NdA recognizing a subset of the ATR1 variants recognized by RPP1-WsB. In this work, we further characterized direct effector recognition through random mutagenesis of an unrecognized ATR1 allele, ATR1-Cala2, screening for gain-of-recognition phenotypes in a tobacco hypersensitive response assay. We identified ATR1 mutants that a) confirm surface-exposed residues contribute to recognition by RPP1, and b) are recognized by and activate the narrow-spectrum allele RPP1-NdA, but not RPP1-WsB, in co-immunoprecipitation and bacterial growth inhibition assays. Thus, RPP1 alleles have distinct recognition specificities, rather than simply different sensitivity to activation. Using chimeric RPP1 constructs, we showed that RPP1-NdA LRRs were sufficient for allele-specific recognition (association with ATR1), but insufficient for receptor activation in the form of HR. Additional inclusion of the RPP1-NdA ARC2 subdomain, from the central NB-ARC domain, was required for a full range of activation specificity. Thus, cooperation between recognition and activation domains seems to be essential for NLR function.
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Ellis JG, Lagudah ES, Spielmeyer W, Dodds PN. The past, present and future of breeding rust resistant wheat. FRONTIERS IN PLANT SCIENCE 2014; 5:641. [PMID: 25505474 PMCID: PMC4241819 DOI: 10.3389/fpls.2014.00641] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/29/2014] [Indexed: 05/17/2023]
Abstract
Two classes of genes are used for breeding rust resistant wheat. The first class, called R (for resistance) genes, are pathogen race specific in their action, effective at all plant growth stages and probably mostly encode immune receptors of the nucleotide binding leucine rich repeat (NB-LRR) class. The second class is called adult plant resistance genes (APR) because resistance is usually functional only in adult plants, and, in contrast to most R genes, the levels of resistance conferred by single APR genes are only partial and allow considerable disease development. Some but not all APR genes provide resistance to all isolates of a rust pathogen species and a subclass of these provides resistance to several fungal pathogen species. Initial indications are that APR genes encode a more heterogeneous range of proteins than R proteins. Two APR genes, Lr34 and Yr36, have been cloned from wheat and their products are an ABC transporter and a protein kinase, respectively. Lr34 and Sr2 have provided long lasting and widely used (durable) partial resistance and are mainly used in conjunction with other R and APR genes to obtain adequate rust resistance. We caution that some APR genes indeed include race specific, weak R genes which may be of the NB-LRR class. A research priority to better inform rust resistance breeding is to characterize further APR genes in wheat and to understand how they function and how they interact when multiple APR and R genes are stacked in a single genotype by conventional and GM breeding. An important message is do not be complacent about the general durability of all APR genes.
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Affiliation(s)
- Jeffrey G. Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
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49
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Chapman S, Stevens LJ, Boevink PC, Engelhardt S, Alexander CJ, Harrower B, Champouret N, McGeachy K, Van Weymers PSM, Chen X, Birch PRJ, Hein I. Detection of the virulent form of AVR3a from Phytophthora infestans following artificial evolution of potato resistance gene R3a. PLoS One 2014; 9:e110158. [PMID: 25340613 PMCID: PMC4207746 DOI: 10.1371/journal.pone.0110158] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/08/2014] [Indexed: 11/24/2022] Open
Abstract
Engineering resistance genes to gain effector recognition is emerging as an important step in attaining broad, durable resistance. We engineered potato resistance gene R3a to gain recognition of the virulent AVR3aEM effector form of Phytophthora infestans. Random mutagenesis, gene shuffling and site-directed mutagenesis of R3a were conducted to produce R3a* variants with gain of recognition towards AVR3aEM. Programmed cell death following gain of recognition was enhanced in iterative rounds of artificial evolution and neared levels observed for recognition of AVR3aKI by R3a. We demonstrated that R3a*-mediated recognition responses, like for R3a, are dependent on SGT1 and HSP90. In addition, this gain of response is associated with re-localisation of R3a* variants from the cytoplasm to late endosomes when co-expressed with either AVR3aKI or AVR3aEM a mechanism that was previously only seen for R3a upon co-infiltration with AVR3aKI. Similarly, AVR3aEM specifically re-localised to the same vesicles upon recognition by R3a* variants, but not with R3a. R3a and R3a* provide resistance to P. infestans isolates expressing AVR3aKI but not those homozygous for AVR3aEM.
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Affiliation(s)
- Sean Chapman
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
| | - Laura J. Stevens
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
| | - Petra C. Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
| | - Stefan Engelhardt
- Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
| | - Colin J. Alexander
- Biomathematics and Statistics Scotland, Invergowrie-Dundee, United Kingdom
| | - Brian Harrower
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
| | - Nicolas Champouret
- J.R. Simplot Company, Simplot Plant Sciences, Boise, Idaho, United States of America
| | - Kara McGeachy
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
| | - Pauline S. M. Van Weymers
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
| | - Xinwei Chen
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
| | - Paul R. J. Birch
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
| | - Ingo Hein
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie-Dundee, United Kingdom
- Dundee Effector Consortium, Invergowrie-Dundee, United Kingdom
- * E-mail:
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50
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Stirnweis D, Milani SD, Brunner S, Herren G, Buchmann G, Peditto D, Jordan T, Keller B. Suppression among alleles encoding nucleotide-binding-leucine-rich repeat resistance proteins interferes with resistance in F1 hybrid and allele-pyramided wheat plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:893-903. [PMID: 24942051 DOI: 10.1111/tpj.12592] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 05/24/2023]
Abstract
The development of high-yielding varieties with broad-spectrum durable disease resistance is the ultimate goal of crop breeding. In plants, immune receptors of the nucleotide-binding-leucine-rich repeat (NB-LRR) class mediate race-specific resistance against pathogen attack. When employed in agriculture this type of resistance is often rapidly overcome by newly adapted pathogen races. The stacking of different resistance genes or alleles in F1 hybrids or in pyramided lines is a promising strategy for achieving more durable resistance. Here, we identify a molecular mechanism which can negatively interfere with the allele-pyramiding approach. We show that pairwise combinations of different alleles of the powdery mildew resistance gene Pm3 in F1 hybrids and stacked transgenic wheat lines can result in suppression of Pm3-based resistance. This effect is independent of the genetic background and solely dependent on the Pm3 alleles. Suppression occurs at the post-translational level, as levels of RNA and protein in the suppressed alleles are unaffected. Using a transient expression system in Nicotiana benthamiana, the LRR domain was identified as the domain conferring suppression. The results of this study suggest that the expression of closely related NB-LRR resistance genes or alleles in the same genotype can lead to dominant-negative interactions. These findings provide a molecular explanation for the frequently observed ineffectiveness of resistance genes introduced from the secondary gene pool into polyploid crop species and mark an important step in overcoming this limitation.
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Affiliation(s)
- Daniel Stirnweis
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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