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Zdrzałek R, Xi Y, Langner T, Bentham AR, Petit-Houdenot Y, De la Concepcion JC, Harant A, Shimizu M, Were V, Talbot NJ, Terauchi R, Kamoun S, Banfield MJ. Bioengineering a plant NLR immune receptor with a robust binding interface toward a conserved fungal pathogen effector. Proc Natl Acad Sci U S A 2024; 121:e2402872121. [PMID: 38968126 PMCID: PMC11252911 DOI: 10.1073/pnas.2402872121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/21/2024] [Indexed: 07/07/2024] Open
Abstract
Bioengineering of plant immune receptors has emerged as a key strategy for generating novel disease resistance traits to counteract the expanding threat of plant pathogens to global food security. However, current approaches are limited by rapid evolution of plant pathogens in the field and may lack durability when deployed. Here, we show that the rice nucleotide-binding, leucine-rich repeat (NLR) immune receptor Pik-1 can be engineered to respond to a conserved family of effectors from the multihost blast fungus pathogen Magnaporthe oryzae. We switched the effector binding and response profile of the Pik NLR from its cognate rice blast effector AVR-Pik to the host-determining factor pathogenicity toward weeping lovegrass 2 (Pwl2) by installing a putative host target, OsHIPP43, in place of the native integrated heavy metal-associated domain (generating Pikm-1OsHIPP43). This chimeric receptor also responded to other PWL alleles from diverse blast isolates. The crystal structure of the Pwl2/OsHIPP43 complex revealed a multifaceted, robust interface that cannot be easily disrupted by mutagenesis, and may therefore provide durable, broad resistance to blast isolates carrying PWL effectors in the field. Our findings highlight how the host targets of pathogen effectors can be used to bioengineer recognition specificities that have more robust properties compared to naturally evolved disease resistance genes.
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Affiliation(s)
- Rafał Zdrzałek
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Yuxuan Xi
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Adam R. Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | | | - Juan Carlos De la Concepcion
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Motoki Shimizu
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate024-0003, Japan
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto606-8501, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Mark J. Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
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Henningsen EC, Lewis D, Nguyen DT, Sperschneider J, Kianian SF, Stone E, Dodds PN, Figueroa M. Virulence Patterns of Oat Crown Rust in Australia - Season 2022. PLANT DISEASE 2024; 108:1959-1963. [PMID: 38277650 DOI: 10.1094/pdis-09-23-1973-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important foliar pathogen of oat which causes crown rust disease. The virulence profile of 48 Pca isolates derived from different locations in Australia was characterized using a collection of oat lines often utilized in rust surveys in the United States and Australia. This analysis indicates that Pca populations in Eastern Australia are broadly virulent, which contrasts with the population in Western Australia (WA). Several oat lines/Pc genes are effective against all rust samples collected from WA, suggesting they may provide useful resistance in this region if deployed in combination. We identified 19 lines from the United States oat differential set that display disease resistance to Pca in WA, with some in agreement with previous rust survey reports. We adopted the 10-letter nomenclature system to define oat crown rust races in Australia and compare the frequency of those virulence traits to published data from the United States. Based on this nomenclature, 42 unique races were detected among the 48 isolates, reflecting the high diversity of virulence phenotypes for Pca in Australia. Nevertheless, the Pca population in the United States is substantially more broadly virulent than that of Australia. Close examination of resistance profiles for the oat differential set lines after infection with Pca supports hypotheses of allelism or redundancy among Pc genes or the presence of several resistance genes in some oat differential lines. These findings illustrate the need to deconvolute the oat differential set using molecular tools.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Eva C Henningsen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - David Lewis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Duong T Nguyen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Adelaide, SA 5064, Australia
| | - Jana Sperschneider
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Shahryar F Kianian
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, St. Paul, MN, U.S.A
| | - Eric Stone
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Biological Data Science Institute, The Australian National University, Canberra, ACT 2601, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
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Dodds PN, Chen J, Outram MA. Pathogen perception and signaling in plant immunity. THE PLANT CELL 2024; 36:1465-1481. [PMID: 38262477 PMCID: PMC11062475 DOI: 10.1093/plcell/koae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Plant diseases are a constant and serious threat to agriculture and ecological biodiversity. Plants possess a sophisticated innate immunity system capable of detecting and responding to pathogen infection to prevent disease. Our understanding of this system has grown enormously over the past century. Early genetic descriptions of plant disease resistance and pathogen virulence were embodied in the gene-for-gene hypothesis, while physiological studies identified pathogen-derived elicitors that could trigger defense responses in plant cells and tissues. Molecular studies of these phenomena have now coalesced into an integrated model of plant immunity involving cell surface and intracellular detection of specific pathogen-derived molecules and proteins culminating in the induction of various cellular responses. Extracellular and intracellular receptors engage distinct signaling processes but converge on many similar outputs with substantial evidence now for integration of these pathways into interdependent networks controlling disease outcomes. Many of the molecular details of pathogen recognition and signaling processes are now known, providing opportunities for bioengineering to enhance plant protection from disease. Here we provide an overview of the current understanding of the main principles of plant immunity, with an emphasis on the key scientific milestones leading to these insights.
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Affiliation(s)
- Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Megan A Outram
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
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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] [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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Figueroa M, Coaker G, Kanyuka K. Focus on the Effectors at the Interface of Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:168-170. [PMID: 38573845 DOI: 10.1094/mpmi-02-24-0010-cm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Affiliation(s)
- Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT 2600, Australia
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Kostya Kanyuka
- National Institute of Agricultural Botany (NIAB), Cambridge, CB3 0LE, U.K
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Lubega J, Figueroa M, Dodds PN, Kanyuka K. Comparative Analysis of the Avirulence Effectors Produced by the Fungal Stem Rust Pathogen of Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:171-178. [PMID: 38170736 DOI: 10.1094/mpmi-10-23-0169-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Crops are constantly exposed to pathogenic microbes. Rust fungi are examples of these harmful microorganisms, which have a major economic impact on wheat production. To protect themselves from pathogens like rust fungi, plants employ a multilayered immune system that includes immunoreceptors encoded by resistance genes. Significant efforts have led to the isolation of numerous resistance genes against rust fungi in cereals, especially in wheat. However, the evolution of virulence of rust fungi hinders the durability of resistance genes as a strategy for crop protection. Rust fungi, like other biotrophic pathogens, secrete an arsenal of effectors to facilitate infection, and these are the molecules that plant immunoreceptors target for pathogen recognition and mounting defense responses. When recognized, these effector proteins are referred to as avirulence (Avr) effectors. Despite the many predicted effectors in wheat rust fungi, only five Avr genes have been identified, all from wheat stem rust. Knowledge of the Avr genes and their variation in the fungal population will inform deployment of the most appropriate wheat disease-resistance genes for breeding and farming. The review provides an overview of methodologies as well as the validation techniques that have been used to characterize Avr effectors from wheat stem rust. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Jibril Lubega
- National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, U.K
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra 2601, Australia
| | - Kostya Kanyuka
- National Institute of Agricultural Botany (NIAB), Cambridge CB3 0LE, U.K
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Hewitt TC, Henningsen EC, Pereira D, McElroy K, Nazareno ES, Dugyala S, Nguyen-Phuc H, Li F, Miller ME, Visser B, Pretorius ZA, Boshoff WHP, Sperschneider J, Stukenbrock EH, Kianian SF, Dodds PN, Figueroa M. Genome-Enabled Analysis of Population Dynamics and Virulence-Associated Loci in the Oat Crown Rust Fungus Puccinia coronata f. sp. avenae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:290-303. [PMID: 37955552 DOI: 10.1094/mpmi-09-23-0126-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against Pca is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of Pca using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse Pca collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of Pca involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved Pca reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate Avr effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked Avr effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Tim C Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva C Henningsen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Danilo Pereira
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva H Stukenbrock
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
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Locci F, Parker JE. Plant NLR immunity activation and execution: a biochemical perspective. Open Biol 2024; 14:230387. [PMID: 38262605 PMCID: PMC10805603 DOI: 10.1098/rsob.230387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.
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Affiliation(s)
- Federica Locci
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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