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Lahfa M, Barthe P, de Guillen K, Cesari S, Raji M, Kroj T, Le Naour-Vernet M, Hoh F, Gladieux P, Roumestand C, Gracy J, Declerck N, Padilla A. The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited. PLoS Pathog 2024; 20:e1012176. [PMID: 38709846 DOI: 10.1371/journal.ppat.1012176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/28/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast disease on numerous cereals and grasses. In spite of high sequence divergence, MAX effectors share a common fold characterized by a ß-sandwich core stabilized by a conserved disulfide bond. In this study, we investigated the structural landscape and diversity within the MAX effector repertoire of P. oryzae. Combining experimental protein structure determination and in silico structure modeling we validated the presence of the conserved MAX effector core domain in 77 out of 94 groups of orthologs (OG) identified in a previous population genomic study. Four novel MAX effector structures determined by NMR were in remarkably good agreement with AlphaFold2 (AF2) predictions. Based on the comparison of the AF2-generated 3D models we propose a classification of the MAX effectors superfamily in 20 structural groups that vary in the canonical MAX fold, disulfide bond patterns, and additional secondary structures in N- and C-terminal extensions. About one-third of the MAX family members remain singletons, without strong structural relationship to other MAX effectors. Analysis of the surface properties of the AF2 MAX models also highlights the high variability within the MAX family at the structural level, potentially reflecting the wide diversity of their virulence functions and host targets.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Philippe Barthe
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Mouna Raji
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marie Le Naour-Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - François Hoh
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Jérôme Gracy
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Nathalie Declerck
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
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Yang T, Song L, Hu J, Qiao L, Yu Q, Wang Z, Chen X, Lu GD. Magnaporthe oryzae effector AvrPik-D targets a transcription factor WG7 to suppress rice immunity. RICE (NEW YORK, N.Y.) 2024; 17:14. [PMID: 38351214 PMCID: PMC10864242 DOI: 10.1186/s12284-024-00693-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases for rice crops, significantly affecting crop yield and quality. During the infection process, M. oryzae secretes effector proteins that help in hijacking the host's immune responses to establish infection. However, little is known about the interaction between the effector protein AvrPik-D and the host protein Pikh, and how AvrPik-D increases disease severity to promote infection. In this study, we show that the M. oryzae effector AvrPik-D interacts with the zinc finger-type transcription factor WG7 in the nucleus and promotes its transcriptional activity. Genetic removal (knockout) of the gene WG7 in transgenic rice enhances resistance to M. oryzae and also results in an increased burst of reactive oxygen species after treatments with chitin. In addition, the hormone level of SA and JA, is increased and decreased respectively in WG7 KO plants, indicating that WG7 may negatively mediate resistance through salicylic acid pathway. Conversely, WG7 overexpression lines reduce resistance to M. oryzae. However, WG7 is not required for the Pikh-mediated resistance against rice blast. In conclusion, our results revealed that the M. oryzae effector AvrPik-D targets and promotes transcriptional activity of WG7 to suppress rice innate immunity to facilitate infection.
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Affiliation(s)
- Tao Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Linlin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Jinxian Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Luao Qiao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Qing Yu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China
- Fujian Universities Engineering Research Center of Marine Biology and Drugs, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Minjiang University, Fuzhou, 350108, China
| | - Xiaofeng Chen
- Fujian Universities Engineering Research Center of Marine Biology and Drugs, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China.
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Minjiang University, Fuzhou, 350108, China.
| | - Guo-Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 35002, China.
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Oliveira-Garcia E, Yan X, Oses-Ruiz M, de Paula S, Talbot NJ. Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae. THE NEW PHYTOLOGIST 2024; 241:1007-1020. [PMID: 38073141 DOI: 10.1111/nph.19446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024]
Abstract
Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae-host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Miriam Oses-Ruiz
- IMAB, Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Navarra, Spain
| | - Samuel de Paula
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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Wei YY, Liang S, Zhu XM, Liu XH, Lin FC. Recent Advances in Effector Research of Magnaporthe oryzae. Biomolecules 2023; 13:1650. [PMID: 38002332 PMCID: PMC10669146 DOI: 10.3390/biom13111650] [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: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Recalcitrant rice blast disease is caused by Magnaporthe oryzae, which has a significant negative economic reverberation on crop productivity. In order to induce the disease onto the host, M. oryzae positively generates many types of small secreted proteins, here named as effectors, to manipulate the host cell for the purpose of stimulating pathogenic infection. In M. oryzae, by engaging with specific receptors on the cell surface, effectors activate signaling channels which control an array of cellular activities, such as proliferation, differentiation and apoptosis. The most recent research on effector identification, classification, function, secretion, and control mechanism has been compiled in this review. In addition, the article also discusses directions and challenges for future research into an effector in M. oryzae.
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Affiliation(s)
- Yun-Yun Wei
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China;
| | - Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
| | - Xue-Ming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
| | - Xiao-Hong Liu
- Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fu-Cheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (S.L.); (X.-M.Z.)
- Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Rozano L, Hane JK, Mancera RL. The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins. Int J Mol Sci 2023; 24:15239. [PMID: 37894919 PMCID: PMC10607590 DOI: 10.3390/ijms242015239] [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: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Fungal effector proteins are important in mediating disease infections in agriculturally important crops. These secreted small proteins are known to interact with their respective host receptor binding partners in the host, either inside the cells or in the apoplastic space, depending on the localisation of the effector proteins. Consequently, it is important to understand the interactions between fungal effector proteins and their target host receptor binding partners, particularly since this can be used for the selection of potential plant resistance or susceptibility-related proteins that can be applied to the breeding of new cultivars with disease resistance. In this study, molecular docking simulations were used to characterise protein-protein interactions between effector and plant receptors. Benchmarking was undertaken using available experimental structures of effector-host receptor complexes to optimise simulation parameters, which were then used to predict the structures and mediating interactions of effector proteins with host receptor binding partners that have not yet been characterised experimentally. Rigid docking was applied for both the so-called bound and unbound docking of MAX effectors with plant HMA domain protein partners. All bound complexes used for benchmarking were correctly predicted, with 84% being ranked as the top docking pose using the ZDOCK scoring function. In the case of unbound complexes, a minimum of 95% of known residues were predicted to be part of the interacting interface on the host receptor binding partner, and at least 87% of known residues were predicted to be part of the interacting interface on the effector protein. Hydrophobic interactions were found to dominate the formation of effector-plant protein complexes. An optimised set of docking parameters based on the use of ZDOCK and ZRANK scoring functions were established to enable the prediction of near-native docking poses involving different binding interfaces on plant HMA domain proteins. Whilst this study was limited by the availability of the experimentally determined complexed structures of effectors and host receptor binding partners, we demonstrated the potential of molecular docking simulations to predict the likely interactions between effectors and their respective host receptor binding partners. This computational approach may accelerate the process of the discovery of putative interacting plant partners of effector proteins and contribute to effector-assisted marker discovery, thereby supporting the breeding of disease-resistant crops.
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Affiliation(s)
- Lina Rozano
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA 6845, Australia
- Curtin Institute for Data Science, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - James K. Hane
- Curtin Institute for Data Science, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA 6845, Australia
- Curtin Institute for Data Science, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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Contreras MP, Lüdke D, Pai H, Toghani A, Kamoun S. NLR receptors in plant immunity: making sense of the alphabet soup. EMBO Rep 2023; 24:e57495. [PMID: 37602936 PMCID: PMC10561179 DOI: 10.15252/embr.202357495] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
Plants coordinately use cell-surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich-repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad-spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi-disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding.
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Affiliation(s)
| | - Daniel Lüdke
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | - Hsuan Pai
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
| | | | - Sophien Kamoun
- The Sainsbury LaboratoryUniversity of East AngliaNorwichUK
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Ruiz-Bedoya T, McTavish KJ, Av-Shalom TV, Desveaux D, Guttman DS. Towards integrative plant pathology. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102430. [PMID: 37542739 DOI: 10.1016/j.pbi.2023.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/03/2023] [Accepted: 07/03/2023] [Indexed: 08/07/2023]
Abstract
The field of plant pathology has revealed many of the mechanisms underlying the arms race, providing crucial knowledge and genetic resources for improving plant health. Although the host-microbe interaction seemingly favors rapidly evolving pathogens, it has also generated a vast evolutionary history of largely unexplored plant immunodiversity. We review studies that characterize the scope and distribution of genetic and ecological diversity in model and non-model systems with specific reference to pathogen effector diversity, plant immunodiversity in both cultivated species and their wild relatives, and diversity in the plant-associated microbiota. We show how the study of evolutionary and ecological processes can reveal patterns of genetic convergence, conservation, and diversification, and that this diversity is increasingly tractable in both experimental and translational systems. Perhaps most importantly, these patterns of diversity provide largely untapped resources that can be deployed for the rational engineering of durable resistance for sustainable agriculture.
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Affiliation(s)
- Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Kathryn J McTavish
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Tamar V Av-Shalom
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
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Bentham AR, De la Concepcion JC, Benjumea JV, Kourelis J, Jones S, Mendel M, Stubbs J, Stevenson CEM, Maidment JHR, Youles M, Zdrzałek R, Kamoun S, Banfield MJ. Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities. THE PLANT CELL 2023; 35:3809-3827. [PMID: 37486356 PMCID: PMC10533329 DOI: 10.1093/plcell/koad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023]
Abstract
Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine-rich repeat (NLR) receptor superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defense responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signaling networks that coevolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. The sensor and helper NLRs of the rice (Oryza sativa) NLR pair Pik have coevolved, and mismatching between noncoevolved alleles triggers constitutive activation and cell death. This limits the extent to which protein modifications can be used to engineer pathogen recognition and enhance disease resistance mediated by these NLRs. Here, we dissected incompatibility determinants in the Pik pair in Nicotiana benthamiana and found that heavy metal-associated (HMA) domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely coevolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities, overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic domains with novel and enhanced recognition specificities. Taken together, our results reveal a strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.
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Affiliation(s)
- Adam R Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Javier Vega Benjumea
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sally Jones
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Melanie Mendel
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jack Stubbs
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Josephine H R Maidment
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark Youles
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Rafał Zdrzałek
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Barr ZK, Werner T, Tilsner J. Heavy Metal-Associated Isoprenylated Plant Proteins (HIPPs) at Plasmodesmata: Exploring the Link between Localization and Function. PLANTS (BASEL, SWITZERLAND) 2023; 12:3015. [PMID: 37631227 PMCID: PMC10459601 DOI: 10.3390/plants12163015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Heavy metal-associated isoprenylated plant proteins (HIPPs) are a metallochaperone-like protein family comprising a combination of structural features unique to vascular plants. HIPPs possess both one or two heavy metal-binding domains and an isoprenylation site, facilitating a posttranslational protein lipid modification. Recent work has characterized individual HIPPs across numerous different species and provided evidence for varied functionalities. Interestingly, a significant number of HIPPs have been identified in proteomes of plasmodesmata (PD)-nanochannels mediating symplastic connectivity within plant tissues that play pivotal roles in intercellular communication during plant development as well as responses to biotic and abiotic stress. As characterized functions of many HIPPs are linked to stress responses, plasmodesmal HIPP proteins are potentially interesting candidate components of signaling events at or for the regulation of PD. Here, we review what is known about PD-localized HIPP proteins specifically, and how the structure and function of HIPPs more generally could link to known properties and regulation of PD.
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Affiliation(s)
- Zoe Kathleen Barr
- Biomedical Sciences Research Complex, University of St Andrews, BMS Building, North Haugh, St Andrews, Fife KY16 9ST, UK;
- Cell & Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Tomáš Werner
- Department of Biology, University of Graz, Schubertstraße 51, 8010 Graz, Austria
| | - Jens Tilsner
- Biomedical Sciences Research Complex, University of St Andrews, BMS Building, North Haugh, St Andrews, Fife KY16 9ST, UK;
- Cell & Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
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Lahfa M, Mouhand A, de Guillen K, Barthe P, Kroj T, Padilla A, Roumestand C. Does a Similar 3D Structure Mean a Similar Folding Pathway? The Presence of a C-Terminal α-Helical Extension in the 3D Structure of MAX60 Drastically Changes the Folding Pathway Described for Other MAX-Effectors from Magnaporthe oryzae. Molecules 2023; 28:6068. [PMID: 37630320 PMCID: PMC10460046 DOI: 10.3390/molecules28166068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Does a similar 3D structure mean a similar folding pathway? This question is particularly meaningful when it concerns proteins sharing a similar 3D structure, but low sequence identity or homology. MAX effectors secreted by the phytopathogenic fungus Magnaporthe oryzae present such characteristics. They share a common 3D structure, a ß-sandwich with the same topology for all the family members, but an extremely low sequence identity/homology. In a previous study, we have investigated the folding of two MAX effectors, AVR-Pia and AVR-Pib, using High-Hydrostatic-Pressure NMR and found that they display a similar folding pathway, with a common folding intermediate. In the present work, we used a similar strategy to investigate the folding conformational landscape of another MAX effector, MAX60, and found a very different folding intermediate. Our analysis strongly supports that the presence of a C-terminal α-helical extension in the 3D structure of MAX60 could be responsible for its different folding pathway.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Assia Mouhand
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Karine de Guillen
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Philippe Barthe
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Thomas Kroj
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34060 Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
| | - Christian Roumestand
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34090 Montpellier, France; (M.L.); (A.M.); (K.d.G.); (P.B.); (A.P.)
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Dutta TK, Vashisth N, Ray S, Phani V, Chinnusamy V, Sirohi A. Functional analysis of a susceptibility gene (HIPP27) in the Arabidopsis thaliana-Meloidogyne incognita pathosystem by using a genome editing strategy. BMC PLANT BIOLOGY 2023; 23:390. [PMID: 37563544 PMCID: PMC10416466 DOI: 10.1186/s12870-023-04401-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Plant-parasitic root-knot nematodes cause immense yield declines in crop plants that ultimately obviate global food security. They maintain an intimate relationship with their host plants and hijack the host metabolic machinery to their own advantage. The existing resistance breeding strategies utilizing RNAi and resistance (R) genes might not be particularly effective. Alternatively, knocking out the susceptibility (S) genes in crop plants appears to be a feasible approach, as the induced mutations in S genes are likely to be long-lasting and may confer broad-spectrum resistance. This could be facilitated by the use of CRISPR/Cas9-based genome editing technology that precisely edits the gene of interest using customizable guide RNAs (gRNAs) and Cas9 endonuclease. RESULTS Initially, we characterized the nematode-responsive S gene HIPP27 from Arabidopsis thaliana by generating HIPP27 overexpression lines, which were inoculated with Meloidogyne incognita. Next, two gRNAs (corresponding to the HIPP27 gene) were artificially synthesized using laboratory protocols, sequentially cloned into a Cas9 editor plasmid, mobilized into Agrobacterium tumefaciens strain GV3101, and transformed into Arabidopsis plants using the floral dip method. Apart from 1-3 bp deletions and 1 bp insertions adjacent to the PAM site, a long deletion of approximately 161 bp was documented in the T0 generation. Phenotypic analysis of homozygous, 'transgene-free' T2 plants revealed reduced nematode infection compared to wild-type plants. Additionally, no growth impairment was observed in gene-edited plants. CONCLUSION Our results suggest that the loss of function of HIPP27 in A. thaliana by CRISPR/Cas9-induced mutagenesis can improve host resistance to M. incognita.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Neeraj Vashisth
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Soham Ray
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Victor Phani
- Department of Agricultural Entomology, College of Agriculture, Uttar Banga Krishi Viswavidyalaya, Dakshin Dinajpur, Balurghat, West Bengal, 733133, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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12
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Zdrzałek R, Stone C, De la Concepcion JC, Banfield MJ, Bentham AR. Pathways to engineering plant intracellular NLR immune receptors. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102380. [PMID: 37187111 DOI: 10.1016/j.pbi.2023.102380] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023]
Abstract
Factors including climate change and increased global exchange are set to escalate the prevalence of plant diseases, posing an unprecedented threat to global food security and making it more challenging to meet the demands of an ever-growing population. As such, new methods of pathogen control are essential to help with the growing danger of crop losses to plant diseases. The intracellular immune system of plants utilizes nucleotide-binding leucine-rich repeat (NLR) receptors to recognize and activate defense responses to pathogen virulence proteins (effectors) delivered to the host. Engineering the recognition properties of plant NLRs toward pathogen effectors is a genetic solution to plant diseases with high specificity, and it is more sustainable than several current methods for pathogen control that frequently rely on agrochemicals. Here, we highlight the pioneering approaches toward enhancing effector recognition in plant NLRs and discuss the barriers and solutions in engineering the plant intracellular immune system.
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Affiliation(s)
- Rafał Zdrzałek
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Caroline Stone
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Adam R Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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13
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Cadiou L, Brunisholz F, Cesari S, Kroj T. Molecular engineering of plant immune receptors for tailored crop disease resistance. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102381. [PMID: 37192575 DOI: 10.1016/j.pbi.2023.102381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/17/2023] [Accepted: 04/17/2023] [Indexed: 05/18/2023]
Abstract
The specific recognition of pathogen effectors by intracellular nucleotide-binding and leucine-rich repeat domain receptors (NLRs) is an important component of plant immunity. Creating NLRs with new bespoke recognition specificities is a major goal in molecular plant pathology as it promises to provide unlimited resources for the resistance of crops against diseases. Recent breakthrough discoveries on the structure and molecular activity of NLRs begin to enable their knowledge-guided molecular engineering. First, studies succeeded to extend or change effector recognition specificities by modifying, in a structure-guided manner, the NLR domains that directly bind effectors. By modifying the LRR domain of the singleton NLR Sr35 or the unconventional decoy domains of the helper NLRs RGA5 or Pik-1, receptors that detected other or additional effectors were created.
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Affiliation(s)
- Lila Cadiou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Francois Brunisholz
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
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14
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Tamborski J, Seong K, Liu F, Staskawicz BJ, Krasileva KV. Altering Specificity and Autoactivity of Plant Immune Receptors Sr33 and Sr50 Via a Rational Engineering Approach. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:434-446. [PMID: 36867580 PMCID: PMC10561695 DOI: 10.1094/mpmi-07-22-0154-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many resistance genes deployed against pathogens in crops are intracellular nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs). The ability to rationally engineer the specificity of NLRs will be crucial in the response to newly emerging crop diseases. Successful attempts to modify NLR recognition have been limited to untargeted approaches or depended on previously available structural information or knowledge of pathogen-effector targets. However, this information is not available for most NLR-effector pairs. Here, we demonstrate the precise prediction and subsequent transfer of residues involved in effector recognition between two closely related NLRs without their experimentally determined structure or detailed knowledge about their pathogen effector targets. By combining phylogenetics, allele diversity analysis, and structural modeling, we successfully predicted residues mediating interaction of Sr50 with its cognate effector AvrSr50 and transferred recognition specificity of Sr50 to the closely related NLR Sr33. We created synthetic versions of Sr33 that contain amino acids from Sr50, including Sr33syn, which gained the ability to recognize AvrSr50 with 12 amino-acid substitutions. Furthermore, we discovered that sites in the LRR domain needed to transfer recognition specificity to Sr33 also influence autoactivity in Sr50. Structural modeling suggests these residues interact with a part of the NB-ARC domain, which we named the NB-ARC latch, to possibly maintain the inactive state of the receptor. Our approach demonstrates rational modifications of NLRs, which could be useful to enhance existing elite crop germplasm. [Formula: see text] Copyright © 2023 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)
- Janina Tamborski
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
| | - Furong Liu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
| | - Brian J. Staskawicz
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
| | - Ksenia V. Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
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15
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Guo L, Mu Y, Wang D, Ye C, Zhu S, Cai H, Zhu Y, Peng Y, Liu J, He X. Structural mechanism of heavy metal-associated integrated domain engineering of paired nucleotide-binding and leucine-rich repeat proteins in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1187372. [PMID: 37448867 PMCID: PMC10338059 DOI: 10.3389/fpls.2023.1187372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023]
Abstract
Plant nucleotide-binding and leucine-rich repeat (NLR) proteins are immune sensors that detect pathogen effectors and initiate a strong immune response. In many cases, single NLR proteins are sufficient for both effector recognition and signaling activation. These proteins possess a conserved architecture, including a C-terminal leucine-rich repeat (LRR) domain, a central nucleotide-binding (NB) domain, and a variable N-terminal domain. Nevertheless, many paired NLRs linked in a head-to-head configuration have now been identified. The ones carrying integrated domains (IDs) can recognize pathogen effector proteins by various modes; these are known as sensor NLR (sNLR) proteins. Structural and biochemical studies have provided insights into the molecular basis of heavy metal-associated IDs (HMA IDs) from paired NLRs in rice and revealed the co-evolution between pathogens and hosts by combining naturally occurring favorable interactions across diverse interfaces. Focusing on structural and molecular models, here we highlight advances in structure-guided engineering to expand and enhance the response profile of paired NLR-HMA IDs in rice to variants of the rice blast pathogen MAX-effectors (Magnaporthe oryzae AVRs and ToxB-like). These results demonstrate that the HMA IDs-based design of rice materials with broad and enhanced resistance profiles possesses great application potential but also face considerable challenges.
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Affiliation(s)
- Liwei Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuanyu Mu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dongli Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hong Cai
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Youliang Peng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Junfeng Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China
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16
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Zhao L, Zhang T, Luo Y, Li L, Cheng R, Shi Z, Wang G, Ren T. Effects of temperature and microwave on the stability of the blast effector complex APikL2A/sHMA25 as determined by molecular dynamics analyses. J Mol Model 2023; 29:134. [PMID: 37041399 DOI: 10.1007/s00894-023-05550-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/04/2023] [Indexed: 04/13/2023]
Abstract
Magnaporthe oryzae is the causal agent of rice blast, and understanding how abiotic stress affects the resistance of plants to this disease is useful for designing disease control strategies. In this paper, the effects of temperature and microwave irradiation on the effector complex comprising APikL2A from M. oryzae and sHMA25 from foxtail millet were investigated by molecular dynamics simulations using the GROMACS software package. While the structure of APikL2A/sHMA25 remained relatively stable in a temperature range of 290 K (16.85 °C) to 320 K (46.85 °C), the concave shape of the temperature-dependent binding free energy curve indicated that there was maximum binding affinity between APikL2A and sHMA25 at 300 K-310 K. This coincided with the optimum infectivity temperature, thus suggesting that coupling of the two polypeptides may play a role in the infection process. A strong oscillating electric field destroyed the structure of APikL2A/sHMA25, although it was stable and not susceptible to weak electric fields.
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Affiliation(s)
- Ling Zhao
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China
| | - Ting Zhang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China
| | - Yanjie Luo
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China
| | - Lin Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China
| | - Zhigang Shi
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Afairs/National Foxtail Millet Improvement Center/Key Laboratory of Minor Cereal Crops of Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, 050035, Shijiazhuang, China.
| | - Tiancong Ren
- School of Resources and Environmental Sciences, Shijiazhuang University, Shijiazhuang, 050035, China.
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17
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Vo KTX, Yi Q, Jeon JS. Engineering effector-triggered immunity in rice: Obstacles and perspectives. PLANT, CELL & ENVIRONMENT 2023; 46:1143-1156. [PMID: 36305486 DOI: 10.1111/pce.14477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Improving rice immunity is one of the most effective approaches to reduce yield loss by biotic factors, with the aim of increasing rice production by 2050 amidst limited natural resources. Triggering a fast and strong immune response to pathogens, effector-triggered immunity (ETI) has intrigued scientists to intensively study and utilize the mechanisms for engineering highly resistant plants. The conservation of ETI components and mechanisms across species enables the use of ETI components to generate broad-spectrum resistance in plants. Numerous efforts have been made to introduce new resistance (R) genes, widen the effector recognition spectrum and generate on-demand R genes. Although engineering ETI across plant species is still associated with multiple challenges, previous attempts have provided an enhanced understanding of ETI mechanisms. Here, we provide a survey of recent reports in the engineering of rice R genes. In addition, we suggest a framework for future studies of R gene-effector interactions, including genome-scale investigations in both rice and pathogens, followed by structural studies of R proteins and effectors, and potential strategies to use important ETI components to improve rice immunity.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Korea
| | - Qi Yi
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Korea
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18
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Al Mamun Khan MA, Ahsan A, Khan MA, Sanjana JM, Biswas S, Saleh MA, Gupta DR, Hoque MN, Sakif TI, Rahman MM, Islam T. In-silico prediction of highly promising natural fungicides against the destructive blast fungus Magnaporthe oryzae. Heliyon 2023; 9:e15113. [PMID: 37123971 PMCID: PMC10130775 DOI: 10.1016/j.heliyon.2023.e15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Magnaporthe oryzae causes destructive blast disease in more than 50 species of the major cereal crops rice, wheat and maize and destroys food of millions of people worldwide. Application of synthetic chemical fungicides are environmentally hazardous and unreliable in controlling M. oryzae. Conversely, naturally occurring biofungicides with multiple modes of actions are needed to be discovered for combatting the blast fungus. To find the effective biofungicides, we performed molecular docking study of some potential antifungal natural compounds targeting two proteins including a single-stranded DNA binding protein MoSub1 (4AGH), and an effector protein AVR-Pik (5E9G) of M. oryzae that regulates transcription in fungus and/or suppresses the host cell immunity. The thirty-nine natural compounds previously shown to inhibit M. oryzae growth and reproduction were put under molecular docking against these two proteins followed by simulation, free energy, and interaction analysis of protein-ligand complexes. The virtual screening revealed that two alkaloidal metabolites, camptothecin and GKK1032A2 showed excellent binding energy with any of these target proteins compared to reference commercial fungicides, azoxystrobin and strobilurin. Of the detected compounds, GKK1032A2 bound to both target proteins of M. oryzae. Both compounds showed excellent bioactivity scores as compared to the reference fungicides. Results of our computational biological study suggest that both camptothecin and GKK1032A2 are potential fungicides that could also be considered as lead compounds to design novel fungicides against the blast fungus. Furthermore, the GKK1032A2 acted as a multi-site mode of action fungicide against M. oryzae.
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Affiliation(s)
- Md Abdullah Al Mamun Khan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Asif Ahsan
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh
- Bio-Bio-1 Bioinformatics Research Foundation, Dhaka, Bangladesh
| | - Jannatul Maowa Sanjana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur 1706, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506-6109, USA
| | - Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
- Corresponding author. Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh.
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Genome-Wide Identification and Characterization of Copper Chaperone for Superoxide Dismutase (CCS) Gene Family in Response to Abiotic Stress in Soybean. Int J Mol Sci 2023; 24:ijms24065154. [PMID: 36982229 PMCID: PMC10048983 DOI: 10.3390/ijms24065154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
Copper Chaperone For Superoxide Dismutase (CCS) genes encode copper chaperone for Superoxide dismutase (SOD) and dramatically affect the activity of SOD through regulating copper delivery from target to SOD. SOD is the effective component of the antioxidant defense system in plant cells to reduce oxidative damage by eliminating Reactive oxygen species (ROS), which are produced during abiotic stress. CCS might play an important role in abiotic stress to eliminate the damage caused by ROS, however, little is known about CCS in soybean in abiotic stress regulation. In this study, 31 GmCCS gene family members were identified from soybean genome. These genes were classified into 4 subfamilies in the phylogenetic tree. Characteristics of 31 GmCCS genes including gene structure, chromosomal location, collinearity, conserved domain, protein motif, cis-elements, and tissue expression profiling were systematically analyzed. RT-qPCR was used to analyze the expression of 31 GmCCS under abiotic stress, and the results showed that 5 GmCCS genes(GmCCS5, GmCCS7, GmCCS8, GmCCS11 and GmCCS24) were significantly induced by some kind of abiotic stress. The functions of these GmCCS genes in abiotic stress were tested using yeast expression system and soybean hairy roots. The results showed that GmCCS7/GmCCS24 participated in drought stress regulation. Soybean hairy roots expressing GmCCS7/GmCCS24 showed improved drought stress tolerance, with increased SOD and other antioxidant enzyme activities. The results of this study provide reference value in-depth study CCS gene family, and important gene resources for the genetic improvement of soybean drought stress tolerance.
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Wang Z, Zhang H, Li Y, Chen Y, Tang X, Zhao J, Yu F, Wang H, Xiao J, Liu J, Zhang X, Sun L, Xie Q, Wang X. Isoprenylation modification is required for HIPP1-mediated powdery mildew resistance in wheat. PLANT, CELL & ENVIRONMENT 2023; 46:288-305. [PMID: 36319595 DOI: 10.1111/pce.14479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/09/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Powdery mildew (Pm), caused by Blumeria graminis f.sp. tritici (Bgt), is one of the most important wheat diseases. Heavy-metal-associated isoprenylated plant protein (HIPP1) has been proved playing important roles in response to biotic and a biotic stress. In present study, we proved HIPP1-V from Haynalidia villosa is a positive regulator in Pm resistance. HIPP1-V was rapidly induced by Bgt. Transiently or stably heterologous overexpressing HIPP1-V in wheat suppressed the haustorium formation and enhanced Pm resistance. HIPP1-V isoprenylation was critical for plasma membrane (PM) localization, interaction with E3-ligase CMPG1-V and function in Pm resistance. Bgt infection recruited the isoprenylated HIPP1-V and CMPG1s on PM; blocking the HIPP1 isoprenylation reduced such recruitment and compromised the resistance of OE-CMPG1-V and OE-HIPP1-V. Overexpressing HIPP1-VC148G could not enhance Pm resistance. These indicated the Pm resistance was dependent on HIPP1-V's isoprenylation. DGEs related to the ROS and SA pathways were remarkably enriched in OE-HIPP1-V, revealing their involvement in Pm resistance. Our results provide evidence on the important role of protein isoprenylation in plant defense.
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Affiliation(s)
- Zongkuan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Heng Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yingbo Li
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yiming Chen
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Xiong Tang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Jia Zhao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Feifei Yu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Haiyan Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Jin Xiao
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Jia Liu
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Xu Zhang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Li Sun
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiue Wang
- State Key Lab of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu, China
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21
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Marchal C, Pai H, Kamoun S, Kourelis J. Emerging principles in the design of bioengineered made-to-order plant immune receptors. CURRENT OPINION IN PLANT BIOLOGY 2022; 70:102311. [PMID: 36379872 DOI: 10.1016/j.pbi.2022.102311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Crop yield and global food security are under constant threat from plant pathogens with the potential to cause epidemics. Traditional breeding for disease resistance can be too slow to counteract these emerging threats, resulting in the need to retool the plant immune system using bioengineered made-to-order immune receptors. Efforts to engineer immune receptors have focused primarily on nucleotide-binding domain and leucine-rich repeat (NLR) immune receptors and proof-of-principles studies. Based upon a near-exhaustive literature search of previously engineered plant immune systems we distil five emerging principles in the design of bioengineered made-to-order plant NLRs and describe approaches based on other components. These emerging principles are anticipated to assist the functional understanding of plant immune receptors, as well as bioengineering novel disease resistance specificities.
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Affiliation(s)
- Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, UK
| | - Hsuan Pai
- 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.
| | - Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, UK.
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22
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De la Concepcion JC, Fujisaki K, Bentham AR, Cruz Mireles N, Sanchez de Medina Hernandez V, Shimizu M, Lawson DM, Kamoun S, Terauchi R, Banfield MJ. A blast fungus zinc-finger fold effector binds to a hydrophobic pocket in host Exo70 proteins to modulate immune recognition in rice. Proc Natl Acad Sci U S A 2022; 119:e2210559119. [PMID: 36252011 PMCID: PMC9618136 DOI: 10.1073/pnas.2210559119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Exocytosis plays an important role in plant-microbe interactions, in both pathogenesis and symbiosis. Exo70 proteins are integral components of the exocyst, an octameric complex that mediates tethering of vesicles to membranes in eukaryotes. Although plant Exo70s are known to be targeted by pathogen effectors, the underpinning molecular mechanisms and the impact of this interaction on infection are poorly understood. Here, we show the molecular basis of the association between the effector AVR-Pii of the blast fungus Maganaporthe oryzae and rice Exo70 alleles OsExo70F2 and OsExo70F3, which is sensed by the immune receptor pair Pii via an integrated RIN4/NOI domain. The crystal structure of AVR-Pii in complex with OsExo70F2 reveals that the effector binds to a conserved hydrophobic pocket in Exo70, defining an effector/target binding interface. Structure-guided and random mutagenesis validates the importance of AVR-Pii residues at the Exo70 binding interface to sustain protein association and disease resistance in rice when challenged with fungal strains expressing effector mutants. Furthermore, the structure of AVR-Pii defines a zinc-finger effector fold (ZiF) distinct from the MAX (Magnaporthe Avrs and ToxB-like) fold previously described for a majority of characterized M. oryzae effectors. Our data suggest that blast fungus ZiF effectors bind a conserved Exo70 interface to manipulate plant exocytosis and that these effectors are also baited by plant immune receptors, pointing to new opportunities for engineering disease resistance.
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Affiliation(s)
| | - Koki Fujisaki
- bDivision of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, 024-0003, Japan
| | - Adam R. Bentham
- aDepartment of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Neftaly Cruz Mireles
- aDepartment of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, United Kingdom
- cThe Sainsbury Laboratory, University of East Anglia, Norwich, NR4 7UH, United Kingdom
| | | | - Motoki Shimizu
- bDivision of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, 024-0003, Japan
| | - David M. Lawson
- aDepartment of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Sophien Kamoun
- cThe Sainsbury Laboratory, University of East Anglia, Norwich, NR4 7UH, United Kingdom
| | - Ryohei Terauchi
- bDivision of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, 024-0003, Japan
- dLaboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8501, Japan
| | - Mark J. Banfield
- aDepartment of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, United Kingdom
- 2To whom correspondence may be addressed.
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23
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Lüdke D, Yan Q, Rohmann PFW, Wiermer M. NLR we there yet? Nucleocytoplasmic coordination of NLR-mediated immunity. THE NEW PHYTOLOGIST 2022; 236:24-42. [PMID: 35794845 DOI: 10.1111/nph.18359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Plant intracellular nucleotide-binding leucine-rich repeat immune receptors (NLRs) perceive the activity of pathogen-secreted effector molecules that, when undetected, promote colonisation of hosts. Signalling from activated NLRs converges with and potentiates downstream responses from activated pattern recognition receptors (PRRs) that sense microbial signatures at the cell surface. Efficient signalling of both receptor branches relies on the host cell nucleus as an integration point for transcriptional reprogramming, and on the macromolecular transport processes that mediate the communication between cytoplasm and nucleoplasm. Studies on nuclear pore complexes (NPCs), the nucleoporin proteins (NUPs) that compose NPCs, and nuclear transport machinery constituents that control nucleocytoplasmic transport, have revealed that they play important roles in regulating plant immune responses. Here, we discuss the contributions of nucleoporins and nuclear transport receptor (NTR)-mediated signal transduction in plant immunity with an emphasis on NLR immune signalling across the nuclear compartment boundary and within the nucleus. We also highlight and discuss cytoplasmic and nuclear functions of NLRs and their signalling partners and further consider the potential implications of NLR activation and resistosome formation in both cellular compartments for mediating plant pathogen resistance and programmed host cell death.
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Affiliation(s)
- Daniel Lüdke
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Qiqi Yan
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Philipp F W Rohmann
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Marcel Wiermer
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
- Biochemistry of Plant-Microbe Interactions, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195, Berlin, Germany
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24
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Lahfa M, Padilla A, de Guillen K, Pissarra J, Raji M, Cesari S, Kroj T, Gladieux P, Roumestand C, Barthe P. 1H, 13C, 15 N backbone and side-chain NMR assignments for three MAX effectors from Magnaporthe oryzae. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:305-309. [PMID: 35657473 DOI: 10.1007/s12104-022-10095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Effectors are small and very diverse proteins secreted by fungi and translocated in plant cells during infection. Among them, MAX effectors (for Magnaporthe Avrs and ToxB) were identified as a family of effectors that share an identical fold topology despite having highly divergent sequences. They are mostly secreted by ascomycetes from the Magnaporthe genus, a fungus that causes the rice blast, a plant disease leading to huge crop losses. As rice is the first source of calories in many countries, especially in Asia and Africa, this constitutes a threat for world food security. Hence, a better understanding of these effectors, including structural and functional characterization, constitutes a strategic milestone in the fight against phytopathogen fungi and may give clues for the development of resistant varieties of rice. We report here the near complete 1H, 15 N and 13C NMR resonance assignment of three new putative MAX effectors (MAX47, MAX60 and MAX67). Secondary structure determination using TALOS-N and CSI.3 demonstrates a high content of β-strands in all the three proteins, in agreement with the canonic ß-sandwich structure of MAX effectors. This preliminary study provides foundations for further structural characterization, that will help in turn to improve sequence predictions of other MAX effectors through data mining.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Joana Pissarra
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Mouna Raji
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France.
| | - Philippe Barthe
- Centre de Biologie Structurale, Univ Montpellier, INSERM U1054, CNRS UMR 5048, Montpellier, France
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25
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Xi Y, Cesari S, Kroj T. Insight into the structure and molecular mode of action of plant paired NLR immune receptors. Essays Biochem 2022; 66:513-526. [PMID: 35735291 PMCID: PMC9528088 DOI: 10.1042/ebc20210079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022]
Abstract
The specific recognition of pathogen effectors by intracellular nucleotide-binding domain and leucine-rich repeat receptors (NLRs) is an important component of plant immunity. NLRs have a conserved modular architecture and can be subdivided according to their signaling domain that is mostly a coiled-coil (CC) or a Toll/Interleukin1 receptor (TIR) domain into CNLs and TNLs. Single NLR proteins are often sufficient for both effector recognition and immune activation. However, sometimes, they act in pairs, where two different NLRs are required for disease resistance. Functional studies have revealed that in these cases one NLR of the pair acts as a sensor (sNLR) and one as a helper (hNLR). The genes corresponding to such resistance protein pairs with one-to-one functional co-dependence are clustered, generally with a head-to-head orientation and shared promoter sequences. sNLRs in such functional NLR pairs have additional, non-canonical and highly diverse domains integrated in their conserved modular architecture, which are thought to act as decoys to trap effectors. Recent structure-function studies on the Arabidopsis thaliana TNL pair RRS1/RPS4 and on the rice CNL pairs RGA4/RGA5 and Pik-1/Pik-2 are unraveling how such protein pairs function together. Focusing on these model NLR pairs and other recent examples, this review highlights the distinctive features of NLR pairs and their various fascinating mode of action in pathogen effector perception. We also discuss how these findings on NLR pairs pave the way toward improved plant disease resistance.
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Affiliation(s)
- Yuxuan Xi
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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26
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Marchal C, Michalopoulou VA, Zou Z, Cevik V, Sarris PF. Show me your ID: NLR immune receptors with integrated domains in plants. Essays Biochem 2022; 66:527-539. [PMID: 35635051 PMCID: PMC9528084 DOI: 10.1042/ebc20210084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
Nucleotide-binding and leucine-rich repeat receptors (NLRs) are intracellular plant immune receptors that recognize pathogen effectors secreted into the plant cell. Canonical NLRs typically contain three conserved domains including a central nucleotide binding (NB-ARC) domain, C-terminal leucine-rich repeats (LRRs) and an N-terminal domain. A subfamily of plant NLRs contain additional noncanonical domain(s) that have potentially evolved from the integration of the effector targets in the canonical NLR structure. These NLRs with extra domains are thus referred to as NLRs with integrated domains (NLR-IDs). Here, we first summarize our current understanding of NLR-ID activation upon effector binding, focusing on the NLR pairs Pik-1/Pik-2, RGA4/RGA5, and RRS1/RPS4. We speculate on their potential oligomerization into resistosomes as it was recently shown for certain canonical plant NLRs. Furthermore, we discuss how our growing understanding of the mode of action of NLR-ID continuously informs engineering approaches to design new resistance specificities in the context of rapidly evolving pathogens.
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Affiliation(s)
- Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Crete, Greece
| | - Zhou Zou
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, United Kingdom
| | - Volkan Cevik
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, United Kingdom
| | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Crete, Greece
- Department of Biology, University of Crete, 714 09 Heraklion, Crete, Greece
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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27
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Sahu PK, Sao R, Choudhary DK, Thada A, Kumar V, Mondal S, Das BK, Jankuloski L, Sharma D. Advancement in the Breeding, Biotechnological and Genomic Tools towards Development of Durable Genetic Resistance against the Rice Blast Disease. PLANTS 2022; 11:plants11182386. [PMID: 36145787 PMCID: PMC9504543 DOI: 10.3390/plants11182386] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 01/02/2023]
Abstract
Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | | | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India
- Correspondence: (L.J.); (D.S.); Tel.: +91-7000591137 (D.S.)
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28
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A genetically linked pair of NLR immune receptors shows contrasting patterns of evolution. Proc Natl Acad Sci U S A 2022; 119:e2116896119. [PMID: 35771942 PMCID: PMC9271155 DOI: 10.1073/pnas.2116896119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Throughout their evolution, plant nucleotide-binding leucine-rich-repeat receptors (NLRs) have acquired widely divergent unconventional integrated domains that enhance their ability to detect pathogen effectors. However, the functional dynamics that drive the evolution of NLRs with integrated domains (NLR-IDs) remain poorly understood. Here, we reconstructed the evolutionary history of an NLR locus prone to unconventional domain integration and experimentally tested hypotheses about the evolution of NLR-IDs. We show that the rice (Oryza sativa) NLR Pias recognizes the effector AVR-Pias of the blast fungal pathogen Magnaporthe oryzae. Pias consists of a functionally specialized NLR pair, the helper Pias-1 and the sensor Pias-2, that is allelic to the previously characterized Pia pair of NLRs: the helper RGA4 and the sensor RGA5. Remarkably, Pias-2 carries a C-terminal DUF761 domain at a similar position to the heavy metal-associated (HMA) domain of RGA5. Phylogenomic analysis showed that Pias-2/RGA5 sensor NLRs have undergone recurrent genomic recombination within the genus Oryza, resulting in up to six sequence-divergent domain integrations. Allelic NLRs with divergent functions have been maintained transspecies in different Oryza lineages to detect sequence-divergent pathogen effectors. By contrast, Pias-1 has retained its NLR helper activity throughout evolution and is capable of functioning together with the divergent sensor-NLR RGA5 to respond to AVR-Pia. These results suggest that opposite selective forces have driven the evolution of paired NLRs: highly dynamic domain integration events maintained by balancing selection for sensor NLRs, in sharp contrast to purifying selection and functional conservation of immune signaling for helper NLRs.
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29
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Outram MA, Figueroa M, Sperschneider J, Williams SJ, Dodds PN. Seeing is believing: Exploiting advances in structural biology to understand and engineer plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102210. [PMID: 35461025 DOI: 10.1016/j.pbi.2022.102210] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/27/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Filamentous plant pathogens cause disease in numerous economically important crops. These pathogens secrete virulence proteins, termed effectors, that modulate host cellular processes and promote infection. Plants have evolved immunity receptors that detect effectors and activate defence pathways, resulting in resistance to the invading pathogen. This leads to an evolutionary arms race between pathogen and host that is characterised by highly diverse effector repertoires in plant pathogens. Here, we review the recent advances in understanding host-pathogen co-evolution provided by the structural determination of effectors alone, and in complex with immunity receptors. We highlight the use of recent advances in structural prediction within this field and its role for future development of designer resistance proteins.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia.
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30
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Ortiz D, Chen J, Outram MA, Saur IM, Upadhyaya NM, Mago R, Ericsson DJ, Cesari S, Chen C, Williams SJ, Dodds PN. The stem rust effector protein AvrSr50 escapes Sr50 recognition by a substitution in a single surface-exposed residue. THE NEW PHYTOLOGIST 2022; 234:592-606. [PMID: 35107838 PMCID: PMC9306850 DOI: 10.1111/nph.18011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/12/2022] [Indexed: 05/28/2023]
Abstract
Pathogen effectors are crucial players during plant colonisation and infection. Plant resistance mostly relies on effector recognition to activate defence responses. Understanding how effector proteins escape from plant surveillance is important for plant breeding and resistance deployment. Here we examined the role of genetic diversity of the stem rust (Puccinia graminis f. sp. tritici (Pgt)) AvrSr50 gene in determining recognition by the corresponding wheat Sr50 resistance gene. We solved the crystal structure of a natural variant of AvrSr50 and used site-directed mutagenesis and transient expression assays to dissect the molecular mechanisms explaining gain of virulence. We report that AvrSr50 can escape recognition by Sr50 through different mechanisms including DNA insertion, stop codon loss or by amino-acid variation involving a single substitution of the AvrSr50 surface-exposed residue Q121. We also report structural homology of AvrSr50 to cupin superfamily members and carbohydrate-binding modules indicating a potential role in binding sugar moieties. This study identifies key polymorphic sites present in AvrSr50 alleles from natural stem rust populations that play important roles to escape from Sr50 recognition. This constitutes an important step to better understand Pgt effector evolution and to monitor AvrSr50 variants in natural rust populations.
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Affiliation(s)
- Diana Ortiz
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
- National Research Institute for AgricultureFood and Environment, Genetics and Breeding of Fruit and Vegetables UnitMontfavet84143France
| | - Jian Chen
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Megan A. Outram
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Isabel M.L. Saur
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologne50829Germany
- University of Plant SciencesUniversity of CologneCologne50674Germany
- Cluster of Excellence on Plant SciencesCologne50674Germany
| | - Narayana M. Upadhyaya
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Rohit Mago
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Daniel J. Ericsson
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Australian SynchrotronMacromolecular CrystallographyClaytonVic.3168Australia
| | - Stella Cesari
- PHIM Plant Health InstituteUniversité de MontpellierINRAE, CIRADInstitut AgroIRDMontpellier34980France
| | - Chunhong Chen
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Simon J. Williams
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Peter N. Dodds
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
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31
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Cesari S, Xi Y, Declerck N, Chalvon V, Mammri L, Pugnière M, Henriquet C, de Guillen K, Chochois V, Padilla A, Kroj T. New recognition specificity in a plant immune receptor by molecular engineering of its integrated domain. Nat Commun 2022; 13:1524. [PMID: 35314704 PMCID: PMC8938504 DOI: 10.1038/s41467-022-29196-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/11/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractPlant nucleotide-binding and leucine-rich repeat domain proteins (NLRs) are immune sensors that recognize pathogen effectors. Here, we show that molecular engineering of the integrated decoy domain (ID) of an NLR can extend its recognition spectrum to a new effector. We relied for this on detailed knowledge on the recognition of the Magnaporthe oryzae effectors AVR-PikD, AVR-Pia, and AVR1-CO39 by, respectively, the rice NLRs Pikp-1 and RGA5. Both receptors detect their effectors through physical binding to their HMA (Heavy Metal-Associated) IDs. By introducing into RGA5_HMA the AVR-PikD binding residues of Pikp-1_HMA, we create a high-affinity binding surface for this effector. RGA5 variants carrying this engineered binding surface perceive the new ligand, AVR-PikD, and still recognize AVR-Pia and AVR1-CO39 in the model plant N. benthamiana. However, they do not confer extended disease resistance specificity against M. oryzae in transgenic rice plants. Altogether, our study provides a proof of concept for the design of new effector recognition specificities in NLRs through molecular engineering of IDs.
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32
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Han J, Dong S, Liu X, Shi Y, Beckles DM, Gu X, Miao H, Zhang S. Fine mapping a quantitative trait locus underlying seedling resistance to gummy stem blight using a residual heterozygous lines-derived strategy in cucumber. FRONTIERS IN PLANT SCIENCE 2022; 13:968811. [PMID: 36119620 PMCID: PMC9480501 DOI: 10.3389/fpls.2022.968811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/12/2022] [Indexed: 05/20/2023]
Abstract
Gummy stem blight (GSB), caused by Didymella bryoniae, is one of the most devastating diseases that severely reduces cucumber production. Developing resistant varieties would be an effective strategy to control GSB. Although several GSB-resistant QTLs have been reported, causal genes for GSB resistance have not yet been identified in cucumber. A novel loci gsb3.1 for seedling GSB resistance from the "PI 183967" genotype was previously identified in a 1.7-Mb interval on chromosome 3. In this study, we developed a residual heterozygous line-derived strategy from Recombinant Inbred Lines to perform fine mapping, and with this approach, the gsb3.1 locus was narrowed to a 38 kb interval. There were six predicted genes at the gsb3.1 locus, four of which differed in expression in the GSB-resistant compared to the susceptible lines after fungal inoculation. These candidate genes (Csa3G020050, Csa3G020060, Csa3G020090, and Csa3G020590) within the gsb3.1 locus could be helpful for the genetic study of GSB resistance and marker-assisted selection in cucumber. Phylogenetic analyses indicated that the resistant gsb3.1 allele may uniquely exist in the wild species present in the Indian group, and that nucleotide diversity was significantly reduced in cultivated accessions. Therefore, the gsb3.1 allele could be introgressed into existing commercial cultivars and combined with other resistance QTLs to provide broad-spectrum and robust GSB resistance in cucumber.
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Affiliation(s)
- Jianan Han
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xingfang Gu,
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Han Miao,
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Shengping Zhang,
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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] [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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34
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De la Concepcion JC, Vega Benjumea J, Bialas A, Terauchi R, Kamoun S, Banfield MJ. Functional diversification gave rise to allelic specialization in a rice NLR immune receptor pair. eLife 2021; 10:e71662. [PMID: 34783652 PMCID: PMC8631799 DOI: 10.7554/elife.71662] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Cooperation between receptors from the nucleotide-binding, leucine-rich repeats (NLR) superfamily is important for intracellular activation of immune responses. NLRs can function in pairs that, upon pathogen recognition, trigger hypersensitive cell death and stop pathogen invasion. Natural selection drives specialization of host immune receptors towards an optimal response, whilst keeping a tight regulation of immunity in the absence of pathogens. However, the molecular basis of co-adaptation and specialization between paired NLRs remains largely unknown. Here, we describe functional specialization in alleles of the rice NLR pair Pik that confers resistance to strains of the blast fungus Magnaporthe oryzae harbouring AVR-Pik effectors. We revealed that matching pairs of allelic Pik NLRs mount effective immune responses, whereas mismatched pairs lead to autoimmune phenotypes, a hallmark of hybrid necrosis in both natural and domesticated plant populations. We further showed that allelic specialization is largely underpinned by a single amino acid polymorphism that determines preferential association between matching pairs of Pik NLRs. These results provide a framework for how functionally linked immune receptors undergo co-adaptation to provide an effective and regulated immune response against pathogens. Understanding the molecular constraints that shape paired NLR evolution has implications beyond plant immunity given that hybrid necrosis can drive reproductive isolation.
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Affiliation(s)
- Juan Carlos De la Concepcion
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of SciencesViennaAustria
- Department of Biological Chemistry and Metabolism, John Innes CentreNorwichUnited Kingdom
| | - Javier Vega Benjumea
- Department of Biological Chemistry and Metabolism, John Innes CentreNorwichUnited Kingdom
- Servicio de Bioquímica-Análisis clínicos, Hospital Universitario Puerta de HierroMadridSpain
| | - Aleksandra Bialas
- The Sainsbury Laboratory, University of East AngliaNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CenterIwateJapan
- Laboratory of Crop Evolution, Graduate School of AgricultureKyotoJapan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East AngliaNorwichUnited Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry and Metabolism, John Innes CentreNorwichUnited Kingdom
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Bentham AR, Petit-Houdenot Y, Win J, Chuma I, Terauchi R, Banfield MJ, Kamoun S, Langner T. A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum. PLoS Pathog 2021; 17:e1009957. [PMID: 34758051 PMCID: PMC8608293 DOI: 10.1371/journal.ppat.1009957] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/22/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Accelerated gene evolution is a hallmark of pathogen adaptation and specialization following host-jumps. However, the molecular processes associated with adaptive evolution between host-specific lineages of a multihost plant pathogen remain poorly understood. In the blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae), host specialization on different grass hosts is generally associated with dynamic patterns of gain and loss of virulence effector genes that tend to define the distinct genetic lineages of this pathogen. Here, we unravelled the biochemical and structural basis of adaptive evolution of APikL2, an exceptionally conserved paralog of the well-studied rice-lineage specific effector AVR-Pik. Whereas AVR-Pik and other members of the six-gene AVR-Pik family show specific patterns of presence/absence polymorphisms between grass-specific lineages of M. oryzae, APikL2 stands out by being ubiquitously present in all blast fungus lineages from 13 different host species. Using biochemical, biophysical and structural biology methods, we show that a single aspartate to asparagine polymorphism expands the binding spectrum of APikL2 to host proteins of the heavy-metal associated (HMA) domain family. This mutation maps to one of the APikL2-HMA binding interfaces and contributes to an altered hydrogen-bonding network. By combining phylogenetic ancestral reconstruction with an analysis of the structural consequences of allelic diversification, we revealed a common mechanism of effector specialization in the AVR-Pik/APikL2 family that involves two major HMA-binding interfaces. Together, our findings provide a detailed molecular evolution and structural biology framework for diversification and adaptation of a fungal pathogen effector family following host-jumps.
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Affiliation(s)
- Adam R. Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Yohann Petit-Houdenot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Izumi Chuma
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Ryohei Terauchi
- Kyoto University, Kyoto, Japan
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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36
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Figueroa M, Ortiz D, Henningsen EC. Tactics of host manipulation by intracellular effectors from plant pathogenic fungi. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102054. [PMID: 33992840 DOI: 10.1016/j.pbi.2021.102054] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Fungal pathogens can secrete hundreds of effectors, some of which are known to promote host susceptibility. This biological complexity, together with the lack of genetic tools in some fungi, presents a substantial challenge to develop a broad picture of the mechanisms these pathogens use for host manipulation. Nevertheless, recent advances in understanding individual effector functions are beginning to flesh out our view of fungal pathogenesis. This review discusses some of the latest findings that illustrate how effectors from diverse species use similar strategies to modulate plant physiology to their advantage. We also summarize recent breakthroughs in the identification of effectors from challenging systems, like obligate biotrophs, and emerging concepts such as the 'iceberg model' to explain how the activation of plant immunity can be turned off by effectors with suppressive activity.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Diana Ortiz
- National Research Institute for Agriculture, Food and Environment, Unit of Genetics and Breeding of Fruit and Vegetables, Domaine St Maurice, CS 60094, F-84143 Montfavet, France
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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37
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CEM, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:e66961. [PMID: 34288868 PMCID: PMC8294853 DOI: 10.7554/elife.66961] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 12/17/2022] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Clare EM Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CentreIwateJapan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto UniversityKyotoJapan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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