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Ijaz U, Zhao C, Shabala S, Zhou M. Molecular Basis of Plant-Pathogen Interactions in the Agricultural Context. BIOLOGY 2024; 13:421. [PMID: 38927301 PMCID: PMC11200688 DOI: 10.3390/biology13060421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.
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Affiliation(s)
- Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia;
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
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2
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Guo T, Bao R, Yang Z, Fu X, Hu L, Wang N, Liu C, Ma F. The m 6 A reader MhYTP2 negatively modulates apple Glomerella leaf spot resistance by binding to and degrading MdRGA2L mRNA. MOLECULAR PLANT PATHOLOGY 2023; 24:1287-1299. [PMID: 37366340 PMCID: PMC10502827 DOI: 10.1111/mpp.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
Glomerella leaf spot (GLS), caused by the fungal pathogen Colletotrichum fructicola, significantly threatens apple production. Some resistances to plant disease are mediated by the accumulation of nucleotide-binding site and leucine-rich repeat (NBS-LRR) proteins that are encoded by a major class of plant disease resistance genes (R genes). However, the R genes that confer resistance to GLS in apple remain largely unclear. Malus hupehensis YT521-B homology domain-containing protein 2 (MhYTP2) was identified as an N6 -methyladenosine RNA methylation (m6 A) modified RNA reader in our previous study. However, whether MhYTP2 binds to mRNAs without m6 A RNA modifications remains unknown. In this study, we discovered that MhYTP2 exerts both m6 A-dependent and -independent functions by analysing previously obtained RNA immunoprecipitation sequencing results. The overexpression of MhYTP2 significantly reduced the resistance of apple to GLS and down-regulated the transcript levels of some R genes whose transcripts do not contain m6 A modifications. Further analysis indicated that MhYTP2 binds to and reduces the stability of MdRGA2L mRNA. MdRGA2L positively regulates resistance to GLS by activating salicylic acid signalling. Our findings revealed that MhYTP2 plays an essential role in the regulation of resistance to GLS and identified a promising R gene, MdRGA2L, for use in developing apple cultivars with GLS resistance.
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Affiliation(s)
- Tianli Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Ru Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Zehua Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Xiaomin Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Liu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Na Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Changhai Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of AppleCollege of Horticulture, Northwest A&F UniversityYanglingChina
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3
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Abstract
Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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4
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Zhang L, Xu Z, Jiang Z, Chen X, Li B, Xu L, Zhang Z. Cloning and functional analysis of the root-knot nematode resistance gene NtRk1 in tobacco. PHYSIOLOGIA PLANTARUM 2023; 175:e13894. [PMID: 36942459 DOI: 10.1111/ppl.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is an economically important crop worldwide. Root-knot nematodes (RKNs) are responsible for yield losses in tobacco and other crops, such as tomato, potato, peanut, and soybean. Therefore, screening for resistance genes that can prevent RKN infestation and the associated damage is crucial. However, there is no report of cloning tobacco RKN resistance genes to date. Here, we cloned the tobacco RKN resistance gene NtRk1 from the resistant variety TI706, using rapid amplification of cDNA ends. NtRk1 has high homology with other RKN resistance genes (CaMi in pepper, Mi-1.1 and Mi-1.2 in tomato). Under normal conditions, NtRk1 was barely expressed in the roots; however, following RKN infection, its expression level rapidly increased. Overexpression of NtRk1 in the susceptible cultivar "Changbohuang" enhanced its resistance to Meloidogyne incognita, while RNA interference of NtRk1 in the resistant cultivar K326 resulted in its susceptibility to M. incognita. Moreover, compared with resistant variety K326, we found the salicylic acid and jasmonic acid contents of RNAi plants decreased after inoculation with M. incognita, and confirmed that the function of NtRk1 is related to these phytohormones. These findings indicate that NtRk1 is an RKN resistance gene, which is abundantly expressed in response to RKN infection and may enhance host defense responses by elevating salicylic acid and jasmonic acid levels.
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Affiliation(s)
- Luyang Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiqiang Xu
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, 310008, China
| | - Zhimin Jiang
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, 310008, China
| | - Xiaoxiang Chen
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, 310008, China
| | - Bo Li
- China Tobacco Zhejiang Industry Co, Ltd, Hangzhou, 310008, China
| | - Liping Xu
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiqiang Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, China
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5
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Garcia AGK, Steinbrenner AD. Bringing Plant Immunity to Light: A Genetically Encoded, Bioluminescent Reporter of Pattern-Triggered Immunity in Nicotiana benthamiana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:139-149. [PMID: 36583694 DOI: 10.1094/mpmi-07-22-0160-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Plants rely on innate immune systems to defend against a wide variety of biotic attackers. Key components of innate immunity include cell-surface pattern-recognition receptors (PRRs), which recognize pest- and pathogen-associated molecular patterns (PAMPs). Unlike other classes of receptors that often have visible cell-death immune outputs upon activation, PRRs generally lack rapid methods for assessing function. Here, we describe a genetically encoded bioluminescent reporter of immune activation by heterologously expressed PRRs in the model organism Nicotiana benthamiana. We characterized N. benthamiana transcriptome changes in response to Agrobacterium tumefaciens and subsequent PAMP treatment to identify pattern-triggered immunity (PTI)-associated marker genes, which were then used to generate promoter-luciferase fusion fungal bioluminescence pathway (FBP) constructs. A reporter construct termed pFBP_2xNbLYS1::LUZ allows for robust detection of PTI activation by heterologously expressed PRRs. Consistent with known PTI signaling pathways, reporter activation by receptor-like protein (RLP) PRRs is dependent on the known adaptor of RLP PRRs, i.e., SOBIR1. The FBP reporter minimizes the amount of labor, reagents, and time needed to assay function of PRRs and displays robust sensitivity at biologically relevant PAMP concentrations, making it ideal for high throughput screens. The tools described in this paper will be powerful for investigations of PRR function and characterization of the structure-function of plant cell-surface receptors. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
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Affiliation(s)
- Anthony G K Garcia
- Department of Biology, University of Washington, Seattle, WA 98195, U.S.A
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6
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Wu Q, Cui Y, Jin X, Wang G, Yan L, Zhong C, Yu M, Li W, Wang Y, Wang L, Wang H, Dang C, Zhang X, Chen Y, Zhang P, Zhao X, Wu J, Fu D, Xia L, Nevo E, Vogel J, Huo N, Li D, Gu YQ, Jackson AO, Zhang Y, Liu Z. The CC-NB-LRR protein BSR1 from Brachypodium confers resistance to Barley stripe mosaic virus in gramineous plants by recognising TGB1 movement protein. THE NEW PHYTOLOGIST 2022; 236:2233-2248. [PMID: 36059081 DOI: 10.1111/nph.18457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Although some nucleotide binding, leucine-rich repeat immune receptor (NLR) proteins conferring resistance to specific viruses have been identified in dicot plants, NLR proteins involved in viral resistance have not been described in monocots. We have used map-based cloning to isolate the CC-NB-LRR (CNL) Barley stripe mosaic virus (BSMV) resistance gene barley stripe resistance 1 (BSR1) from Brachypodium distachyon Bd3-1 inbred line. Stable BSR1 transgenic Brachypodium line Bd21-3, barley (Golden Promise) and wheat (Kenong 199) plants developed resistance against BSMV ND18 strain. Allelic variation analyses indicated that BSR1 is present in several Brachypodium accessions collected from countries in the Middle East. Protein domain swaps revealed that the intact LRR domain and the C-terminus of BSR1 are required for resistance. BSR1 interacts with the BSMV ND18 TGB1 protein in planta and shows temperature-sensitive antiviral resistance. The R390 and T392 residues of TGB1ND (ND18 strain) and the G196 and K197 residues within the BSR1 P-loop motif are key amino acids required for immune activation. BSR1 is the first cloned virus resistance gene encoding a typical CNL protein in monocots, highlighting the utility of the Brachypodium model for isolation and analysis of agronomically important genes for crop improvement.
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Affiliation(s)
- Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Guoxin Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chenchen Zhong
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Meihua Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wenli Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ling Wang
- 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
| | - Hao Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Dang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xinyu Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Panpan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhao
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiajie Wu
- College of Agronomy, Shandong Agriculture University, Taian, 271018, China
| | - Daolin Fu
- College of Agronomy, Shandong Agriculture University, Taian, 271018, China
| | - Lanqin Xia
- Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Eviatar Nevo
- Institute of Evolution, Haifa University, Haifa, 31905, Israel
| | - John Vogel
- Joint Genome Institute, DOE, Walnut Creek, CA, 94598, USA
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yong Q Gu
- USDA-ARS Western Regional Research Center, Albany, CA, 94710, USA
| | - Andrew O Jackson
- Department of Plant and Microbiology, University of California, Berkeley, CA, 94720, USA
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Martin EC, Ion CF, Ifrimescu F, Spiridon L, Bakker J, Goverse A, Petrescu AJ. NLRscape: an atlas of plant NLR proteins. Nucleic Acids Res 2022; 51:D1470-D1482. [PMID: 36350627 PMCID: PMC9825502 DOI: 10.1093/nar/gkac1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
NLRscape is a webserver that curates a collection of over 80 000 plant protein sequences identified in UniProtKB to contain NOD-like receptor signatures, and hosts in addition a number of tools aimed at the exploration of the complex sequence landscape of this class of plant proteins. Each entry gathers sequence information, domain and motif annotations from multiple third-party sources but also in-house advanced annotations aimed at addressing caveats of the existing broad-based annotations. NLRscape provides a top-down perspective of the NLR sequence landscape but also services for assisting a bottom-up approach starting from a given input sequence. Sequences are clustered by their domain organization layout, global homology and taxonomic spread-in order to allow analysis of how particular traits of an NLR family are scattered within the plant kingdom. Tools are provided for users to locate their own protein of interest in the overall NLR landscape, generate custom clusters centered around it and perform a large number of sequence and structural analyses using included interactive online instruments. Amongst these, we mention: taxonomy distribution plots, homology cluster graphs, identity matrices and interactive MSA synchronizing secondary structure and motif predictions. NLRscape can be found at: https://nlrscape.biochim.ro/.
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Affiliation(s)
- Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Catalin F Ion
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Florin Ifrimescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Laurentiu Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest 060031, Romania
| | - Jaap Bakker
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University and Research, Wageningen 6700ES, The Netherlands
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8
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Cantila AY, Thomas WJW, Bayer PE, Edwards D, Batley J. Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species. PLANTS (BASEL, SWITZERLAND) 2022; 11:3010. [PMID: 36432742 PMCID: PMC9693284 DOI: 10.3390/plants11223010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Brassicaceae crops, including Brassica, Camelina and Raphanus species, are among the most economically important crops globally; however, their production is affected by several diseases. To predict cloned disease resistance (R) gene homologs (CDRHs), we used the protein sequences of 49 cloned R genes against fungal and bacterial diseases in Brassicaceae species. In this study, using 20 Brassicaceae genomes (17 wild and 3 domesticated species), 3172 resistance gene analogs (RGAs) (2062 nucleotide binding-site leucine-rich repeats (NLRs), 497 receptor-like protein kinases (RLKs) and 613 receptor-like proteins (RLPs)) were identified. CDRH clusters were also observed in Arabis alpina, Camelina sativa and Cardamine hirsuta with assigned chromosomes, consisting of 62 homogeneous (38 NLR, 17 RLK and 7 RLP clusters) and 10 heterogeneous RGA clusters. This study highlights the prevalence of CDRHs in the wild relatives of the Brassicaceae family, which may lay the foundation for rapid identification of functional genes and genomics-assisted breeding to develop improved disease-resistant Brassicaceae crop cultivars.
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9
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Direct recognition of pathogen effectors by plant NLR immune receptors and downstream signalling. Essays Biochem 2022; 66:471-483. [PMID: 35731245 PMCID: PMC9528080 DOI: 10.1042/ebc20210072] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022]
Abstract
Plants deploy extracellular and intracellular immune receptors to sense and restrict pathogen attacks. Rapidly evolving pathogen effectors play crucial roles in suppressing plant immunity but are also monitored by intracellular nucleotide-binding, leucine-rich repeat immune receptors (NLRs), leading to effector-triggered immunity (ETI). Here, we review how NLRs recognize effectors with a focus on direct interactions and summarize recent research findings on the signalling functions of NLRs. Coiled-coil (CC)-type NLR proteins execute immune responses by oligomerizing to form membrane-penetrating ion channels after effector recognition. Some CC-NLRs function in sensor-helper networks with the sensor NLR triggering oligomerization of the helper NLR. Toll/interleukin-1 receptor (TIR)-type NLR proteins possess catalytic activities that are activated upon effector recognition-induced oligomerization. Small molecules produced by TIR activity are detected by additional signalling partners of the EDS1 lipase-like family (enhanced disease susceptibility 1), leading to activation of helper NLRs that trigger the defense response.
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10
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Zhao Y, Zhu X, Chen X, Zhou JM. From plant immunity to crop disease resistance. J Genet Genomics 2022; 49:693-703. [PMID: 35728759 DOI: 10.1016/j.jgg.2022.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaobo Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu Sichuan 611130, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainai 572025, China.
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11
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Indirect recognition of pathogen effectors by NLRs. Essays Biochem 2022; 66:485-500. [PMID: 35535995 DOI: 10.1042/ebc20210097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
To perceive pathogen threats, plants utilize both plasma membrane-localized and intracellular receptors. Nucleotide-binding domain leucine-rich repeat containing (NLR) proteins are key receptors that can recognize pathogen-derived intracellularly delivered effectors and activate downstream defense. Exciting recent findings have propelled our understanding of the various recognition and activation mechanisms of plant NLRs. Some NLRs directly bind to effectors, but others can perceive effector-induced changes on targeted host proteins (guardees), or non-functional host protein mimics (decoys). Such guarding strategies are thought to afford the host more durable resistance to quick-evolving and diverse pathogens. Here, we review classic and recent examples of indirect effector recognition by NLRs and discuss strategies for the discovery and study of new NLR-decoy/guardee systems. We also provide a perspective on how executor NLRs and helper NLRs (hNLRs) provide recognition for a wider range of effectors through sensor NLRs and how this can be considered an expanded form of indirect recognition. Furthermore, we summarize recent structural findings on NLR activation and resistosome formation upon indirect recognition. Finally, we discuss existing and potential applications that harness NLR indirect recognition for plant disease resistance and crop resilience.
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12
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Lapin D, Johanndrees O, Wu Z, Li X, Parker JE. Molecular innovations in plant TIR-based immunity signaling. THE PLANT CELL 2022; 34:1479-1496. [PMID: 35143666 PMCID: PMC9153377 DOI: 10.1093/plcell/koac035] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 05/19/2023]
Abstract
A protein domain (Toll and Interleukin-1 receptor [TIR]-like) with homology to animal TIRs mediates immune signaling in prokaryotes and eukaryotes. Here, we present an overview of TIR evolution and the molecular versatility of TIR domains in different protein architectures for host protection against microbial attack. Plant TIR-based signaling emerges as being central to the potentiation and effectiveness of host defenses triggered by intracellular and cell-surface immune receptors. Equally relevant for plant fitness are mechanisms that limit potent TIR signaling in healthy tissues but maintain preparedness for infection. We propose that seed plants evolved a specialized protein module to selectively translate TIR enzymatic activities to defense outputs, overlaying a more general function of TIRs.
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Affiliation(s)
- Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht 3584 CH, The Netherlands
- Author for correspondence: (D.L.), (J.E.P.)
| | - Oliver Johanndrees
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Zhongshou Wu
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Labs and Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Duesseldorf 40225, Germany
- Author for correspondence: (D.L.), (J.E.P.)
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13
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Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:biology11030421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Simple Summary Plants, unlike animals, do not have defender cells or an adaptive immune system. Instead, plants rely on each cell’s innate immunity and systemic signals emitted from infection sites. On the other hand, not all plants, even within the same species, are genetically identical, and their genetic backgrounds determine how well they respond to stress factors. Through evolution, plants have acquired various defense mechanisms that play important roles in the never-ending fight between plants and pathogens. Genetic variation in relation to plant disease resistance can thus be contextualized to provide new insights into these defense mechanisms and evolutionary processes that lead to resistance to pathogens. By focusing on genetic variations and mutational events linked with plant–pathogen interactions, the paper explores how genome compartments facilitate plant and pathogen evolutionary processes. Abstract Phytopathologists are actively researching the molecular basis of plant–pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant–microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant–pathogen interactions and discusses how these genome compartments enhance plants’ and pathogens’ evolutionary processes.
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14
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Maruta N, Burdett H, Lim BYJ, Hu X, Desa S, Manik MK, Kobe B. Structural basis of NLR activation and innate immune signalling in plants. Immunogenetics 2022; 74:5-26. [PMID: 34981187 PMCID: PMC8813719 DOI: 10.1007/s00251-021-01242-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
Animals and plants have NLRs (nucleotide-binding leucine-rich repeat receptors) that recognize the presence of pathogens and initiate innate immune responses. In plants, there are three types of NLRs distinguished by their N-terminal domain: the CC (coiled-coil) domain NLRs, the TIR (Toll/interleukin-1 receptor) domain NLRs and the RPW8 (resistance to powdery mildew 8)-like coiled-coil domain NLRs. CC-NLRs (CNLs) and TIR-NLRs (TNLs) generally act as sensors of effectors secreted by pathogens, while RPW8-NLRs (RNLs) signal downstream of many sensor NLRs and are called helper NLRs. Recent studies have revealed three dimensional structures of a CNL (ZAR1) including its inactive, intermediate and active oligomeric state, as well as TNLs (RPP1 and ROQ1) in their active oligomeric states. Furthermore, accumulating evidence suggests that members of the family of lipase-like EDS1 (enhanced disease susceptibility 1) proteins, which are uniquely found in seed plants, play a key role in providing a link between sensor NLRs and helper NLRs during innate immune responses. Here, we summarize the implications of the plant NLR structures that provide insights into distinct mechanisms of action by the different sensor NLRs and discuss plant NLR-mediated innate immune signalling pathways involving the EDS1 family proteins and RNLs.
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Affiliation(s)
- Natsumi Maruta
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Hayden Burdett
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Bryan Y J Lim
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiahao Hu
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sneha Desa
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mohammad Kawsar Manik
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, 4072, Australia.
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15
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Xiao K, Zhu H, Zhu X, Liu Z, Wang Y, Pu W, Guan P, Hu J. Overexpression of PsoRPM3, an NBS-LRR gene isolated from myrobalan plum, confers resistance to Meloidogyne incognita in tobacco. PLANT MOLECULAR BIOLOGY 2021; 107:129-146. [PMID: 34596818 DOI: 10.1007/s11103-021-01185-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGES We reported an NBS-LRR gene, PsoRPM3, is highly expressed following RKN infection, initiating an HR response that promotes plant resistance. Meloidogyne spp. are root-knot nematodes (RKNs) that cause substantial economic losses worldwide. Screening for resistant tree resources and identifying plant resistance genes is currently the most effective way to prevent RKN infestations. Here, we cloned a novel TIR-NB-LRR-type resistance gene, PsoRPM3, from Xinjiang wild myrobalan plum (Prunus sogdiana Vassilcz.) and demonstrated that its protein product localized to the nucleus. In response to Meloidogyne incognita infection, PsoRPM3 gene expression levels were significantly higher in resistant myrobalan plum plants compared to susceptible plants. We investigated this difference, discovering that the - 309 to - 19 bp region of the susceptible PsoRPM3 promoter was highly methylated. Indeed, heterologous expression of PsoRPM3 significantly enhanced the resistance of susceptible tobacco plants to M. incognita. Moreover, transient expression of PsoRPM3 induced a hypersensitive response in tobacco, whereas RNAi-mediated silencing of PsoRPM3 in transgenic tobacco reduced this hypersensitive response. Several hypersensitive response marker genes were considerably up-regulated in resistant myrobalan plum plants when compared with susceptible counterparts inoculated with M. incognita. PsoPR1a (a SA marker gene), PsoPR2 (a JA marker gene), and PsoACS6 (an ET signaling marker gene) were all more highly expressed in resistant than in susceptible plants. Together, these results support a model in which PsoRPM3 is highly expressed following RKN infection, initiating an HR response that promotes plant resistance through activated salicylic acid, jasmonic acid, and ethylene signaling pathways.
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Affiliation(s)
- Kun Xiao
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Haifeng Zhu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Xiang Zhu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
- Institute of Laboratory Animal Science, Guizhou University of Traditional Chinese, Guiyang, China
| | - Zhenhua Liu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Yan Wang
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Wenjiang Pu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Pingyin Guan
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Jianfang Hu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China.
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16
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Bi G, Zhou JM. Regulation of Cell Death and Signaling by Pore-Forming Resistosomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:239-263. [PMID: 33957051 DOI: 10.1146/annurev-phyto-020620-095952] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) are the largest class of immune receptors in plants. They play a key role in the plant surveillance system by monitoring pathogen effectors that are delivered into the plant cell. Recent structural biology and biochemical analyses have uncovered how NLRs are activated to form oligomeric resistosomes upon the recognition of pathogen effectors. In the resistosome, the signaling domain of the NLR is brought to the center of a ringed structure to initiate immune signaling and regulated cell death (RCD). The N terminus of the coiled-coil (CC) domain of the NLR protein HOPZ-ACTIVATED RESISTANCE 1 likely forms a pore in the plasma membrane to trigger RCD in a way analogous to animal pore-forming proteins that trigger necroptosis or pyroptosis. NLRs that carry TOLL-INTERLEUKIN1-RECEPTOR as a signaling domain may also employ pore-forming resistosomes for RCD execution. In addition, increasing evidence supports intimate connections between NLRs and surface receptors in immune signaling. These new findings are rapidly advancing our understanding of the plant immune system.
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Affiliation(s)
- Guozhi Bi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Kahveci E, Devran Z, Özkaynak E, Hong Y, Studholme DJ, Tör M. Genomic-Assisted Marker Development Suitable for CsCvy-1 Selection in Cucumber Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:691576. [PMID: 34489994 PMCID: PMC8416629 DOI: 10.3389/fpls.2021.691576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 06/02/2023]
Abstract
Cucumber is a widely grown vegetable crop plant and a host to many different plant pathogens. Cucumber vein yellowing virus (CVYV) causes economic losses on cucumber crops in Mediterranean countries and in some part of India such as West Bengal and in African countries such as Sudan. CVYV is an RNA potyvirus transmitted mechanically and by whitefly (Bemisia tabaci) in a semipersistent manner. Control of this virus is heavily dependent on the management of the insect vector and breeding virus-resistant lines. DNA markers have been used widely in conventional plant breeding programs via marker-assisted selection (MAS). However, very few resistance sources against CVYV in cucumber exist, and also the lack of tightly linked molecular markers to these sources restricts the rapid generation of resistant lines. In this work, we used genomics coupled with the bulked segregant analysis method and generated the MAS-friendly Kompetitive allele specific PCR (KASP) markers suitable for CsCvy-1 selection in cucumber breeding using a segregating F2 mapping population and commercial plant lines. Variant analysis was performed to generate single-nucleotide polymorphism (SNP)-based markers for mapping the population and genotyping the commercial lines. We fine-mapped the region by generating new markers down to 101 kb with eight genes. We provided SNP data for this interval, which could be useful for breeding programs and cloning the candidate genes.
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Affiliation(s)
- Erdem Kahveci
- M.Y. Genetik Tarim Tek. Lab. Tic. Ltd. Sti., Antalya, Turkey
| | - Zübeyir Devran
- Department of Plant Protection, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - David J. Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mahmut Tör
- Department of Biology, School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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18
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Chang J, Liu X, Ren H, Lu S, Li M, Zhang S, Zhao K, Li H, Zhou X, Peng L, Liu Z, Hu P. Pseudomonas Exotoxin A-Based Immunotherapy Targeting CCK2R-Expressing Colorectal Malignancies: An In Vitro and In Vivo Evaluation. Mol Pharm 2021; 18:2285-2297. [PMID: 33998814 DOI: 10.1021/acs.molpharmaceut.1c00095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cholecystokinin-2 receptor (CCK2R) has been proven to be a specific biomarker for colorectal malignancies. Immunotoxins are a valuable class of immunotherapy agents consisting of a targeting element and a bacterial or plant toxin. Previous work demonstrated that targeting CCK2R is a good therapeutic strategy for the treatment of colorectal cancer (CRC). In the present study, we developed a new version of CCK2R-targeting immunotoxin GD9P using a targeted peptide, GD9, as the binding motif and a truncated Pseudomonas exotoxin A (PE38) as the cytokiller. BALB/c nude mice were treated with different doses of GD9P, and pharmacodynamics, pharmacokinetic, and toxicological data were obtained throughout this study. Compared to the parental immunotoxin rCCK8PE38, GD9P exhibited about 1.5-fold yield, higher fluorescence intensity, and increased antitumor activity against human CRC in vitro and in vivo. The IC50 values of GD9P in vitro ranged from 1.61 to 4.55 nM. Pharmacokinetic studies were conducted in mice with a T1/2 of 69.315 min. When tumor-bearing nude mice were treated with GD9P at doses ≥2 mg/kg for five doses, a rapid shrinkage in tumor volume and, in some cases, complete remission was observed. A preliminary safety evaluation demonstrated a good safety profile of GD9P as a Pseudomonas exotoxin A-based immunotherapy. The therapy in combination with oxaliplatin can increase the antitumor efficacy and reduce the toxic side effects caused by chemotherapy. In conclusion, the data support the use of GD9P as a promising immunotherapy targeting CCK2R-expressing colorectal malignancies.
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Affiliation(s)
- Jiang Chang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Xilin Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Honglin Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Shiying Lu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Meng Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Song Zhang
- Shenzhen Lifotronic Technology Co., Ltd., 1008 Songbai Road, Shenzhen 518055, China
| | - Ke Zhao
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Hanxiao Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Xiaoshi Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Lixiong Peng
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Zengshan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
| | - Pan Hu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis/College of Veterinary Medicine/Double-First Class Discipline of Human-Animal Medicine, China-Japan Union Hospital, Jilin University, Changchun 130062, China
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19
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Ordon J, Martin P, Erickson JL, Ferik F, Balcke G, Bonas U, Stuttmann J. Disentangling cause and consequence: genetic dissection of the DANGEROUS MIX2 risk locus, and activation of the DM2h NLR in autoimmunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1008-1023. [PMID: 33629456 DOI: 10.1111/tpj.15215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/07/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Nucleotide-binding domain-leucine-rich repeat-type immune receptors (NLRs) protect plants against pathogenic microbes through intracellular detection of effector proteins. However, this comes at a cost, as NLRs can also induce detrimental autoimmunity in genetic interactions with foreign alleles. This may occur when independently evolved genomes are combined in inter- or intraspecific crosses, or when foreign alleles are introduced by mutagenesis or transgenesis. Most autoimmunity-inducing NLRs are encoded within highly variable NLR gene clusters with no known immune functions, which were termed autoimmune risk loci. Whether risk NLRs differ from sensor NLRs operating in natural pathogen resistance and how risk NLRs are activated in autoimmunity is unknown. Here, we analyzed the DANGEROUS MIX2 risk locus, a major autoimmunity hotspot in Arabidopsis thaliana. By gene editing and heterologous expression, we show that a single gene, DM2h, is necessary and sufficient for autoimmune induction in three independent cases of autoimmunity in accession Landsberg erecta. We focus on autoimmunity provoked by an EDS1-yellow fluorescent protein (YFP)NLS fusion protein to characterize DM2h functionally and determine features of EDS1-YFPNLS activating the immune receptor. Our data suggest that risk NLRs function in a manner reminiscent of sensor NLRs, while autoimmunity-inducing properties of EDS1-YFPNLS in this context are unrelated to the protein's functions as an immune regulator. We propose that autoimmunity, at least in some cases, may be caused by spurious, stochastic interactions of foreign alleles with coincidentally matching risk NLRs.
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Affiliation(s)
- Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Patrick Martin
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jessica Lee Erickson
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Filiz Ferik
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Gerd Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
| | - Ulla Bonas
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
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20
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Kang H, Nguyen QM, Iswanto ABB, Hong JC, Bhattacharjee S, Gassmann W, Kim SH. Nuclear Localization of HopA1 Pss61 Is Required for Effector-Triggered Immunity. PLANTS 2021; 10:plants10050888. [PMID: 33924988 PMCID: PMC8145104 DOI: 10.3390/plants10050888] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/17/2021] [Accepted: 04/23/2021] [Indexed: 01/13/2023]
Abstract
Plant resistance proteins recognize cognate pathogen avirulence proteins (also named effectors) to implement the innate immune responses called effector-triggered immunity. Previously, we reported that hopA1 from Pseudomonas syringae pv. syringae strain 61 was identified as an avr gene for Arabidopsis thaliana. Using a forward genetic screen approach, we cloned a hopA1-specific TIR-NBS-LRR class disease resistance gene, RESISTANCE TO PSEUDOMONAS SYRINGAE6 (RPS6). Many resistance proteins indirectly recognize effectors, and RPS6 is thought to interact with HopA1Pss61 indirectly by surveillance of an effector target. However, the involved target protein is currently unknown. Here, we show RPS6 is the only R protein that recognizes HopA1Pss61 in Arabidopsis wild-type Col-0 accession. Both RPS6 and HopA1Pss61 are co-localized to the nucleus and cytoplasm. HopA1Pss61 is also distributed in plasma membrane and plasmodesmata. Interestingly, nuclear localization of HopA1Pss61 is required to induce cell death as NES-HopA1Pss61 suppresses the level of cell death in Nicotiana benthamiana. In addition, in planta expression of hopA1Pss61 led to defense responses, such as a dwarf morphology, a cell death response, inhibition of bacterial growth, and increased accumulation of defense marker proteins in transgenic Arabidopsis. Functional characterization of HopA1Pss61 and RPS6 will provide an important piece of the ETI puzzle.
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Affiliation(s)
- Hobin Kang
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea; (H.K.); (Q.-M.N.); (A.B.B.I.); (J.C.H.)
| | - Quang-Minh Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea; (H.K.); (Q.-M.N.); (A.B.B.I.); (J.C.H.)
| | - Arya Bagus Boedi Iswanto
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea; (H.K.); (Q.-M.N.); (A.B.B.I.); (J.C.H.)
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea; (H.K.); (Q.-M.N.); (A.B.B.I.); (J.C.H.)
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
| | - Saikat Bhattacharjee
- Laboratory of Signal Transduction and Plant Resistance, UNESCO—Regional Centre for Biotechnology (RCB), NCR—Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, India;
| | - Walter Gassmann
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA;
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea; (H.K.); (Q.-M.N.); (A.B.B.I.); (J.C.H.)
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
- Correspondence:
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21
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Baudin M, Martin EC, Sass C, Hassan JA, Bendix C, Sauceda R, Diplock N, Specht CD, Petrescu AJ, Lewis JD. A natural diversity screen in Arabidopsis thaliana reveals determinants for HopZ1a recognition in the ZAR1-ZED1 immune complex. PLANT, CELL & ENVIRONMENT 2021; 44:629-644. [PMID: 33103794 DOI: 10.1111/pce.13927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
Pathogen pressure on hosts can lead to the evolution of genes regulating the innate immune response. By characterizing naturally occurring polymorphisms in immune receptors, we can better understand the molecular determinants of pathogen recognition. ZAR1 is an ancient Arabidopsis thaliana NLR (Nucleotide-binding [NB] Leucine-rich-repeat [LRR] Receptor) that recognizes multiple secreted effector proteins from the pathogenic bacteria Pseudomonas syringae and Xanthomonas campestris through its interaction with receptor-like cytoplasmic kinases (RLCKs). ZAR1 was first identified for its role in recognizing P. syringae effector HopZ1a, through its interaction with the RLCK ZED1. To identify additional determinants of HopZ1a recognition, we performed a computational screen for ecotypes from the 1001 Genomes project that were likely to lack HopZ1a recognition, and tested ~300 ecotypes. We identified ecotypes containing polymorphisms in ZAR1 and ZED1. Using our previously established Nicotiana benthamiana transient assay and Arabidopsis ecotypes, we tested for the effect of naturally occurring polymorphisms on ZAR1 interactions and the immune response. We identified key residues in the NB or LRR domain of ZAR1 that impact the interaction with ZED1. We demonstrate that natural diversity combined with functional assays can help define the molecular determinants and interactions necessary to regulate immune induction in response to pathogens.
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Affiliation(s)
- Maël Baudin
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Eliza C Martin
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Chodon Sass
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Jana A Hassan
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Claire Bendix
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Rolin Sauceda
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Nathan Diplock
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Chelsea D Specht
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, New York, USA
| | - Andrei J Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Jennifer D Lewis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
- Plant Gene Expression Center, United States Department of Agriculture, Albany, California, USA
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22
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Wan WL, Kim ST, Castel B, Charoennit N, Chae E. Genetics of autoimmunity in plants: an evolutionary genetics perspective. THE NEW PHYTOLOGIST 2021; 229:1215-1233. [PMID: 32970825 DOI: 10.1111/nph.16947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 05/14/2023]
Abstract
Autoimmunity in plants has been found in numerous hybrids as a form of hybrid necrosis and mutant panels. Uncontrolled cell death is a main cellular outcome of autoimmunity, which negatively impacts growth. Its occurrence highlights the vulnerable nature of the plant immune system. Genetic investigation of autoimmunity in hybrid plants revealed that extreme variation in the immune receptor repertoire is a major contributor, reflecting an evolutionary conundrum that plants face in nature. In this review, we discuss natural variation in the plant immune system and its contribution to fitness. The value of autoimmunity genetics lies in its ability to identify combinations of a natural immune receptor and its partner that are predisposed to triggering autoimmunity. The network of immune components for autoimmunity becomes instrumental in revealing mechanistic details of how immune receptors recognize cellular invasion and activate signaling. The list of autoimmunity-risk variants also allows us to infer evolutionary processes contributing to their maintenance in the natural population. Our approach to autoimmunity, which integrates mechanistic understanding and evolutionary genetics, has the potential to serve as a prognosis tool to optimize immunity in crops.
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Affiliation(s)
- Wei-Lin Wan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Sang-Tae Kim
- Department of Life Sciences, The Catholic University of Korea, Bucheon, Gyeonggi-do, 14662, South Korea
| | - Baptiste Castel
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Nuri Charoennit
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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23
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Barragan AC, Collenberg M, Wang J, Lee RRQ, Cher WY, Rabanal FA, Ashkenazy H, Weigel D, Chae E. A Truncated Singleton NLR Causes Hybrid Necrosis in Arabidopsis thaliana. Mol Biol Evol 2021; 38:557-574. [PMID: 32966577 PMCID: PMC7826191 DOI: 10.1093/molbev/msaa245] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies 3 weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation of most NLR (nucleotide-binding site leucine-rich repeat) disease-resistance genes. This is due to an incompatible interaction between the singleton TIR-NLR gene DANGEROUS MIX 10 (DM10), which was recently relocated from a larger NLR cluster, and an unlinked locus, DANGEROUS MIX 11 (DM11). There are multiple DM10 allelic variants in the global A. thaliana population, several of which have premature stop codons. One of these, which has a truncated LRR-PL (leucine-rich repeat [LRR]-post-LRR) region, corresponds to the DM10 risk allele. The DM10 locus and the adjacent genomic region in the risk allele carriers are highly differentiated from those in the nonrisk carriers in the global A. thaliana population, suggesting that this allele became geographically widespread only relatively recently. The DM11 risk allele is much rarer and found only in two accessions from southwestern Spain-a region from which the DM10 risk haplotype is absent-indicating that the ranges of DM10 and DM11 risk alleles may be nonoverlapping.
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Affiliation(s)
- Ana Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jinge Wang
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Rachelle R Q Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Wei Yuan Cher
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Fernando A Rabanal
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Haim Ashkenazy
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Department of Biological Sciences, National University of Singapore, Singapore
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24
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Ma S, Lapin D, Liu L, Sun Y, Song W, Zhang X, Logemann E, Yu D, Wang J, Jirschitzka J, Han Z, Schulze-Lefert P, Parker JE, Chai J. Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme. Science 2021; 370:370/6521/eabe3069. [PMID: 33273071 DOI: 10.1126/science.abe3069] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The Hyaloperonospora arabidopsidis effector ATR1 activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of Arabidopsis NLR RPP1. We report a cryo-electron microscopy structure of RPP1 bound by ATR1. The structure reveals a C-terminal jelly roll/Ig-like domain (C-JID) for specific ATR1 recognition. Biochemical and functional analyses show that ATR1 binds to the C-JID and the LRRs to induce an RPP1 tetrameric assembly required for nicotinamide adenine dinucleotide hydrolase (NADase) activity. RPP1 tetramerization creates two potential active sites, each formed by an asymmetric TIR homodimer. Our data define the mechanism of direct effector recognition by a plant NLR leading to formation of a signaling-active holoenzyme.
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Affiliation(s)
- Shoucai Ma
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Dmitry Lapin
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Li Liu
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Yue Sun
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Wen Song
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Xiaoxiao Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Elke Logemann
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Dongli Yu
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Jia Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jan Jirschitzka
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Zhifu Han
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. .,Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. .,Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Jijie Chai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, Centre for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. .,Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany.,Cluster of Excellence in Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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25
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Li L, Habring A, Wang K, Weigel D. Atypical Resistance Protein RPW8/HR Triggers Oligomerization of the NLR Immune Receptor RPP7 and Autoimmunity. Cell Host Microbe 2020; 27:405-417.e6. [PMID: 32101702 DOI: 10.1016/j.chom.2020.01.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/30/2019] [Accepted: 01/17/2020] [Indexed: 01/08/2023]
Abstract
In certain plant hybrids, immunity signaling is initiated when immune components interact in the absence of a pathogen trigger. In Arabidopsis thaliana, such autoimmunity and cell death are linked to variants of the NLR RPP7 and the RPW8 proteins involved in broad-spectrum resistance. We uncover the molecular basis for this autoimmunity and demonstrate that a homolog of RPW8, HR4Fei-0, can trigger the assembly of a higher-order RPP7 complex, with autoimmunity signaling as a consequence. HR4Fei-0-mediated RPP7 oligomerization occurs via the RPP7 C-terminal leucine-rich repeat (LRR) domain and ATP-binding P-loop. RPP7 forms a higher-order complex only in the presence of HR4Fei-0 and not with the standard HR4 variant, which is distinguished from HR4Fei-0 by length variation in C-terminal repeats. Additionally, HR4Fei-0 can independently form self-oligomers, which directly kill cells in an RPP7-independent manner. Our work provides evidence for a plant resistosome complex and the mechanisms by which RPW8/HR proteins trigger cell death.
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Affiliation(s)
- Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Anette Habring
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Kai Wang
- Department of Cell Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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26
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Herlihy J, Ludwig NR, van den Ackerveken G, McDowell JM. Oomycetes Used in Arabidopsis Research. THE ARABIDOPSIS BOOK 2019; 17:e0188. [PMID: 33149730 PMCID: PMC7592078 DOI: 10.1199/tab.0188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Arabidopsis plants in their natural environment are susceptible to infection by oomycete pathogens, in particular to downy mildew and white rust diseases. These naturally occurring infectious agents have imposed evolutionary pressures on Arabidopsis populations and are therefore highly relevant for the study of host-pathogen co-evolution. In addition, the study of oomycete diseases, including infections caused by several Phytophthora species, has led to many scientific discoveries on Arabidopsis immunity and disease. Herein, we describe the major oomycete species used for experiments on Arabidopsis, and how these pathosystems have been used to provide significant insights into mechanistic and evolutionary aspects of plant-oomycete interactions. We also highlight understudied aspects of plant-oomycete interactions, as well as translational approaches, that can be productively addressed using the reference pathosystems described in this article.
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Affiliation(s)
- John Herlihy
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Nora R. Ludwig
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Guido van den Ackerveken
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - John M. McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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27
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Engqvist MKM, Rabe KS. Applications of Protein Engineering and Directed Evolution in Plant Research. PLANT PHYSIOLOGY 2019; 179:907-917. [PMID: 30626612 PMCID: PMC6393796 DOI: 10.1104/pp.18.01534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/25/2018] [Indexed: 05/06/2023]
Abstract
Engineered proteins can be used to optimize desired traits in plants; even though recent advances have resulted in new application areas, certain methodological challenges remain.
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Affiliation(s)
- Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Division of Systems and Synthetic Biology, Gothenburg, Sweden
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Group for Molecular Evolution, Karlsruhe, Germany
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28
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Zhang Y, Zhang Q, Hao L, Wang S, Wang S, Zhang W, Xu C, Yu Y, Li T. A novel miRNA negatively regulates resistance to Glomerella leaf spot by suppressing expression of an NBS gene in apple. HORTICULTURE RESEARCH 2019; 6:93. [PMID: 31645951 PMCID: PMC6804642 DOI: 10.1038/s41438-019-0175-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 06/15/2019] [Indexed: 05/07/2023]
Abstract
Glomerella leaf spot (GLS) of apple (Malus×domestica Borkh.), caused by Glomerella cingulata, is an emerging fungal epidemic threatening the apple industry. Little is known about the molecular mechanism underlying resistance to this devastating fungus. In this study, high-throughput sequencing technology was used to identify microRNAs (miRNAs) involved in GLS resistance in apple. We focused on miRNAs that target genes related to disease and found that expression of a novel miRNA, Md-miRln20, was higher in susceptible apple varieties than in resistant ones. Furthermore, its target gene Md-TN1-GLS exhibited the opposite expression pattern, which suggested that the expression levels of Md-miRln20 and its target gene are closely related to apple resistance to GLS. Furthermore, downregulation of Md-miRln20 in susceptible apple leaves resulted in upregulation of Md-TN1-GLS and reduced the disease incidence. Conversely, overexpression of Md-miRln20 in resistant apple leaves suppressed Md-TN1-GLS expression, with increased disease incidence. We demonstrated that Md-miRln20 negatively regulates resistance to GLS by suppressing Md-TN1-GLS expression and showed, for the first time, a crucial role for miRNA in response to GLS in apple.
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Affiliation(s)
- Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Wenna Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Chaoran Xu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Yunfei Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
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29
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Qi T, Seong K, Thomazella DPT, Kim JR, Pham J, Seo E, Cho MJ, Schultink A, Staskawicz BJ. NRG1 functions downstream of EDS1 to regulate TIR-NLR-mediated plant immunity in Nicotiana benthamiana. Proc Natl Acad Sci U S A 2018; 115:E10979-E10987. [PMID: 30373842 PMCID: PMC6243234 DOI: 10.1073/pnas.1814856115] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Effector-triggered immunity (ETI) in plants involves a large family of nucleotide-binding leucine-rich repeat (NLR) immune receptors, including Toll/IL-1 receptor-NLRs (TNLs) and coiled-coil NLRs (CNLs). Although various NLR immune receptors are known, a mechanistic understanding of NLR function in ETI remains unclear. The TNL Recognition of XopQ 1 (Roq1) recognizes the effectors XopQ and HopQ1 from Xanthomonas and Pseudomonas, respectively, which activates resistance to Xanthomonas euvesicatoria and Xanthomonas gardneri in an Enhanced Disease Susceptibility 1 (EDS1)-dependent way in Nicotiana benthamiana In this study, we found that the N. benthamiana N requirement gene 1 (NRG1), a CNL protein required for the tobacco TNL protein N-mediated resistance to tobacco mosaic virus, is also essential for immune signaling [including hypersensitive response (HR)] triggered by the TNLs Roq1 and Recognition of Peronospora parasitica 1 (RPP1), but not by the CNLs Bs2 and Rps2, suggesting that NRG1 may be a conserved key component in TNL signaling pathways. Besides EDS1, Roq1 and NRG1 are necessary for resistance to Xanthomonas and Pseudomonas in N. benthamiana NRG1 functions downstream of Roq1 and EDS1 and physically associates with EDS1 in mediating XopQ-Roq1-triggered immunity. Moreover, RNA sequencing analysis showed that XopQ-triggered gene-expression profile changes in N. benthamiana were almost entirely mediated by Roq1 and EDS1 and were largely regulated by NRG1. Overall, our study demonstrates that NRG1 is a key component that acts downstream of EDS1 to mediate various TNL signaling pathways, including Roq1 and RPP1-mediated HR, resistance to Xanthomonas and Pseudomonas, and XopQ-regulated transcriptional changes in N. benthamiana.
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Affiliation(s)
- Tiancong Qi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120
| | - Daniela P T Thomazella
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120
| | - Joonyoung Ryan Kim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120
| | - Julie Pham
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | - Eunyoung Seo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | - Alex Schultink
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3120;
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
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30
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De la Concepcion JC, Franceschetti M, Maqbool A, Saitoh H, Terauchi R, Kamoun S, Banfield MJ. Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. NATURE PLANTS 2018; 4:576-585. [PMID: 29988155 DOI: 10.1038/s41477-018-0194-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Accelerated adaptive evolution is a hallmark of plant-pathogen interactions. Plant intracellular immune receptors (NLRs) often occur as allelic series with differential pathogen specificities. The determinants of this specificity remain largely unknown. Here, we unravelled the biophysical and structural basis of expanded specificity in the allelic rice NLR Pik, which responds to the effector AVR-Pik from the rice blast pathogen Magnaporthe oryzae. Rice plants expressing the Pikm allele resist infection by blast strains expressing any of three AVR-Pik effector variants, whereas those expressing Pikp only respond to one. Unlike Pikp, the integrated heavy metal-associated (HMA) domain of Pikm binds with high affinity to each of the three recognized effector variants, and variation at binding interfaces between effectors and Pikp-HMA or Pikm-HMA domains encodes specificity. By understanding how co-evolution has shaped the response profile of an allelic NLR, we highlight how natural selection drove the emergence of new receptor specificities. This work has implications for the engineering of NLRs with improved utility in agriculture.
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Affiliation(s)
| | - Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Abbas Maqbool
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Hiromasa Saitoh
- Laboratory of Plant Symbiotic and Parasitic Microbes, Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK.
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31
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Zhang Q, Ma C, Zhang Y, Gu Z, Li W, Duan X, Wang S, Hao L, Wang Y, Wang S, Li T. A Single-Nucleotide Polymorphism in the Promoter of a Hairpin RNA Contributes to Alternaria alternata Leaf Spot Resistance in Apple ( Malus × domestica). THE PLANT CELL 2018; 30:1924-1942. [PMID: 30065047 PMCID: PMC6139694 DOI: 10.1105/tpc.18.00042] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/11/2018] [Accepted: 07/26/2018] [Indexed: 05/04/2023]
Abstract
Apple leaf spot caused by the Alternaria alternata f. sp mali (ALT1) fungus is one of the most devastating diseases of apple (Malus × domestica). We identified a hairpin RNA (hpRNA) named MdhpRNA277 that produces small RNAs and is induced by ALT1 infection in 'Golden Delicious' apple. MdhpRNA277 produces mdm-siR277-1 and mdm-siR277-2, which target five resistance (R) genes that are expressed at high levels in resistant apple variety 'Hanfu' and at low levels in susceptible variety 'Golden Delicious' following ALT1 infection. MdhpRNA277 was strongly induced in 'Golden Delicious' but not 'Hanfu' following ALT1 inoculation. MdhpRNA277 promoter activity was much stronger in inoculated 'Golden Delicious' versus 'Hanfu'. We identified a single-nucleotide polymorphism (SNP) in the MdhpRNA277 promoter region between 'Golden Delicious' (pMdhpRNA277-GD) and 'Hanfu' (pMdhpRNA277-HF). The transcription factor MdWHy binds to pMdhpRNA277-GD, but not to pMdhpRNA277-HF Transgenic 'GL-3' apple expressing pMdhpRNA277-GD:MdhpRNA277 was more susceptible to ALT1 infection than plants expressing pMdhpRNA277-HF:MdhpRNA277 due to induced mdm-siR277 accumulation and reduced expression of the five target R genes. We confirmed that the SNP in pMdhpRNA277 is associated with A. alternata leaf spot resistance by crossing. This SNP could be used as a marker to distinguish between apple varieties that are resistant or susceptible to A. alternata leaf spot.
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Affiliation(s)
- Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chao Ma
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yi Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhaoyu Gu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Wei Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuwei Duan
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yuanhua Wang
- Jiangsu Polytechnic College of Agriculture and Forestry, Zhenjiang, Jiangsu 212400, China
| | - Shengyuan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
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32
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Atanasov KE, Liu C, Erban A, Kopka J, Parker JE, Alcázar R. NLR Mutations Suppressing Immune Hybrid Incompatibility and Their Effects on Disease Resistance. PLANT PHYSIOLOGY 2018; 177:1152-1169. [PMID: 29794019 PMCID: PMC6052992 DOI: 10.1104/pp.18.00462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/15/2018] [Indexed: 05/12/2023]
Abstract
Genetic divergence between populations can lead to reproductive isolation. Hybrid incompatibilities (HI) represent intermediate points along a continuum toward speciation. In plants, genetic variation in disease resistance (R) genes underlies several cases of HI. The progeny of a cross between Arabidopsis (Arabidopsis thaliana) accessions Landsberg erecta (Ler, Poland) and Kashmir2 (Kas2, central Asia) exhibits immune-related HI. This incompatibility is due to a genetic interaction between a cluster of eight TNL (TOLL/INTERLEUKIN1 RECEPTOR-NUCLEOTIDE BINDING-LEU RICH REPEAT) RPP1 (RECOGNITION OF PERONOSPORA PARASITICA1)-like genes (R1-R8) from Ler and central Asian alleles of a Strubbelig-family receptor-like kinase (SRF3) from Kas2. In characterizing mutants altered in Ler/Kas2 HI, we mapped multiple mutations to the RPP1-like Ler locus. Analysis of these suppressor of Ler/Kas2 incompatibility (sulki) mutants reveals complex, additive and epistatic interactions underlying RPP1-like Ler locus activity. The effects of these mutations were measured on basal defense, global gene expression, primary metabolism, and disease resistance to a local Hyaloperonospora arabidopsidis isolate (Hpa Gw) collected from Gorzów (Gw), where the Landsberg accession originated. Gene expression sectors and metabolic hallmarks identified for HI are both dependent and independent of RPP1-like Ler members. We establish that mutations suppressing immune-related Ler/Kas2 HI do not compromise resistance to Hpa Gw. QTL mapping analysis of Hpa Gw resistance point to RPP7 as the causal locus. This work provides insight into the complex genetic architecture of the RPP1-like Ler locus and immune-related HI in Arabidopsis and into the contributions of RPP1-like genes to HI and defense.
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Affiliation(s)
- Kostadin E Atanasov
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Changxin Liu
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
| | - Alexander Erban
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Rubén Alcázar
- Department of Biology, Healthcare and Environment, Section of Plant Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08028 Barcelona, Spain
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33
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Ma LS, Pellegrin C, Kahmann R. Repeat-containing effectors of filamentous pathogens and symbionts. Curr Opin Microbiol 2018; 46:123-130. [PMID: 29929732 DOI: 10.1016/j.mib.2018.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 11/26/2022]
Abstract
Pathogenic and symbiotic filamentous microbes secrete effectors which suppress host immune responses and promote a successful colonization. Pathogen effectors are engaged in the arms race with their hosts and because of this they are subject to intense evolutionary pressure. Effectors particularly prone to rapid evolution display repeat-containing domains which can easily expand or contract and accumulate point mutations without altering their original function. In this review we address the diversity of function in such repeat-containing effectors, focus on new findings and point out avenues for future work.
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34
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Funk A, Galewski P, McGrath JM. Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:659-671. [PMID: 29797366 DOI: 10.1111/tpj.13977] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/19/2018] [Accepted: 05/04/2018] [Indexed: 05/28/2023]
Abstract
Nucleotide-binding (NB-ARC), leucine-rich-repeat genes (NLRs) account for 60.8% of resistance (R) genes molecularly characterized from plants. NLRs exist as large gene families prone to tandem duplication and transposition, with high sequence diversity among crops and their wild relatives. This diversity can be a source of new disease resistance, but difficulty in distinguishing specific sequences from homologous gene family members hinders characterization of resistance for improving crop varieties. Current genome sequencing and assembly technologies, especially those using long-read sequencing, are improving resolution of repeat-rich genomic regions and clarifying locations of duplicated genes, such as NLRs. Using the conserved NB-ARC domain as a model, 231 tentative NB-ARC loci were identified in a highly contiguous genome assembly of sugar beet, revealing diverged and truncated NB-ARC signatures as well as full-length sequences. The NB-ARC-associated proteins contained NLR resistance gene domains, including TIR, CC and LRR, as well as other integrated domains. Phylogenetic relationships of partial and complete domains were determined, and patterns of physical clustering in the genome were evaluated. Comparison of sugar beet NB-ARC domains to validated R-genes from monocots and eudicots suggested extensive Beta vulgaris-specific subfamily expansions. The NLR landscape in the rhizomania resistance conferring Rz region of Chromosome 3 was characterized, identifying 26 NLR-like sequences spanning 20 MB. This work presents the first detailed view of NLR family composition in a member of the Caryophyllales, builds a foundation for additional disease resistance work in B. vulgaris, and demonstrates an additional nucleic-acid-based method for NLR prediction in non-model plant species.
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Affiliation(s)
- Andrew Funk
- Department of Plant, Soil, and Microbial Science, Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Paul Galewski
- Department of Plant, Soil, and Microbial Science, Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI, 48824, USA
| | - J Mitchell McGrath
- USDA-ARS, Sugarbeet and Bean Research Unit, 1066 Bogue Street, 494 PSSB, East Lansing, MI, 48824, USA
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Woods-Tör A, Studholme DJ, Cevik V, Telli O, Holub EB, Tör M. A Suppressor/Avirulence Gene Combination in Hyaloperonospora arabidopsidis Determines Race Specificity in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:265. [PMID: 29545818 PMCID: PMC5838922 DOI: 10.3389/fpls.2018.00265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/14/2018] [Indexed: 05/23/2023]
Abstract
The pathosystem of Arabidopsis thaliana and diploid biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) has been a model for investigating the molecular basis of Flor's gene-for-gene hypothesis. The isolates Hpa-Noks1 and Hpa-Cala2 are virulent on Arabidopsis accession RMX-A02 whilst an F1 generated from a cross between these two isolates was avirulent. The F2 progeny segregated 3,1 (avirulent, virulent), indicating a single major effect AVR locus in this pathogen. SNP-based linkage mapping confirmed a single AVR locus within a 14 kb map interval containing two genes encoding putative effectors. The Hpa-Cala2 allele of one gene, designated H. arabidopsidiscryptic1 (HAC1), encodes a protein with a signal peptide and an RxLR/dEER motif, and triggers a defense response in RMX-A02. The second gene is heterozygous in Hpa-Cala2. One allele, designated Suppressor ofHAC1Cala2 (S-HAC1Cala2 ) encodes a protein with a signal peptide and a dKEE motif with no RxLR motif; the other allele (s-hac1Cala2 ) encodes a protein with a signal peptide, a dEEE motif and is divergent in sequence from the S-HAC1Cala2 allele. In selfed progeny from Hpa-Cala2, dominant S-HAC1Cala2 allele carrying progeny correlates with virulence in RMX-A02, whereas homozygous recessive s-hac1Cala2 carrying progeny were avirulent. Genetic investigations suggested other heterozygous suppressor loci might exist in the Hpa-Cala2 genome.
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Affiliation(s)
- Alison Woods-Tör
- Institute of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - David J. Studholme
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Volkan Cevik
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Osman Telli
- Institute of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Eric B. Holub
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Mahmut Tör
- Institute of Science and the Environment, University of Worcester, Worcester, United Kingdom
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Kourelis J, van der Hoorn RAL. Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function. THE PLANT CELL 2018; 30:285-299. [PMID: 29382771 PMCID: PMC5868693 DOI: 10.1105/tpc.17.00579] [Citation(s) in RCA: 433] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/14/2017] [Accepted: 01/29/2018] [Indexed: 05/18/2023]
Abstract
Plants have many, highly variable resistance (R) gene loci, which provide resistance to a variety of pathogens. The first R gene to be cloned, maize (Zea mays) Hm1, was published over 25 years ago, and since then, many different R genes have been identified and isolated. The encoded proteins have provided clues to the diverse molecular mechanisms underlying immunity. Here, we present a meta-analysis of 314 cloned R genes. The majority of R genes encode cell surface or intracellular receptors, and we distinguish nine molecular mechanisms by which R proteins can elevate or trigger disease resistance: direct (1) or indirect (2) perception of pathogen-derived molecules on the cell surface by receptor-like proteins and receptor-like kinases; direct (3) or indirect (4) intracellular detection of pathogen-derived molecules by nucleotide binding, leucine-rich repeat receptors, or detection through integrated domains (5); perception of transcription activator-like effectors through activation of executor genes (6); and active (7), passive (8), or host reprogramming-mediated (9) loss of susceptibility. Although the molecular mechanisms underlying the functions of R genes are only understood for a small proportion of known R genes, a clearer understanding of mechanisms is emerging and will be crucial for rational engineering and deployment of novel R genes.
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Affiliation(s)
- Jiorgos Kourelis
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
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Zhu X, Xiao K, Cui H, Hu J. Overexpression of the Prunus sogdiana NBS-LRR Subgroup Gene PsoRPM2 Promotes Resistance to the Root-Knot Nematode Meloidogyne incognita in Tobacco. Front Microbiol 2017; 8:2113. [PMID: 29163405 PMCID: PMC5671597 DOI: 10.3389/fmicb.2017.02113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/17/2017] [Indexed: 12/12/2022] Open
Abstract
Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are the most devastating soil-borne pathogens that significantly affect the production of Prunus spp. fruit. RKN infection is difficult to control and consequently causes massive yield losses each year. However, several germplasms of wild Prunus spp. have been shown to display resistance to M. incognita. Consequently, both the isolation of novel plant resistance (R) genes and the characterization of their resistance mechanisms are important strategies for future disease control. R proteins require the co-chaperone protein HSP90-SGT1-RAR1 to achieve correct folding, maturation, and stabilization. Here, we used homologous cloning to isolate the R gene PsoRPM2 from the RKN-resistant species Prunus sogdiana. PsoRPM2 was found to encode a TIR-NB-LRR-type protein and react with significantly elevated PsoRPM2 expression levels in response to RKN infection. Transient expression assays indicated PsoRPM2 to be located in both the cytoplasm and the nucleus. Four transgenic tobacco lines that heterologously expressed PsoRPM2 showed enhanced resistance to M. incognita. Yeast two-hybrid analysis and bimolecular fluorescence complementation analysis demonstrated that both PsoRAR1 and PsoRPM2 interacted with PsoHSP90-1 and PsoSGT1, but not with one another. These results indicate that the observed PsoRPM2-mediated RKN resistance requires both PsoHSP90-1 and PsoSGT1, further suggesting that PsoRAR1 plays a functionally redundant role in the HSP90-SGT1-RAR1 co-chaperone.
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Affiliation(s)
| | | | | | - Jianfang Hu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
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38
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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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Rodriguez-Moreno L, Song Y, Thomma BP. Transfer and engineering of immune receptors to improve recognition capacities in crops. CURRENT OPINION IN PLANT BIOLOGY 2017; 38:42-49. [PMID: 28472757 DOI: 10.1016/j.pbi.2017.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 05/23/2023]
Abstract
Immune receptors are pivotal elements of the plant immune system that act as sentinels for microbial invasion. Knowingly or unknowingly, breeding for resistance has largely relied on the transfer of immune receptor recognition specificities between plant genotypes. For decades such transfers were limited to crossable species. However, advents in transgene technologies have allowed overcoming species barriers. Novel strategies for mining of recognition specificities, combined with our recently increased understanding of immune receptor functioning, allows to increase and alter recognition specificities, which should ultimately increase the spectrum of recognition specificities that are available to control plant diseases in crops.
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Affiliation(s)
- Luis Rodriguez-Moreno
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Yin Song
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart Phj Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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40
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Petit-Houdenot Y, Fudal I. Complex Interactions between Fungal Avirulence Genes and Their Corresponding Plant Resistance Genes and Consequences for Disease Resistance Management. FRONTIERS IN PLANT SCIENCE 2017; 8:1072. [PMID: 28670324 PMCID: PMC5472840 DOI: 10.3389/fpls.2017.01072] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/02/2017] [Indexed: 05/07/2023]
Abstract
During infection, pathogens secrete an arsenal of molecules, collectively called effectors, key elements of pathogenesis which modulate innate immunity of the plant and facilitate infection. Some of these effectors can be recognized directly or indirectly by resistance (R) proteins from the plant and are then called avirulence (AVR) proteins. This recognition usually triggers defense responses including the hypersensitive response and results in resistance of the plant. R-AVR gene interactions are frequently exploited in the field to control diseases. Recently, the availability of fungal genomes has accelerated the identification of AVR genes in plant pathogenic fungi, including in fungi infecting agronomically important crops. While single AVR genes recognized by their corresponding R gene were identified, more and more complex interactions between AVR and R genes are reported (e.g., AVR genes recognized by several R genes, R genes recognizing several AVR genes in distinct organisms, one AVR gene suppressing recognition of another AVR gene by its corresponding R gene, two cooperating R genes both necessary to recognize an AVR gene). These complex interactions were particularly reported in pathosystems showing a long co-evolution with their host plant but could also result from the way agronomic crops were obtained and improved (e.g., through interspecific hybridization or introgression of resistance genes from wild related species into cultivated crops). In this review, we describe some complex R-AVR interactions between plants and fungi that were recently reported and discuss their implications for AVR gene evolution and R gene management.
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Affiliation(s)
- Yohann Petit-Houdenot
- UMR BIOGER, Institut National De La Recherche Agronomique, AgroParisTech, Université Paris SaclayThiverval-Grignon, France
| | - Isabelle Fudal
- UMR BIOGER, Institut National De La Recherche Agronomique, AgroParisTech, Université Paris SaclayThiverval-Grignon, France
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41
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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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Ortiz D, de Guillen K, Cesari S, Chalvon V, Gracy J, Padilla A, Kroj T. Recognition of the Magnaporthe oryzae Effector AVR-Pia by the Decoy Domain of the Rice NLR Immune Receptor RGA5. THE PLANT CELL 2017; 29:156-168. [PMID: 28087830 PMCID: PMC5304345 DOI: 10.1105/tpc.16.00435] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/09/2016] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
Nucleotide binding domain and leucine-rich repeat proteins (NLRs) are important receptors in plant immunity that allow recognition of pathogen effectors. The rice (Oryza sativa) NLR RGA5 recognizes the Magnaporthe oryzae effector AVR-Pia through direct interaction. Here, we gained detailed insights into the molecular and structural bases of AVR-Pia-RGA5 interaction and the role of the RATX1 decoy domain of RGA5. NMR titration combined with in vitro and in vivo protein-protein interaction analyses identified the AVR-Pia interaction surface that binds to the RATX1 domain. Structure-informed AVR-Pia mutants showed that, although AVR-Pia associates with additional sites in RGA5, binding to the RATX1 domain is necessary for pathogen recognition but can be of moderate affinity. Therefore, RGA5-mediated resistance is highly resilient to mutations in the effector. We propose a model that explains such robust effector recognition as a consequence, and an advantage, of the combination of integrated decoy domains with additional independent effector-NLR interactions.
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Affiliation(s)
- Diana Ortiz
- INRA, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, 34398 Montpellier, France
| | - Karine de Guillen
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, 34090 Montpellier, France
| | - Stella Cesari
- INRA, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, 34398 Montpellier, France
- CSIRO Agriculture Flagship, Canberra ACT 2601, Australia
| | - Véronique Chalvon
- INRA, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, 34398 Montpellier, France
| | - Jérome Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, 34090 Montpellier, France
| | - André Padilla
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, 34090 Montpellier, France
| | - Thomas Kroj
- INRA, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, 34398 Montpellier, France
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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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Choi K, Reinhard C, Serra H, Ziolkowski PA, Underwood CJ, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP, Henderson IR. Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet 2016; 12:e1006179. [PMID: 27415776 PMCID: PMC4945094 DOI: 10.1371/journal.pgen.1006179] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/15/2016] [Indexed: 12/31/2022] Open
Abstract
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Carsten Reinhard
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Charles J. Underwood
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Xiaohui Zhao
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Thomas J. Hardcastle
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Griffin
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Jackson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles, France
| | - Gil McVean
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ian R. Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
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45
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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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Goritschnig S, Steinbrenner AD, Grunwald DJ, Staskawicz BJ. Structurally distinct Arabidopsis thaliana NLR immune receptors recognize tandem WY domains of an oomycete effector. THE NEW PHYTOLOGIST 2016; 210:984-96. [PMID: 26725254 DOI: 10.1111/nph.13823] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/18/2015] [Indexed: 05/27/2023]
Abstract
Nucleotide-binding leucine-rich repeat (NB-LRR, or NLR) receptors mediate pathogen recognition. The Arabidopsis thaliana NLR RPP1 recognizes the tandem WY-domain effector ATR1 from the oomycete Hyaloperonospora arabidopsidis through direct association with C-terminal LRRs. We isolated and characterized homologous NLR genes RPP1-EstA and RPP1-ZdrA from two Arabidopsis ecotypes, Estland (Est-1) and Zdarec (Zdr-1), responsible for recognizing a novel spectrum of ATR1 alleles. RPP1-EstA and -ZdrA encode nearly identical NLRs that are phylogenetically distinct from known immunity-activating RPP1 homologs and possess greatly expanded LRR domains. Site-directed mutagenesis and truncation analysis of ATR1 suggests that these homologs recognize a novel surface of the 2(nd) WY domain of ATR1, partially specified by a C-terminal region of the LRR domain. Synteny comparison with RPP1 loci involved in hybrid incompatibility suggests that these functions evolved independently. Closely related RPP1 homologs have diversified their recognition spectra through LRR expansion and sequence variation, allowing them to detect multiple surfaces of the same pathogen effector. Engineering NLR receptor specificity may require a similar combination of repeat expansion and tailored amino acid variation.
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Affiliation(s)
- Sandra Goritschnig
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Adam D Steinbrenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Derrick J Grunwald
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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Wang K, Remigi P, Anisimova M, Lonjon F, Kars I, Kajava A, Li CH, Cheng CP, Vailleau F, Genin S, Peeters N. Functional assignment to positively selected sites in the core type III effector RipG7 from Ralstonia solanacearum. MOLECULAR PLANT PATHOLOGY 2016; 17:553-64. [PMID: 26300048 PMCID: PMC6638336 DOI: 10.1111/mpp.12302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The soil-borne pathogen Ralstonia solanacearum causes bacterial wilt in a broad range of plants. The main virulence determinants of R. solanacearum are the type III secretion system (T3SS) and its associated type III effectors (T3Es), translocated into the host cells. Of the conserved T3Es among R. solanacearum strains, the Fbox protein RipG7 is required for R. solanacearum pathogenesis on Medicago truncatula. In this work, we describe the natural ripG7 variability existing in the R. solanacearum species complex. We show that eight representative ripG7 orthologues have different contributions to pathogenicity on M. truncatula: only ripG7 from Asian or African strains can complement the absence of ripG7 in GMI1000 (Asian reference strain). Nonetheless, RipG7 proteins from American and Indonesian strains can still interact with M. truncatula SKP1-like/MSKa protein, essential for the function of RipG7 in virulence. This indicates that the absence of complementation is most likely a result of the variability in the leucine-rich repeat (LRR) domain of RipG7. We identified 11 sites under positive selection in the LRR domains of RipG7. By studying the functional impact of these 11 sites, we show the contribution of five positively selected sites for the function of RipG7CMR15 in M. truncatula colonization. This work reveals the genetic and functional variation of the essential core T3E RipG7 from R. solanacearum. This analysis is the first of its kind on an essential disease-controlling T3E, and sheds light on the co-evolutionary arms race between the bacterium and its hosts.
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Affiliation(s)
- Keke Wang
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Philippe Remigi
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Gruenalstrasse 14, 8820, Wädesnwil, Switzerland
| | - Fabien Lonjon
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Ilona Kars
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Andrey Kajava
- Centre de Recherche de Biochimie Macromoléculaire, CNRS, UMR5237, 1919 Route de Mende, 34000, Montpellier, France
| | - Chien-Hui Li
- Institute of Plant Biology, National Taiwan University, Taipei, 11529, Taiwan, R.O.C
| | - Chiu-Ping Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 11529, Taiwan, R.O.C
| | - Fabienne Vailleau
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- Université de Toulouse, INP, ENSAT, 18 Chemin de Borde Rouge, Castanet-Tolosan, 31326, France
| | - Stéphane Genin
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
| | - Nemo Peeters
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR441, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
- CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR2594, CS52627 Chemin de Borde Rouge, 31326, Castanet-Tolosan, France
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Stuttmann J, Peine N, Garcia AV, Wagner C, Choudhury SR, Wang Y, James GV, Griebel T, Alcázar R, Tsuda K, Schneeberger K, Parker JE. Arabidopsis thaliana DM2h (R8) within the Landsberg RPP1-like Resistance Locus Underlies Three Different Cases of EDS1-Conditioned Autoimmunity. PLoS Genet 2016; 12:e1005990. [PMID: 27082651 PMCID: PMC4833295 DOI: 10.1371/journal.pgen.1005990] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 03/24/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have a large panel of nucleotide-binding/leucine rich repeat (NLR) immune receptors which monitor host interference by diverse pathogen molecules (effectors) and trigger disease resistance pathways. NLR receptor systems are necessarily under tight control to mitigate the trade-off between induced defenses and growth. Hence, mis-regulated NLRs often cause autoimmunity associated with stunting and, in severe cases, necrosis. Nucleocytoplasmic ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) is indispensable for effector-triggered and autoimmune responses governed by a family of Toll-Interleukin1-Receptor-related NLR receptors (TNLs). EDS1 operates coincidently or immediately downstream of TNL activation to transcriptionally reprogram cells for defense. We show here that low levels of nuclear-enforced EDS1 are sufficient for pathogen resistance in Arabidopsis thaliana, without causing negative effects. Plants expressing higher nuclear EDS1 amounts have the genetic, phenotypic and transcriptional hallmarks of TNL autoimmunity. In a screen for genetic suppressors of nuclear EDS1 autoimmunity, we map multiple, independent mutations to one gene, DM2h, lying within the polymorphic DANGEROUS MIX2 cluster of TNL RPP1-like genes from A. thaliana accession Landsberg erecta (Ler). The DM2 locus is a known hotspot for deleterious epistatic interactions leading to immune-related incompatibilities between A. thaliana natural accessions. We find that DM2hLer underlies two further genetic incompatibilities involving the RPP1-likeLer locus and EDS1. We conclude that the DM2hLer TNL protein and nuclear EDS1 cooperate, directly or indirectly, to drive cells into an immune response at the expense of growth. A further conclusion is that regulating the available EDS1 nuclear pool is fundamental for maintaining homeostatic control of TNL immune pathways. Plants tune their cellular and developmental programs to different environmental stimuli. Central players in the plant biotic stress response network are intracellular NLR receptors which intercept specific disease-inducing molecules (effectors) produced by pathogenic microbes. Variation in NLR gene repertoires between plant genetic lines is driven by pathogen selection pressure. One evolutionary question is how new, functional NLRs are assembled within a plant genome without mis-activating defense pathways, which can have strong negative effects on growth and fitness. This study focuses on a large, polymorphic sub-class of NLR receptors called TNLs present in dicotyledenous plant lineages. TNL receptors confer immunity to a broad range of pathogens. They also frequently underlie autoimmunity caused by their mis-regulation or deleterious allelic interactions with other genes in crosses between different genetic lines (hybrid incompatibility, HI). TNL pathogen-triggered and autoimmune responses require the conserved nucleocytoplasmic protein EDS1 to transcriptionally reprogram cells for defense. We discover in Arabidopsis thaliana that high levels of nuclear-enriched EDS1 induce transcriptional activation of defenses and growth inhibition without a pathogen effector stimulus. In a mutational screen, we identify one rapidly evolving TNL gene, DM2hLer, as a driver of nuclear EDS1 autoimmunity. DM2hLer also contributes to two separate cases of EDS1-dependent autoimmunity. Genetic cooperation between DM2hLer and EDS1 suggests a functional relationship in the transcriptional feed-forward regulation of defense pathways.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
- * E-mail: (JS); (JEP)
| | - Nora Peine
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ana V. Garcia
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Christine Wagner
- Department of Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Sayan R. Choudhury
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yiming Wang
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Thomas Griebel
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Alcázar
- Department of Natural Products, Plant Biology and Soil Science, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail: (JS); (JEP)
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49
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Bernoux M, Burdett H, Williams SJ, Zhang X, Chen C, Newell K, Lawrence GJ, Kobe B, Ellis JG, Anderson PA, Dodds PN. Comparative Analysis of the Flax Immune Receptors L6 and L7 Suggests an Equilibrium-Based Switch Activation Model. THE PLANT CELL 2016; 28:146-59. [PMID: 26744216 PMCID: PMC4746675 DOI: 10.1105/tpc.15.00303] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 12/10/2015] [Accepted: 01/06/2016] [Indexed: 05/18/2023]
Abstract
NOD-like receptors (NLRs) are central components of the plant immune system. L6 is a Toll/interleukin-1 receptor (TIR) domain-containing NLR from flax (Linum usitatissimum) conferring immunity to the flax rust fungus. Comparison of L6 to the weaker allele L7 identified two polymorphic regions in the TIR and the nucleotide binding (NB) domains that regulate both effector ligand-dependent and -independent cell death signaling as well as nucleotide binding to the receptor. This suggests that a negative functional interaction between the TIR and NB domains holds L7 in an inactive/ADP-bound state more tightly than L6, hence decreasing its capacity to adopt the active/ATP-bound state and explaining its weaker activity in planta. L6 and L7 variants with a more stable ADP-bound state failed to bind to AvrL567 in yeast two-hybrid assays, while binding was detected to the signaling active variants. This contrasts with current models predicting that effectors bind to inactive receptors to trigger activation. Based on the correlation between nucleotide binding, effector interaction, and immune signaling properties of L6/L7 variants, we propose that NLRs exist in an equilibrium between ON and OFF states and that effector binding to the ON state stabilizes this conformation, thereby shifting the equilibrium toward the active form of the receptor to trigger defense signaling.
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Affiliation(s)
| | - Hayden Burdett
- School of Biological Sciences, Flinders University, Adelaide SA 5001, Australia
| | - Simon J Williams
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane QLD 4072, Australia
| | | | | | - Kim Newell
- CSIRO Agriculture, Canberra ACT 2601, Australia
| | | | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane QLD 4072, Australia
| | | | - Peter A Anderson
- School of Biological Sciences, Flinders University, Adelaide SA 5001, Australia
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Anderson RG, Deb D, Fedkenheuer K, McDowell JM. Recent Progress in RXLR Effector Research. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1063-72. [PMID: 26125490 DOI: 10.1094/mpmi-01-15-0022-cr] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.
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Affiliation(s)
- Ryan G Anderson
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Devdutta Deb
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Kevin Fedkenheuer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - John M McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
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