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Jones JDG, Staskawicz BJ, Dangl JL. The plant immune system: From discovery to deployment. Cell 2024; 187:2095-2116. [PMID: 38670067 DOI: 10.1016/j.cell.2024.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/08/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Plant diseases cause famines, drive human migration, and present challenges to agricultural sustainability as pathogen ranges shift under climate change. Plant breeders discovered Mendelian genetic loci conferring disease resistance to specific pathogen isolates over 100 years ago. Subsequent breeding for disease resistance underpins modern agriculture and, along with the emergence and focus on model plants for genetics and genomics research, has provided rich resources for molecular biological exploration over the last 50 years. These studies led to the identification of extracellular and intracellular receptors that convert recognition of extracellular microbe-encoded molecular patterns or intracellular pathogen-delivered virulence effectors into defense activation. These receptor systems, and downstream responses, define plant immune systems that have evolved since the migration of plants to land ∼500 million years ago. Our current understanding of plant immune systems provides the platform for development of rational resistance enhancement to control the many diseases that continue to plague crop production.
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Affiliation(s)
- Jonathan D G Jones
- Sainsbury Lab, University of East Anglia, Colney Lane, Norwich NR4 7UH, UK.
| | - Brian J Staskawicz
- Department of Plant and Microbial Biology and Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill and Howard Hughes Medical Institute, Chapel Hill, NC 27599, USA
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2
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Nirwan S, Chatterjee A, Cevik V, Holub EB, Jones JDG, Tewari AK, Shrivastava N, Agnihotri A, Sharma P. Genetic manipulation of Indian mustard genotypes with WRR-gene(s) confers resistance against Albugo candida. Mol Biol Rep 2024; 51:199. [PMID: 38270712 DOI: 10.1007/s11033-023-09040-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/26/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Brassica species is the second most important edible oilseed crop in India. Albugo candida (Pers.) Kuntze, a major oomycete disease of oilseed brassica causing white rust, leads to 60% yield loss globally. The prevalence of A. candida race 2 (Ac2V) that specifically infects B. juncea, coupled with limitations of conventional methods has resulted in a dearth of white rust resistance resources in cultivated varieties. METHODS AND RESULTS In an effort to develop resistant plants, Agrobacterium mediated genetic transformation of three B. juncea genotypes viz., susceptible host var. Varuna, along with its doubled haploid mutant lines C66 and C69 (showing moderate tolerance to field isolates of A. candida) was initiated to transfer resistance genes (WRR8Sf-2 and WRR9Hi-0) identified in Arabidopsis thaliana against race Ac2V, that encode for Toll-like/interleukin-1 receptor-nucleotide binding-leucine-rich repeat proteins that recognize effectors of the pathogen races. CONCLUSIONS Our results demonstrate that introduction of resistance genes from a tertiary gene pool by genetic transformation enhances disease resistance in B. juncea genotypes to a highly virulent Ac2V isolate.
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Affiliation(s)
- Shradha Nirwan
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, 201303, India
| | - Anupriya Chatterjee
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, 201303, India
| | - Volkan Cevik
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK.
| | - Eric B Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, CV35 9EF, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich, NR4 7UH, UK
| | - Anand Kumar Tewari
- Department of Plant Pathology, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Neeraj Shrivastava
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, 201303, India
| | - Abha Agnihotri
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, 201303, India.
| | - Pankaj Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, 201303, India.
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3
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Lee ES, Heo J, Bang WY, Chougule KM, Waminal NE, Hong NT, Kim MJ, Beak HK, Kim YJ, Priatama RA, Jang JI, Cha KI, Son SH, Rajendran S, Choo Y, Bae JH, Kim CM, Lee YK, Bae S, Jones JDG, Sohn KH, Lee J, Kim HH, Hong JC, Ware D, Kim K, Park SJ. Engineering homoeologs provide a fine scale for quantitative traits in polyploid. Plant Biotechnol J 2023; 21:2458-2472. [PMID: 37530518 PMCID: PMC10651150 DOI: 10.1111/pbi.14141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/20/2023] [Indexed: 08/03/2023]
Abstract
Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.
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Affiliation(s)
- Eun Song Lee
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Jung Heo
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Woo Young Bang
- Biological and Genetic Resources Assessment DivisionNational Institute of Biological ResourcesIncheonKorea
| | | | - Nomar Espinosa Waminal
- Leibniz Institute of Plant Genetics and Crop Plant ResearchGaterslebenGermany
- BioScience Institute, Department of Chemistry & Life ScienceSahmyook UniversitySeoulKorea
| | - Nguyen Thi Hong
- BioScience Institute, Department of Chemistry & Life ScienceSahmyook UniversitySeoulKorea
| | - Min Ji Kim
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Hong Kwan Beak
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Yong Jun Kim
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Ryza A. Priatama
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Institute of Plasma TechnologyKorea Institute of Fusion EnergyGunsan‐siKorea
| | - Ji In Jang
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Kang Il Cha
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Seung Han Son
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | | | - Young‐Kug Choo
- Division of Biological SciencesWonkwang UniversityIksanKorea
| | - Jong Hyang Bae
- Division of Horticulture IndustryWonkwang UniversityIksanKorea
| | - Chul Min Kim
- Division of Horticulture IndustryWonkwang UniversityIksanKorea
| | - Young Koung Lee
- Institute of Plasma TechnologyKorea Institute of Fusion EnergyGunsan‐siKorea
| | - Sangsu Bae
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulSouth Korea
| | - Jonathan D. G. Jones
- The Sainsbury LaboratoryUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Kee Hoon Sohn
- Department of Agricultural Biotechnology, Plant Immunity Research Center, Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource CenterKorea Research Institute of Bioscience and BiotechnologyJeongeupKorea
| | - Hyun Hee Kim
- BioScience Institute, Department of Chemistry & Life ScienceSahmyook UniversitySeoulKorea
| | - Jong Chan Hong
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Doreen Ware
- Cold Spring Harbor LaboratoryCold Spring HarborNYUSA
- U.S. Department of Agriculture‐Agricultural Research ServiceNEA Robert W. Holley Center for Agriculture and HealthIthacaNYUSA
| | - Keunhwa Kim
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
| | - Soon Ju Park
- Division of Biological SciencesWonkwang UniversityIksanKorea
- Division of Applied Life Science (BK21 four) and Plant Molecular Biology and Biotechnology Research Center (PMBBRC)Gyeongsang National UniversityJinjuKorea
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4
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Wang MY, Chen JB, Wu R, Guo HL, Chen Y, Li ZJ, Wei LY, Liu C, He SF, Du MD, Guo YL, Peng YL, Jones JDG, Weigel D, Huang JH, Zhu WS. The plant immune receptor SNC1 monitors helper NLRs targeted by a bacterial effector. Cell Host Microbe 2023; 31:1792-1803.e7. [PMID: 37944492 DOI: 10.1016/j.chom.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/01/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Plants deploy intracellular receptors to counteract pathogen effectors that suppress cell-surface-receptor-mediated immunity. To what extent pathogens manipulate intracellular receptor-mediated immunity, and how plants tackle such manipulation, remains unknown. Arabidopsis thaliana encodes three similar ADR1 class helper nucleotide-binding domain leucine-rich repeat receptors (ADR1, ADR1-L1, and ADR1-L2), which are crucial in plant immunity initiated by intracellular receptors. Here, we report that Pseudomonas syringae effector AvrPtoB suppresses ADR1-L1- and ADR1-L2-mediated cell death. ADR1, however, evades such suppression by diversifying into two ubiquitination sites targeted by AvrPtoB. The intracellular sensor SNC1 interacts with and guards the CCR domains of ADR1-L1/L2. Removal of ADR1-L1/L2 or delivery of AvrPtoB activates SNC1, which then signals through ADR1 to trigger immunity. Our work elucidates the long-sought-after function of SNC1 in defense, and also how plants can use dual strategies, sequence diversification, and a multi-layered guard-guardee system, to counteract pathogen's attack on core immunity functions.
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Affiliation(s)
- Ming-Yu Wang
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Jun-Bin Chen
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Rui Wu
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Hai-Long Guo
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yan Chen
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Zhen-Ju Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Lu-Yang Wei
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Chuang Liu
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Sheng-Feng He
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Mei-Da Du
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - You-Liang Peng
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Jian-Hua Huang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Wang-Sheng Zhu
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, and College of Plant Protection, State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing 100193, China.
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5
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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Publisher Correction: Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1779. [PMID: 37749249 PMCID: PMC10562209 DOI: 10.1038/s41588-023-01550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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6
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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1579-1588. [PMID: 37640880 PMCID: PMC10484786 DOI: 10.1038/s41588-023-01486-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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Asai S, Cevik V, Jones JDG, Shirasu K. Cell-specific RNA profiling reveals host genes expressed in Arabidopsis cells haustoriated by downy mildew. Plant Physiol 2023; 193:259-270. [PMID: 37307565 PMCID: PMC10469357 DOI: 10.1093/plphys/kiad326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/21/2023] [Accepted: 05/15/2023] [Indexed: 06/14/2023]
Abstract
The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infects Arabidopsis (Arabidopsis thaliana) by forming structures called haustoria inside host cells. Previous transcriptome analyses have revealed that host genes are specifically induced during infection; however, RNA profiling from whole-infected tissues may fail to capture key transcriptional events occurring exclusively in haustoriated host cells, where the pathogen injects virulence effectors to modulate host immunity. To determine interactions between Arabidopsis and H. arabidopsidis at the cellular level, we devised a translating ribosome affinity purification system using 2 high-affinity binding proteins, colicin E9 and Im9 (immunity protein of colicin E9), applicable to pathogen-responsive promoters, thus enabling haustoriated cell-specific RNA profiling. Among the host genes specifically expressed in H. arabidopsidis-haustoriated cells, we found genes that promote either susceptibility or resistance to the pathogen, providing insights into the Arabidopsis-downy mildew interaction. We propose that our protocol for profiling cell-specific transcripts will apply to several stimulus-specific contexts and other plant-pathogen interactions.
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Affiliation(s)
- Shuta Asai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Volkan Cevik
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
| | | | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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Gu B, Parkes T, Rabanal F, Smith C, Lu FH, McKenzie N, Dong H, Weigel D, Jones JDG, Cevik V, Bevan MW. The integrated LIM-peptidase domain of the CSA1-CHS3/DAR4 paired immune receptor detects changes in DA1 peptidase inhibitors in Arabidopsis. Cell Host Microbe 2023; 31:949-961.e5. [PMID: 37167970 DOI: 10.1016/j.chom.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 03/09/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
White blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Brassica relative Arabidopsis thaliana uses the paired immune receptor complex CSA1-CHS3/DAR4 to resist Albugo infection. The CHS3/DAR4 sensor NLR, which functions together with its partner, the helper NLR CSA1, carries an integrated domain (ID) with homology to DA1 peptidases. Using domain swaps with several DA1 homologs, we show that the LIM-peptidase domain of the family member CHS3/DAR4 functions as an integrated decoy for the family member DAR3, which interacts with and inhibits the peptidase activities of the three closely related peptidases DA1, DAR1, and DAR2. Albugo infection rapidly lowers DAR3 levels and activates DA1 peptidase activity, thereby promoting endoreduplication of host tissues to support pathogen growth. We propose that the paired immune receptor CSA1-CHS3/DAR4 detects the actions of a putative Albugo effector that reduces DAR3 levels, resulting in defense activation.
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Affiliation(s)
- Benguo Gu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Toby Parkes
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Fernando Rabanal
- Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Caroline Smith
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Fu-Hao Lu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neil McKenzie
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hui Dong
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Detlef Weigel
- Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK.
| | - Volkan Cevik
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK.
| | - Michael W Bevan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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9
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Yu G, Matny O, Gourdoupis S, Rayapuram N, Aljedaani FR, Wang YL, Nürnberger T, Johnson R, Crean EE, Saur IML, Gardener C, Yue Y, Kangara N, Steuernagel B, Hayta S, Smedley M, Harwood W, Patpour M, Wu S, Poland J, Jones JDG, Reuber TL, Ronen M, Sharon A, Rouse MN, Xu S, Holušová K, Bartoš J, Molnár I, Karafiátová M, Hirt H, Blilou I, Jaremko Ł, Doležel J, Steffenson BJ, Wulff BBH. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase. Nat Genet 2023:10.1038/s41588-023-01402-1. [PMID: 37217714 DOI: 10.1038/s41588-023-01402-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
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Affiliation(s)
- Guotai Yu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Spyridon Gourdoupis
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Naganand Rayapuram
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Fatimah R Aljedaani
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Yan L Wang
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Ryan Johnson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Emma E Crean
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Isabel M-L Saur
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Catherine Gardener
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yajuan Yue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Shuangye Wu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - T Lynne Reuber
- 2Blades Foundation, Evanston, IL, USA
- Enko Chem, Mystic, CT, USA
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, and the School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, USA
| | - Steven Xu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Kateřina Holušová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - István Molnár
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
- Centre for Agricultural Research, ELKH, Agricultural Institute, Martonvásár, Hungary
| | - Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Heribert Hirt
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Ikram Blilou
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
- Red Sea Research Center, BESE, KAUST, Thuwal, Saudi Arabia
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia.
- John Innes Centre, Norwich Research Park, Norwich, UK.
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10
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Larson ER, Armstrong EM, Harper H, Knapp S, Edwards KJ, Grierson D, Poppy G, Chase MW, Jones JDG, Bastow R, Jellis G, Barnes S, Temple P, Clarke M, Oldroyd G, Grierson CS. One hundred important questions for plant science - reflecting on a decade of plant research. New Phytol 2023; 238:464-469. [PMID: 36924326 DOI: 10.1111/nph.18663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 06/18/2023]
Affiliation(s)
- Emily R Larson
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Emily May Armstrong
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Helen Harper
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Keith J Edwards
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Don Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, nr Loughborough, LE12 5RD, UK
| | - Guy Poppy
- Biological Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Mark W Chase
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6845, Australia
- Royal Botanic Gardens Kew, Richmond, London, TW9 3AE, UK
| | | | - Ruth Bastow
- Crop Health and Protection Ltd, York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Graham Jellis
- Agrifood Charities Partnership, The Bullock Building, University Way, Cranfield, Bedford, MK43 OGH, UK
| | | | - Paul Temple
- Wold Farm, Driffield, East Yorkshire, YO25 3BB, UK
| | - Matthew Clarke
- Bayer - Crop Science, Monsanto UK Ltd, 230 Science Park, Cambridge, CB4 0WB, UK
| | - Giles Oldroyd
- Crop Science Centre, Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Claire S Grierson
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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11
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Ahn H, Lin X, Olave‐Achury AC, Derevnina L, Contreras MP, Kourelis J, Wu C, Kamoun S, Jones JDG. Effector-dependent activation and oligomerization of plant NRC class helper NLRs by sensor NLR immune receptors Rpi-amr3 and Rpi-amr1. EMBO J 2023; 42:e111484. [PMID: 36592032 PMCID: PMC9975942 DOI: 10.15252/embj.2022111484] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 01/03/2023] Open
Abstract
Plant pathogens compromise crop yields. Plants have evolved robust innate immunity that depends in part on intracellular Nucleotide-binding, Leucine rich-Repeat (NLR) immune receptors that activate defense responses upon detection of pathogen-derived effectors. Most "sensor" NLRs that detect effectors require the activity of "helper" NLRs, but how helper NLRs support sensor NLR function is poorly understood. Many Solanaceae NLRs require NRC (NLR-Required for Cell death) class of helper NLRs. We show here that Rpi-amr3, a sensor NLR from Solanum americanum, detects AVRamr3 from the potato late blight pathogen, Phytophthora infestans, and activates oligomerization of helper NLRs NRC2 and NRC4 into high-molecular-weight resistosomes. In contrast, recognition of P. infestans effector AVRamr1 by another sensor NLR Rpi-amr1 induces formation of only the NRC2 resistosome. The activated NRC2 oligomer becomes enriched in membrane fractions. ATP-binding motifs of both Rpi-amr3 and NRC2 are required for NRC2 resistosome formation, but not for the interaction of Rpi-amr3 with its cognate effector. NRC2 resistosome can be activated by Rpi-amr3 upon detection of AVRamr3 homologs from other Phytophthora species. Mechanistic understanding of NRC resistosome formation will underpin engineering crops with durable disease resistance.
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Affiliation(s)
- Hee‐Kyung Ahn
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Xiao Lin
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | | | - Lida Derevnina
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
- Present address:
Department of Plant Sciences, Crop Science CentreUniversity of CambridgeCambridgeUK
| | | | | | - Chih‐Hang Wu
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
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12
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Arora S, Steed A, Goddard R, Gaurav K, O'Hara T, Schoen A, Rawat N, Elkot AF, Korolev AV, Chinoy C, Nicholson MH, Asuke S, Antoniou-Kourounioti R, Steuernagel B, Yu G, Awal R, Forner-Martínez M, Wingen L, Baggs E, Clarke J, Saunders DGO, Krasileva KV, Tosa Y, Jones JDG, Tiwari VK, Wulff BBH, Nicholson P. A wheat kinase and immune receptor form host-specificity barriers against the blast fungus. Nat Plants 2023; 9:385-392. [PMID: 36797350 PMCID: PMC10027608 DOI: 10.1038/s41477-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/20/2023] [Indexed: 05/18/2023]
Abstract
Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. Here we show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes will enable study of the molecular interaction between pathogen effector and host resistance genes.
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Affiliation(s)
- Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Andrew Steed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Rachel Goddard
- John Innes Centre, Norwich Research Park, Norwich, UK
- Limagrain UK Ltd, Lincolnshire, UK
| | - Kumar Gaurav
- John Innes Centre, Norwich Research Park, Norwich, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK
| | - Tom O'Hara
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ahmed F Elkot
- Wheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | | | | | | | - Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Rea Antoniou-Kourounioti
- John Innes Centre, Norwich Research Park, Norwich, UK
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, UK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rajani Awal
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Luzie Wingen
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | | | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, UK.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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13
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Redkar A, Cevik V, Bailey K, Zhao H, Kim DS, Zou Z, Furzer OJ, Fairhead S, Borhan MH, Holub EB, Jones JDG. The Arabidopsis WRR4A and WRR4B paralogous NLR proteins both confer recognition of multiple Albugo candida effectors. New Phytol 2023; 237:532-547. [PMID: 35838065 PMCID: PMC10087428 DOI: 10.1111/nph.18378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 05/26/2023]
Abstract
The oomycete Albugo candida causes white blister rust, an important disease of Brassica crops. Distinct races of A. candida are defined by their capacity to infect different host plant species. Each A. candida race encodes secreted proteins with a CX2 CX5 G ('CCG') motif that are polymorphic and show presence/absence variation, and are therefore candidate effectors. The White Rust Resistance 4 (WRR4) locus in Arabidopsis thaliana accession Col-0 contains three genes that encode intracellular nucleotide-binding domain leucine-rich repeat immune receptors. The Col-0 alleles of WRR4A and WRR4B confer resistance to multiple A. candida races, although both WRR4A and WRR4B can be overcome by the Col-0-virulent race 4 isolate AcEx1. Comparison of CCG candidate effectors in avirulent and virulent races, and transient co-expression of CCG effectors from four A. candida races in Nicotiana sp. or A. thaliana, revealed CCG effectors that trigger WRR4A- or WRR4B-dependent hypersensitive responses. We found eight WRR4A-recognised CCGs and four WRR4B-recognised CCGs, the first recognised proteins from A. candida for which the cognate immune receptors in A. thaliana are known. This multiple recognition capacity potentially explains the broad-spectrum resistance to several A. candida races conferred by WRR4 paralogues. We further show that of five tested CCGs, three confer enhanced disease susceptibility when expressed in planta, consistent with A. candida CCG proteins being effectors.
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Affiliation(s)
- Amey Redkar
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Department of BotanySavitribai Phule Pune UniversityGaneshkhindPune411007India
| | - Volkan Cevik
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBathBA2 7AYUK
| | - Kate Bailey
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
| | - He Zhao
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
| | - Dae Sung Kim
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Present address:
State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei UniversityWuhan430062China
| | - Zhou Zou
- The Milner Centre for Evolution, Department of Biology and BiochemistryUniversity of BathBathBA2 7AYUK
| | - Oliver J. Furzer
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- Department of BiologyUniversity of North CarolinaChapel HillNC27599USA
| | - Sebastian Fairhead
- The Sainsbury LaboratoryUniversity of East AngliaNorwichNR4 7UHUK
- School of Life SciencesWarwick Crop Centre, University of WarwickWellesbourneCV35 9EFUK
| | - M. Hossein Borhan
- Agriculture and Agri‐Food Canada107 Science PlaceSaskatoonSKS7N 0X2Canada
| | - Eric B. Holub
- School of Life SciencesWarwick Crop Centre, University of WarwickWellesbourneCV35 9EFUK
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14
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Abstract
Interview with Jonathan Jones, who studies plant pathology.
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Affiliation(s)
- Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
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15
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Ngou BPM, Heal R, Wyler M, Schmid MW, Jones JDG. Concerted expansion and contraction of immune receptor gene repertoires in plant genomes. Nat Plants 2022; 8:1146-1152. [PMID: 36241733 PMCID: PMC9579050 DOI: 10.1038/s41477-022-01260-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 09/09/2022] [Indexed: 05/10/2023]
Abstract
Recent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether they co-evolve is unclear. Here we determined the numbers of cell-surface and intracellular immune receptors in 350 species. Surprisingly, the number of receptor genes that are predicted to encode cell-surface and intracellular immune receptors is strongly correlated. We suggest this is consistent with mutual potentiation of immunity initiated by cell-surface and intracellular receptors being reflected in the concerted co-evolution of the size of their repertoires across plant species.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | | | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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16
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Lin X, Olave-Achury A, Heal R, Pais M, Witek K, Ahn HK, Zhao H, Bhanvadia S, Karki HS, Song T, Wu CH, Adachi H, Kamoun S, Vleeshouwers VGAA, Jones JDG. A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector. Mol Plant 2022; 15:1457-1469. [PMID: 35915586 DOI: 10.1016/j.molp.2022.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/15/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Species of the genus Phytophthora, the plant killer, cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) immune receptor proteins that recognize RXLR (Arg-X-Leu-Arg) effectors. However, whether NLR proteins can recognize RXLR effectors from multiple Phytophthora species has rarely been investigated. Here, we identified a new RXLR-WY effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from a wild Solanaceae species Solanum americanum. Rpi-amr3 associates with AVRamr3 in planta. AVRamr3 is broadly conserved in many different Phytophthora species, and the recognition of AVRamr3 homologs by Rpi-amr3 activates resistance against multiple Phytophthora pathogens, including the tobacco black shank disease and cacao black pod disease pathogens P. parasitica and P. palmivora. Rpi-amr3 is thus the first characterized resistance gene that acts against P. parasitica or P. palmivora. These findings suggest a novel path to redeploy known R genes against different important plant pathogens.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Marina Pais
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - He Zhao
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Shivani Bhanvadia
- Wageningen UR Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK
| | - Vivianne G A A Vleeshouwers
- Wageningen UR Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, UK.
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17
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Michalopoulou VA, Mermigka G, Kotsaridis K, Mentzelopoulou A, Celie PHN, Moschou PN, Jones JDG, Sarris PF. The host exocyst complex is targeted by a conserved bacterial type-III effector that promotes virulence. Plant Cell 2022; 34:3400-3424. [PMID: 35640532 PMCID: PMC9421483 DOI: 10.1093/plcell/koac162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/23/2022] [Indexed: 05/30/2023]
Abstract
For most Gram-negative bacteria, pathogenicity largely depends on the type-III secretion system that delivers virulence effectors into eukaryotic host cells. The subcellular targets for the majority of these effectors remain unknown. Xanthomonas campestris, the causal agent of black rot disease of crucifers such as Brassica spp., radish, and turnip, delivers XopP, a highly conserved core-effector protein produced by X. campestris, which is essential for virulence. Here, we show that XopP inhibits the function of the host-plant exocyst complex by direct targeting of Exo70B, a subunit of the exocyst complex, which plays a significant role in plant immunity. XopP interferes with exocyst-dependent exocytosis and can do this without activating a plant NOD-like receptor that guards Exo70B in Arabidopsis. In this way, Xanthomonas efficiently inhibits the host's pathogen-associated molecular pattern (PAMP)-triggered immunity by blocking exocytosis of pathogenesis-related protein-1A, callose deposition, and localization of the FLAGELLIN SENSITIVE2 (FLS2) immune receptor to the plasma membrane, thus promoting successful infection. Inhibition of exocyst function without activating the related defenses represents an effective virulence strategy, indicating the ability of pathogens to adapt to host defenses by avoiding host immunity responses.
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Affiliation(s)
- Vassiliki A Michalopoulou
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Glykeria Mermigka
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | - Konstantinos Kotsaridis
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
| | | | - Patrick H N Celie
- Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Panagiotis N Moschou
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Uppsala S-75007, Sweden
| | | | - Panagiotis F Sarris
- Department of Biology, University of Crete, Heraklion, Crete 714 09, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete 70013, Greece
- Biosciences, University of Exeter, Exeter, UK
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18
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Grech‐Baran M, Witek K, Poznański JT, Grupa‐Urbańska A, Malinowski T, Lichocka M, Jones JDG, Hennig J. The Ry sto immune receptor recognises a broadly conserved feature of potyviral coat proteins. New Phytol 2022; 235:1179-1195. [PMID: 35491734 PMCID: PMC9322412 DOI: 10.1111/nph.18183] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/13/2022] [Indexed: 05/05/2023]
Abstract
Knowledge of the immune mechanisms responsible for viral recognition is critical for understanding durable disease resistance and successful crop protection. We determined how potato virus Y (PVY) coat protein (CP) is recognised by Rysto , a TNL immune receptor. We applied structural modelling, site-directed mutagenesis, transient overexpression, co-immunoprecipitation, infection assays and physiological cell death marker measurements to investigate the mechanism of Rysto -CP interaction. Rysto associates directly with PVY CP in planta that is conditioned by the presence of a CP central 149 amino acids domain. Each deletion that affects the CP core region impairs the ability of Rysto to trigger defence. Point mutations in the amino acid residues Ser125 , Arg157 , and Asp201 of the conserved RNA-binding pocket of potyviral CP reduce or abolish Rysto binding and Rysto -dependent responses, demonstrating that appropriate folding of the CP core is crucial for Rysto -mediated recognition. Rysto recognises the CPs of at least 10 crop-damaging viruses that share a similar core region. It confers immunity to plum pox virus and turnip mosaic virus in both Solanaceae and Brassicaceae systems, demonstrating potential utility in engineering virus resistance in various crops. Our findings shed new light on how R proteins detect different viruses by sensing conserved structural patterns.
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Affiliation(s)
- Marta Grech‐Baran
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichNR4 7UHUK
- The 2Blades FoundationEvanstonIL60201USA
| | - Jarosław T. Poznański
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Anna Grupa‐Urbańska
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
- Plant Breeding and Acclimatization Institute‐National Research InstitutePlatanowa 19Młochów05‐831Poland
| | - Tadeusz Malinowski
- The National Institute of Horticultural ResearchKonstytucji 3. Maja 1/3Skierniewice96‐100Poland
| | - Małgorzata Lichocka
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Jonathan D. G. Jones
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichNR4 7UHUK
| | - Jacek Hennig
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
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19
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Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: Zig-zag through the plant immune system. Plant Cell 2022; 34:1447-1478. [PMID: 35167697 PMCID: PMC9048904 DOI: 10.1093/plcell/koac041] [Citation(s) in RCA: 231] [Impact Index Per Article: 115.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
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Affiliation(s)
| | - Pingtao Ding
- Author for correspondence: (B.P.M.N.); (P.D.); (J.J.)
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20
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Abstract
Plants have both cell-surface and intracellular receptors to recognize diverse self- and non-self molecules. Cell-surface pattern recognition receptors (PRRs) recognize extracellular pathogen-/damage-derived molecules or apoplastic pathogen-derived effectors. Intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) recognize pathogen effectors. Activation of both PRRs and NLRs elevates defense gene expression and accumulation of the phytohormone salicylic acid (SA), which results in SA-dependent transcriptional reprogramming. These receptors, together with their coreceptors, form networks to mediate downstream immune responses. In addition, cell-surface and intracellular immune systems are interdependent and function synergistically to provide robust resistance against pathogens. Here, we summarize the interactions between these immune systems and attempt to provide a holistic picture of plant immune networks. We highlight current challenges and discuss potential new research directions.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333, BE, The Netherlands.
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21
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Furzer OJ, Cevik V, Fairhead S, Bailey K, Redkar A, Schudoma C, MacLean D, Holub EB, Jones JDG. An Improved Assembly of the Albugo candida Ac2V Genome Reveals the Expansion of the "CCG" Class of Effectors. Mol Plant Microbe Interact 2022; 35:39-48. [PMID: 34546764 DOI: 10.1094/mpmi-04-21-0075-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Kate Bailey
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- Department of Genetics, University of Córdoba, Córdoba 14071, Spain
| | - Christian Schudoma
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Eric B Holub
- University of Warwick, School of Life Sciences, Warwick Crop Centre, Wellesbourne, CV35 9EF, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
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22
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Mukhi N, Brown H, Gorenkin D, Ding P, Bentham AR, Stevenson CEM, Jones JDG, Banfield MJ. Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor. Proc Natl Acad Sci U S A 2021; 118:e2113996118. [PMID: 34880132 PMCID: PMC8685902 DOI: 10.1073/pnas.2113996118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
Plants use intracellular nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)-containing immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving the structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. Here, we report the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY Perception of AvrRps4C by RRS1WRKY is mediated by the β2-β3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C Structure-based mutations that disrupt AvrRps4C-RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA-binding domain of AtWRKY41, with similar binding affinities and how effector binding interferes with WRKY-W-box DNA interactions. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity.
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Affiliation(s)
- Nitika Mukhi
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Hannah Brown
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Danylo Gorenkin
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Adam R Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom;
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23
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Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. J Exp Bot 2021; 72:7927-7941. [PMID: 34387350 DOI: 10.1093/jxb/erab373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
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Affiliation(s)
- Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ram Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nicolas Manosalva Perez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shengbo He
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Xiaoqi Feng
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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24
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Wang H, Trusch F, Turnbull D, Aguilera-Galvez C, Breen S, Naqvi S, Jones JDG, Hein I, Tian Z, Vleeshouwers V, Gilroy E, Birch PRJ. Evolutionarily distinct resistance proteins detect a pathogen effector through its association with different host targets. New Phytol 2021; 232:1368-1381. [PMID: 34339518 DOI: 10.1111/nph.17660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Knowledge of the evolutionary processes which govern pathogen recognition is critical to understanding durable disease resistance. We determined how Phytophthora infestans effector PiAVR2 is recognised by evolutionarily distinct resistance proteins R2 and Rpi-mcq1. We employed yeast two-hybrid, co-immunoprecipitation, virus-induced gene silencing, transient overexpression, and phosphatase activity assays to investigate the contributions of BSL phosphatases to R2- and Rpi-mcq1-mediated hypersensitive response (R2 HR and Rpi-mcq1 HR, respectively). Silencing PiAVR2 target BSL1 compromises R2 HR. Rpi-mcq1 HR is compromised only when BSL2 and BSL3 are silenced. BSL1 overexpression increases R2 HR and compromises Rpi-mcq1. However, overexpression of BSL2 or BSL3 enhances Rpi-mcq1 and compromises R2 HR. Okadaic acid, which inhibits BSL phosphatase activity, suppresses both recognition events. Moreover, expression of a BSL1 phosphatase-dead (PD) mutant suppresses R2 HR, whereas BSL2-PD and BSL3-PD mutants suppress Rpi-mcq1 HR. R2 interacts with BSL1 in the presence of PiAVR2, but not with BSL2 and BSL3, whereas no interactions were detected between Rpi-mcq1 and BSLs. Thus, BSL1 activity and association with R2 determine recognition of PiAVR2 by R2, whereas BSL2 and BSL3 mediate Rpi-mcq1 perception of PiAVR2. R2 and Rpi-mcq1 utilise distinct mechanisms to detect PiAVR2 based on association with different BSLs, highlighting central roles of these effector targets for both disease and disease resistance.
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Affiliation(s)
- Haixia Wang
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Rd, Invergowrie, Dundee, DD2 5DA, UK
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Franziska Trusch
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Rd, Invergowrie, Dundee, DD2 5DA, UK
| | - Dionne Turnbull
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Rd, Invergowrie, Dundee, DD2 5DA, UK
| | - Carolina Aguilera-Galvez
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Susan Breen
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 DA, UK
- School of Life Sciences, The University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Shaista Naqvi
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Rd, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Ingo Hein
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Rd, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 DA, UK
| | - Zhendong Tian
- Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Vivianne Vleeshouwers
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Eleanor Gilroy
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 DA, UK
| | - Paul R J Birch
- Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Rd, Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 DA, UK
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25
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Castel B, Fairhead S, Furzer OJ, Redkar A, Wang S, Cevik V, Holub EB, Jones JDG. Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida race recognition specificities. Plant J 2021; 107:1490-1502. [PMID: 34181787 DOI: 10.1111/tpj.15396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR) genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Columbia (Col-0) provides resistance to many but not all white rust races, and encodes a nucleotide-binding, leucine-rich repeat immune receptor. Col-0 WRR4A resistance is broken by AcEx1, an isolate of A. candida. We identified an allele of WRR4A in Arabidopsis accession Øystese-0 (Oy-0) and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed in the oilseed crop Camelina sativa.
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Affiliation(s)
- Baptiste Castel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Warwick Crop Centre, School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, United Kingdom
| | - Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Genetics, University of Cordoba, 14071, Cordoba, Spain
| | - Shanshan Wang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, BA2 7AY, Bath, United Kingdom
| | - Eric B Holub
- Warwick Crop Centre, School of Life Sciences, University of Warwick, CV35 9EF, Wellesbourne, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
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26
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Jones JDG, Dangl JL. Editorial overview: An embarrassment of riches. Curr Opin Plant Biol 2021; 62:102105. [PMID: 34479723 DOI: 10.1016/j.pbi.2021.102105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Jonathan D G Jones
- The Sainsbury Lab, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jeffery L Dangl
- Howard Hughes Medical Institute and Dept. of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.
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27
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Sun X, Lapin D, Feehan JM, Stolze SC, Kramer K, Dongus JA, Rzemieniewski J, Blanvillain-Baufumé S, Harzen A, Bautor J, Derbyshire P, Menke FLH, Finkemeier I, Nakagami H, Jones JDG, Parker JE. Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity. Nat Commun 2021; 12:3335. [PMID: 34099661 PMCID: PMC8185089 DOI: 10.1038/s41467-021-23614-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
Plants utilise intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors to detect pathogen effectors and activate local and systemic defence. NRG1 and ADR1 "helper" NLRs (RNLs) cooperate with enhanced disease susceptibility 1 (EDS1), senescence-associated gene 101 (SAG101) and phytoalexin-deficient 4 (PAD4) lipase-like proteins to mediate signalling from TIR domain NLR receptors (TNLs). The mechanism of RNL/EDS1 family protein cooperation is not understood. Here, we present genetic and molecular evidence for exclusive EDS1/SAG101/NRG1 and EDS1/PAD4/ADR1 co-functions in TNL immunity. Using immunoprecipitation and mass spectrometry, we show effector recognition-dependent interaction of NRG1 with EDS1 and SAG101, but not PAD4. An EDS1-SAG101 complex interacts with NRG1, and EDS1-PAD4 with ADR1, in an immune-activated state. NRG1 requires an intact nucleotide-binding P-loop motif, and EDS1 a functional EP domain and its partner SAG101, for induced association and immunity. Thus, two distinct modules (NRG1/EDS1/SAG101 and ADR1/EDS1/PAD4) mediate TNL receptor defence signalling.
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Affiliation(s)
- Xinhua Sun
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Joanna M Feehan
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Sara C Stolze
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Katharina Kramer
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Joram A Dongus
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jakub Rzemieniewski
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Servane Blanvillain-Baufumé
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Iris Finkemeier
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biology and Biotechnology of Plants, University of Muenster, Muenster, Germany
| | - Hirofumi Nakagami
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Proteomics group, 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.
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
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Sun X, Lapin D, Feehan JM, Stolze SC, Kramer K, Dongus JA, Rzemieniewski J, Blanvillain-Baufumé S, Harzen A, Bautor J, Derbyshire P, Menke FLH, Finkemeier I, Nakagami H, Jones JDG, Parker JE. Pathogen effector recognition-dependent association of NRG1 with EDS1 and SAG101 in TNL receptor immunity. Nat Commun 2021; 12:3335. [PMID: 34099661 DOI: 10.1101/2020.12.21.423810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/30/2021] [Indexed: 05/21/2023] Open
Abstract
Plants utilise intracellular nucleotide-binding, leucine-rich repeat (NLR) immune receptors to detect pathogen effectors and activate local and systemic defence. NRG1 and ADR1 "helper" NLRs (RNLs) cooperate with enhanced disease susceptibility 1 (EDS1), senescence-associated gene 101 (SAG101) and phytoalexin-deficient 4 (PAD4) lipase-like proteins to mediate signalling from TIR domain NLR receptors (TNLs). The mechanism of RNL/EDS1 family protein cooperation is not understood. Here, we present genetic and molecular evidence for exclusive EDS1/SAG101/NRG1 and EDS1/PAD4/ADR1 co-functions in TNL immunity. Using immunoprecipitation and mass spectrometry, we show effector recognition-dependent interaction of NRG1 with EDS1 and SAG101, but not PAD4. An EDS1-SAG101 complex interacts with NRG1, and EDS1-PAD4 with ADR1, in an immune-activated state. NRG1 requires an intact nucleotide-binding P-loop motif, and EDS1 a functional EP domain and its partner SAG101, for induced association and immunity. Thus, two distinct modules (NRG1/EDS1/SAG101 and ADR1/EDS1/PAD4) mediate TNL receptor defence signalling.
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Affiliation(s)
- Xinhua Sun
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitry Lapin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Joanna M Feehan
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Sara C Stolze
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Katharina Kramer
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Joram A Dongus
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jakub Rzemieniewski
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Servane Blanvillain-Baufumé
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Anne Harzen
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Iris Finkemeier
- Proteomics group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biology and Biotechnology of Plants, University of Muenster, Muenster, Germany
| | - Hirofumi Nakagami
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Proteomics group, 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.
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany.
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Abstract
Plant intracellular NLR proteins detect pathogen effectors and then form multimeric protein complexes ("resistosomes") that activate immune responses and cell death through unknown mechanisms. In this issue of Cell, Bi et al. show that the ZAR1 resistosome exhibits cation channel activity, enabling calcium influx that activates defense mechanisms and culminates in cell death.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
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30
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Guo H, Wang S, Jones JDG. Autoactive Arabidopsis RPS4 alleles require partner protein RRS1-R. Plant Physiol 2021; 185:761-764. [PMID: 33793895 PMCID: PMC8133560 DOI: 10.1093/plphys/kiaa076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Autoactivity of an executor immune receptor due to mutations in putative ATP hydrolysis motifs requires the full-length allele of the cognate sensor immune receptor.
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Affiliation(s)
- Hailong Guo
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shanshan Wang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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31
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Ngou BPM, Ahn HK, Ding P, Jones JDG. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature 2021; 592:110-115. [PMID: 33692545 DOI: 10.1101/2020.04.10.034173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/01/2021] [Indexed: 05/25/2023]
Abstract
The plant immune system involves cell-surface receptors that detect intercellular pathogen-derived molecules, and intracellular receptors that activate immunity upon detection of pathogen-secreted effector proteins that act inside the plant cell. Immunity mediated by surface receptors has been extensively studied1, but that mediated by intracellular receptors has rarely been investigated in the absence of surface-receptor-mediated immunity. Furthermore, interactions between these two immune pathways are poorly understood. Here, by activating intracellular receptors without inducing surface-receptor-mediated immunity, we analyse interactions between these two distinct immune systems in Arabidopsis. Pathogen recognition by surface receptors activates multiple protein kinases and NADPH oxidases, and we find that intracellular receptors primarily potentiate the activation of these proteins by increasing their abundance through several mechanisms. Likewise, the hypersensitive response that depends on intracellular receptors is strongly enhanced by the activation of surface receptors. Activation of either immune system alone is insufficient to provide effective resistance against the bacterial pathogen Pseudomonas syringae. Thus, immune pathways activated by cell-surface and intracellular receptors in plants mutually potentiate to activate strong defences against pathogens. These findings reshape our understanding of plant immunity and have broad implications for crop improvement.
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Affiliation(s)
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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32
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Ngou BPM, Ahn HK, Ding P, Jones JDG. Mutual potentiation of plant immunity by cell-surface and intracellular receptors. Nature 2021; 592:110-115. [PMID: 33692545 DOI: 10.1038/s41586-021-03315-7] [Citation(s) in RCA: 396] [Impact Index Per Article: 132.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/01/2021] [Indexed: 02/03/2023]
Abstract
The plant immune system involves cell-surface receptors that detect intercellular pathogen-derived molecules, and intracellular receptors that activate immunity upon detection of pathogen-secreted effector proteins that act inside the plant cell. Immunity mediated by surface receptors has been extensively studied1, but that mediated by intracellular receptors has rarely been investigated in the absence of surface-receptor-mediated immunity. Furthermore, interactions between these two immune pathways are poorly understood. Here, by activating intracellular receptors without inducing surface-receptor-mediated immunity, we analyse interactions between these two distinct immune systems in Arabidopsis. Pathogen recognition by surface receptors activates multiple protein kinases and NADPH oxidases, and we find that intracellular receptors primarily potentiate the activation of these proteins by increasing their abundance through several mechanisms. Likewise, the hypersensitive response that depends on intracellular receptors is strongly enhanced by the activation of surface receptors. Activation of either immune system alone is insufficient to provide effective resistance against the bacterial pathogen Pseudomonas syringae. Thus, immune pathways activated by cell-surface and intracellular receptors in plants mutually potentiate to activate strong defences against pathogens. These findings reshape our understanding of plant immunity and have broad implications for crop improvement.
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Affiliation(s)
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK. .,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
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33
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Moon H, Pandey A, Yoon H, Choi S, Jeon H, Prokchorchik M, Jung G, Witek K, Valls M, McCann HC, Kim M, Jones JDG, Segonzac C, Sohn KH. Identification of RipAZ1 as an avirulence determinant of Ralstonia solanacearum in Solanum americanum. Mol Plant Pathol 2021; 22:317-333. [PMID: 33389783 PMCID: PMC7865085 DOI: 10.1111/mpp.13030] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
Ralstonia solanacearum causes bacterial wilt disease in many plant species. Type III-secreted effectors (T3Es) play crucial roles in bacterial pathogenesis. However, some T3Es are recognized by corresponding disease resistance proteins and activate plant immunity. In this study, we identified the R. solanacearum T3E protein RipAZ1 (Ralstonia injected protein AZ1) as an avirulence determinant in the black nightshade species Solanum americanum. Based on the S. americanum accession-specific avirulence phenotype of R. solanacearum strain Pe_26, 12 candidate avirulence T3Es were selected for further analysis. Among these candidates, only RipAZ1 induced a cell death response when transiently expressed in a bacterial wilt-resistant S. americanum accession. Furthermore, loss of ripAZ1 in the avirulent R. solanacearum strain Pe_26 resulted in acquired virulence. Our analysis of the natural sequence and functional variation of RipAZ1 demonstrated that the naturally occurring C-terminal truncation results in loss of RipAZ1-triggered cell death. We also show that the 213 amino acid central region of RipAZ1 is sufficient to induce cell death in S. americanum. Finally, we show that RipAZ1 may activate defence in host cell cytoplasm. Taken together, our data indicate that the nucleocytoplasmic T3E RipAZ1 confers R. solanacearum avirulence in S. americanum. Few avirulence genes are known in vascular bacterial phytopathogens and ripAZ1 is the first one in R. solanacearum that is recognized in black nightshades. This work thus opens the way for the identification of disease resistance genes responsible for the specific recognition of RipAZ1, which can be a source of resistance against the devastating bacterial wilt disease.
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Affiliation(s)
- Hayoung Moon
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Ankita Pandey
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hayeon Yoon
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Sera Choi
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Hyelim Jeon
- Department of Agriculture, Forestry and BioresourcesSeoul National UniversitySeoulRepublic of Korea
- Plant Immunity Research CenterSeoul National UniversitySeoulRepublic of Korea
| | - Maxim Prokchorchik
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Gayoung Jung
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Marc Valls
- Department of GeneticsUniversity of BarcelonaBarcelonaSpain
- Centre for Research in Agricultural Genomics (CSIC‐IRTA‐UAB‐UB)BellaterraSpain
| | - Honour C. McCann
- New Zealand Institute of Advanced StudiesMassey UniversityAucklandNew Zealand
- Max Planck Institute for Developmental BiologyTübingenGermany
| | - Min‐Sung Kim
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
- Division of Integrative Biosciences and BiotechnologyPohang University of Science and TechnologyRepublic of Korea
| | | | - Cécile Segonzac
- Department of Agriculture, Forestry and BioresourcesSeoul National UniversitySeoulRepublic of Korea
- Plant Immunity Research CenterSeoul National UniversitySeoulRepublic of Korea
- Department of Plant Science, Plant Genomics and Breeding InstituteAgricultural Life Science Research InstituteSeoul National UniversitySeoulRepublic of Korea
| | - Kee Hoon Sohn
- Department of Life SciencesPohang University of Science and TechnologyPohangRepublic of Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangRepublic of Korea
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34
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Torti S, Schlesier R, Thümmler A, Bartels D, Römer P, Koch B, Werner S, Panwar V, Kanyuka K, Wirén NV, Jones JDG, Hause G, Giritch A, Gleba Y. Transient reprogramming of crop plants for agronomic performance. Nat Plants 2021; 7:159-171. [PMID: 33594264 DOI: 10.1038/s41477-021-00851-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/11/2021] [Indexed: 05/02/2023]
Abstract
The development of a new crop variety is a time-consuming and costly process due to the reliance of plant breeding on gene shuffling to introduce desired genes into elite germplasm, followed by backcrossing. Here, we propose alternative technology that transiently targets various regulatory circuits within a plant, leading to operator-specified alterations of agronomic traits, such as time of flowering, vernalization requirement, plant height or drought tolerance. We redesigned techniques of gene delivery, amplification and expression around RNA viral transfection methods that can be implemented on an industrial scale and with many crop plants. The process does not involve genetic modification of the plant genome and is thus limited to a single plant generation, is broadly applicable, fast, tunable and versatile, and can be used throughout much of the crop cultivation cycle. The RNA-based reprogramming may be especially useful in plant pathogen pandemics but also for commercial seed production and for rapid adaptation of orphan crops.
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Affiliation(s)
| | | | | | | | | | | | - Stefan Werner
- Nomad Bioscience GmbH, Halle, Germany
- Icon Genetics GmbH, Halle, Germany
| | - Vinay Panwar
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Germany
| | | | - Gerd Hause
- Biocenter, Electron Microscopy, Martin Luther University of Halle-Wittenberg, Halle, Germany
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35
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Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, Stam R, van Oosterhout C, Fairhead S, Heal R, Cocker JM, Bhanvadia S, Barrett W, Wu CH, Adachi H, Song T, Kamoun S, Vleeshouwers VGAA, Tomlinson L, Wulff BBH, Jones JDG. A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector. Nat Plants 2021; 7:198-208. [PMID: 33574576 PMCID: PMC7116783 DOI: 10.1038/s41477-021-00854-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/12/2021] [Indexed: 05/05/2023]
Abstract
Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only ~90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologues and paralogues. We propose that Rpi-amr1 gene family diversity assists detection of diverse paralogues and alleles of the recognized effector, facilitating durable resistance against P. infestans.
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Affiliation(s)
- Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- US Department of Agriculture-Agricultural Research Service, Madison, WI, USA
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Bayer Crop Science, Chesterfield, MO, USA
| | - Agnieszka I Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Remco Stam
- Phytopathology, Technical University Munich, Freising, Germany
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan M Cocker
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- University of Hull, Hull, UK
| | - Shivani Bhanvadia
- Plant Breeding, Wageningen University and Research, Wageningen, the Netherlands
| | - William Barrett
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- The New Zealand Institute for Plant & Food Research Ltd, Nelson, New Zealand
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, P. R. China
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | | | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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36
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Lin X, Song T, Fairhead S, Witek K, Jouet A, Jupe F, Witek AI, Karki HS, Vleeshouwers VGAA, Hein I, Jones JDG. Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq). Mol Plant Pathol 2020; 21:1502-1512. [PMID: 32935441 DOI: 10.1101/2020.05.14.095158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 05/23/2023]
Abstract
Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Agathe Jouet
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Florian Jupe
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Hari S Karki
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Ingo Hein
- School of Life Sciences, Division of Plant Sciences, University of Dundee, Dundee, UK
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
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37
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Lin X, Song T, Fairhead S, Witek K, Jouet A, Jupe F, Witek AI, Karki HS, Vleeshouwers VGAA, Hein I, Jones JDG. Identification of Avramr1 from Phytophthora infestans using long read and cDNA pathogen-enrichment sequencing (PenSeq). Mol Plant Pathol 2020; 21:1502-1512. [PMID: 32935441 PMCID: PMC7548994 DOI: 10.1111/mpp.12987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 05/22/2023]
Abstract
Potato late blight, caused by the oomycete pathogen Phytophthora infestans, significantly hampers potato production. Recently, a new Resistance to Phytophthora infestans (Rpi) gene, Rpi-amr1, was cloned from a wild Solanum species, Solanum americanum. Identification of the corresponding recognized effector (Avirulence or Avr) genes from P. infestans is key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance. To identify the P. infestans effector recognized by Rpi-amr1, we screened available RXLR effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on four P. infestans isolates to explore the untested effectors. Using single-molecule real-time sequencing (SMRT) and cDNA PenSeq, we identified 47 highly expressed effectors from P. infestans, including PITG_07569, which triggers a highly specific cell death response when transiently coexpressed with Rpi-amr1 in Nicotiana benthamiana, suggesting that PITG_07569 is Avramr1. Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RXLR effector families and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RXLR effector family that is associated with the recognition by Rpi-amr1.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East AngliaNorwichUK
| | - Tianqiao Song
- The Sainsbury Laboratory, University of East AngliaNorwichUK
- Present address:
Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | | | - Kamil Witek
- The Sainsbury Laboratory, University of East AngliaNorwichUK
| | - Agathe Jouet
- The Sainsbury Laboratory, University of East AngliaNorwichUK
| | - Florian Jupe
- The Sainsbury Laboratory, University of East AngliaNorwichUK
- Present address:
Bayer Crop ScienceChesterfieldMissouriUSA
| | | | - Hari S. Karki
- The Sainsbury Laboratory, University of East AngliaNorwichUK
- Present address:
U.S. Department of Agriculture–Agricultural Research ServiceMadisonWisconsinUSA
| | | | - Ingo Hein
- School of Life SciencesDivision of Plant SciencesUniversity of DundeeDundeeUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrie, DundeeUK
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38
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Saile SC, Jacob P, Castel B, Jubic LM, Salas-Gonzáles I, Bäcker M, Jones JDG, Dangl JL, El Kasmi F. Two unequally redundant "helper" immune receptor families mediate Arabidopsis thaliana intracellular "sensor" immune receptor functions. PLoS Biol 2020; 18:e3000783. [PMID: 32925907 PMCID: PMC7514072 DOI: 10.1371/journal.pbio.3000783] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 09/24/2020] [Accepted: 08/17/2020] [Indexed: 01/08/2023] Open
Abstract
Plant nucleotide-binding (NB) leucine-rich repeat (LRR) receptor (NLR) proteins function as intracellular immune receptors that perceive the presence of pathogen-derived virulence proteins (effectors) to induce immune responses. The 2 major types of plant NLRs that “sense” pathogen effectors differ in their N-terminal domains: these are Toll/interleukin-1 receptor resistance (TIR) domain-containing NLRs (TNLs) and coiled-coil (CC) domain-containing NLRs (CNLs). In many angiosperms, the RESISTANCE TO POWDERY MILDEW 8 (RPW8)-CC domain containing NLR (RNL) subclass of CNLs is encoded by 2 gene families, ACTIVATED DISEASE RESISTANCE 1 (ADR1) and N REQUIREMENT GENE 1 (NRG1), that act as “helper” NLRs during multiple sensor NLR-mediated immune responses. Despite their important role in sensor NLR-mediated immunity, knowledge of the specific, redundant, and synergistic functions of helper RNLs is limited. We demonstrate that the ADR1 and NRG1 families act in an unequally redundant manner in basal resistance, effector-triggered immunity (ETI) and regulation of defense gene expression. We define RNL redundancy in ETI conferred by some TNLs and in basal resistance against virulent pathogens. We demonstrate that, in Arabidopsis thaliana, the 2 RNL families contribute specific functions in ETI initiated by specific CNLs and TNLs. Time-resolved whole genome expression profiling revealed that RNLs and “classical” CNLs trigger similar transcriptome changes, suggesting that RNLs act like other CNLs to mediate ETI downstream of sensor NLR activation. Together, our genetic data confirm that RNLs contribute to basal resistance, are fully required for TNL signaling, and can also support defense activation during CNL-mediated ETI. This study shows that two intracellular plant Nod-like immune receptor (NLR-) subfamilies act with unequal redundancy in their roles in plant disease resistance to virulent and avirulent pathogens, in effector-triggered immunity induced gene expression and in immunity-associated cell death. This function is most likely in parallel with, and not downstream of, other canonical intracellular plant immune receptors.
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Affiliation(s)
- Svenja C. Saile
- Center for Plant Molecular Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Pierre Jacob
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Baptiste Castel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Lance M. Jubic
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isai Salas-Gonzáles
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Marcel Bäcker
- Center for Plant Molecular Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Jeffery L. Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Farid El Kasmi
- Center for Plant Molecular Biology, Eberhard Karls University of Tübingen, Tübingen, Germany
- * E-mail:
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39
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Ding P, Ngou BPM, Furzer OJ, Sakai T, Shrestha RK, MacLean D, Jones JDG. High-resolution expression profiling of selected gene sets during plant immune activation. Plant Biotechnol J 2020; 18:1610-1619. [PMID: 31916350 PMCID: PMC7292544 DOI: 10.1111/pbi.13327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 05/08/2023]
Abstract
The plant immune system involves detection of pathogens via both cell-surface and intracellular receptors. Both receptor classes can induce transcriptional reprogramming that elevates disease resistance. To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I). We designed and synthesized biotinylated single-strand RNA bait libraries targeted to a subset of defense genes, and generated sequence capture data from 99 RNA-seq libraries. We built a data processing pipeline to quantify the RNA-CAP-I-seq data, and visualize differential gene expression. Sequence capture in combination with quantitative RNA-seq enabled cost-effective assessment of the expression profile of a specified subset of genes. Quantitative sequence capture is not limited to RNA-seq or any specific organism and can potentially be incorporated into automated platforms for high-throughput sequencing.
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Affiliation(s)
- Pingtao Ding
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Bruno Pok Man Ngou
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Oliver J. Furzer
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichUK
- Present address:
The University of North CarolinaChapel HillNCUSA
| | - Toshiyuki Sakai
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichUK
| | | | - Dan MacLean
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNorwichUK
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40
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Affiliation(s)
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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41
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Steuernagel B, Witek K, Krattinger SG, Ramirez-Gonzalez RH, Schoonbeek HJ, Yu G, Baggs E, Witek AI, Yadav I, Krasileva KV, Jones JDG, Uauy C, Keller B, Ridout CJ, Wulff BBH. The NLR-Annotator Tool Enables Annotation of the Intracellular Immune Receptor Repertoire. Plant Physiol 2020; 183:468-482. [PMID: 32184345 PMCID: PMC7271791 DOI: 10.1104/pp.19.01273] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/06/2020] [Indexed: 05/19/2023]
Abstract
Disease resistance genes encoding nucleotide-binding and leucine-rich repeat (NLR) intracellular immune receptor proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR-encoding genes. The availability of the hexaploid wheat (Triticum aestivum) cultivar Chinese Spring reference genome allows a detailed study of its NLR complement. However, low NLR expression and high intrafamily sequence homology hinder their accurate annotation. Here, we developed NLR-Annotator, a software tool for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. We applied our tool to wheat and combined it with a transcript-validated subset of genes from the reference gene annotation to characterize the structure, phylogeny, and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci, of which 1,560 were confirmed as expressed genes with intact open reading frames. NLRs with integrated domains mostly group in specific subclades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains, suggesting a paired helper function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts). In young leaves subjected to biotic stress, we found up-regulation of 266 of the NLRs To illustrate the utility of our tool for the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease-resistant varieties.
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Affiliation(s)
| | - Kamil Witek
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Erin Baggs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Agnieszka I Witek
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Dr. G.S. Khush Laboratories, Punjab Agricultural University, Ludhiana-141 004, Punjab, India
| | - Ksenia V Krasileva
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom
| | - Jonathan D G Jones
- Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | | | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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42
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Guo H, Ahn HK, Sklenar J, Huang J, Ma Y, Ding P, Menke FLH, Jones JDG. Phosphorylation-Regulated Activation of the Arabidopsis RRS1-R/RPS4 Immune Receptor Complex Reveals Two Distinct Effector Recognition Mechanisms. Cell Host Microbe 2020; 27:769-781.e6. [PMID: 32234500 DOI: 10.1016/j.chom.2020.03.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/20/2019] [Accepted: 03/12/2020] [Indexed: 12/26/2022]
Abstract
The Arabidopsis immune receptors RPS4 and RRS1 interact to co-confer responsiveness to bacterial effectors. The RRS1-R allele, with RPS4, responds to AvrRps4 and PopP2, whereas RRS1-S responds only to AvrRps4. Here, we show that the C terminus of RRS1-R but not RRS1-S is phosphorylated. Phosphorylation at Thr1214 in the WRKY domain maintains RRS1-R in its inactive state and also inhibits acetylation of RRS1-R by PopP2. PopP2 in turn catalyzes O-acetylation at the same site, thereby preventing its phosphorylation. Phosphorylation at other sites is required for PopP2 but not AvrRps4 responsiveness and facilitates the interaction of RRS1's C terminus with its TIR domain. Derepression of RRS1-R or RRS1-S involves effector-triggered proximity between their TIR domain and C termini. This effector-promoted interaction between these domains relieves inhibition of TIRRPS4 by TIRRRS1. Our data reveal effector-triggered and phosphorylation-regulated conformational changes within RRS1 that results in distinct modes of derepression of the complex by PopP2 and AvrRps4.
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Affiliation(s)
- Hailong Guo
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jianhua Huang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yan Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
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43
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Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 2020; 178:1260-1272.e14. [PMID: 31442410 PMCID: PMC6709784 DOI: 10.1016/j.cell.2019.07.038] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/13/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes. Species-wide NLR diversity is high but not unlimited A large fraction of NLR diversity is recovered with 40–50 accessions Presence/absence variation in NLRs is widespread, resulting in a mosaic population A high diversity of NLR-integrated domains favor known virulence targets
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Affiliation(s)
- Anna-Lena Van de Weyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Freddy Monteiro
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Oliver J Furzer
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Milner Centre for Evolution & Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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44
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Andolfo G, Di Donato A, Chiaiese P, De Natale A, Pollio A, Jones JDG, Frusciante L, Ercolano MR. Alien Domains Shaped the Modular Structure of Plant NLR Proteins. Genome Biol Evol 2020; 11:3466-3477. [PMID: 31730154 PMCID: PMC7145615 DOI: 10.1093/gbe/evz248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2019] [Indexed: 12/20/2022] Open
Abstract
Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multitaxa reconstruction of NB-domain associations allowed us to identify the first NB–LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from Toll/interleukin receptor–NB–LRR members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis support the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell-surface LRR receptors.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | - Antimo Di Donato
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | | | - Antonino Pollio
- Department of Biology, University of Naples "Federico II", Italy
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, United Kingdom
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
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Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG. Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. J Exp Bot 2020; 71:2186-2197. [PMID: 32050020 PMCID: PMC7242080 DOI: 10.1093/jxb/erz571] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/14/2020] [Indexed: 05/18/2023]
Abstract
Plant nucleotide-binding domain, leucine-rich repeat receptor (NLR) proteins play important roles in recognition of pathogen-derived effectors. However, the mechanism by which plant NLRs activate immunity is still largely unknown. The paired Arabidopsis NLRs RRS1-R and RPS4, that confer recognition of bacterial effectors AvrRps4 and PopP2, are well studied, but how the RRS1/RPS4 complex activates early immediate downstream responses upon effector detection is still poorly understood. To study RRS1/RPS4 responses without the influence of cell surface receptor immune pathways, we generated an Arabidopsis line with inducible expression of the effector AvrRps4. Induction does not lead to hypersensitive cell death response (HR) but can induce electrolyte leakage, which often correlates with plant cell death. Activation of RRS1 and RPS4 without pathogens cannot activate mitogen-associated protein kinase cascades, but still activates up-regulation of defence genes, and therefore resistance against bacteria.
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Affiliation(s)
- Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Genetics, University of Córdoba, Córdoba, Spain
| | - Hannah Brown
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yan Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Mark Youles
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Laurence Tomlinson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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Grech-Baran M, Witek K, Szajko K, Witek AI, Morgiewicz K, Wasilewicz-Flis I, Jakuczun H, Marczewski W, Jones JDG, Hennig J. Extreme resistance to Potato virus Y in potato carrying the Ry sto gene is mediated by a TIR-NLR immune receptor. Plant Biotechnol J 2020. [PMID: 31397954 DOI: 10.1101/445031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto , from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single-molecule real-time sequencing). Rysto was found to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto -dependent extreme resistance was temperature-independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.
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Affiliation(s)
- Marta Grech-Baran
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Katarzyna Szajko
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | | | - Karolina Morgiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute-National Research Institute, Młochów, Poland
| | | | - Jacek Hennig
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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47
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Grech‐Baran M, Witek K, Szajko K, Witek AI, Morgiewicz K, Wasilewicz‐Flis I, Jakuczun H, Marczewski W, Jones JDG, Hennig J. Extreme resistance to Potato virus Y in potato carrying the Ry sto gene is mediated by a TIR-NLR immune receptor. Plant Biotechnol J 2020; 18:655-667. [PMID: 31397954 PMCID: PMC7004898 DOI: 10.1111/pbi.13230] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 05/19/2023]
Abstract
Potato virus Y (PVY) is a major potato (Solanum tuberosum L.) pathogen that causes severe annual crop losses worth billions of dollars worldwide. PVY is transmitted by aphids, and successful control of virus transmission requires the extensive use of environmentally damaging insecticides to reduce vector populations. Rysto , from the wild relative S. stoloniferum, confers extreme resistance (ER) to PVY and related viruses and is a valuable trait that is widely employed in potato resistance breeding programmes. Rysto was previously mapped to a region of potato chromosome XII, but the specific gene has not been identified to date. In this study, we isolated Rysto using resistance gene enrichment sequencing (RenSeq) and PacBio SMRT (Pacific Biosciences single-molecule real-time sequencing). Rysto was found to encode a nucleotide-binding leucine-rich repeat (NLR) protein with an N-terminal TIR domain and was sufficient for PVY perception and ER in transgenic potato plants. Rysto -dependent extreme resistance was temperature-independent and requires EDS1 and NRG1 proteins. Rysto may prove valuable for creating PVY-resistant cultivars of potato and other Solanaceae crops.
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Affiliation(s)
- Marta Grech‐Baran
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Kamil Witek
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Katarzyna Szajko
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | | | - Karolina Morgiewicz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Iwona Wasilewicz‐Flis
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | - Henryka Jakuczun
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute‐National Research InstituteMłochówPoland
| | | | - Jacek Hennig
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
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48
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Jones JDG. The curious case of the bacterial engineer. Nat Plants 2019; 5:906-907. [PMID: 31477890 DOI: 10.1038/s41477-019-0516-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Jonathan D G Jones
- Sainsbury Laboratory, Norwich Research Park, University of East Anglia, Norwich, UK.
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49
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Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 2019. [PMID: 31442410 DOI: 10.1101/537001v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes.
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Affiliation(s)
- Anna-Lena Van de Weyer
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Freddy Monteiro
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Oliver J Furzer
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA; The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Milner Centre for Evolution & Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jeffery L Dangl
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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50
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Jones JDG. Flor-iculture: Ellis and Dodds' Illumination of Gene-for-Gene Biology. Plant Cell 2019; 31:1204-1205. [PMID: 31036596 PMCID: PMC6588296 DOI: 10.1105/tpc.19.00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Jonathan D G Jones
- The Sainsbury Laboratory University of East AngliaNorwich, United Kingdom
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