1
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [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: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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2
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Greenwood JR, Lacorte-Apostol V, Kroj T, Padilla J, Telebanco-Yanoria MJ, Glaus AN, Roulin A, Padilla A, Zhou B, Keller B, Krattinger SG. Genome-wide association analysis uncovers rice blast resistance alleles of Ptr and Pia. Commun Biol 2024; 7:607. [PMID: 38769168 PMCID: PMC11106262 DOI: 10.1038/s42003-024-06244-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
A critical step to maximize the usefulness of genome-wide association studies (GWAS) in plant breeding is the identification and validation of candidate genes underlying genetic associations. This is of particular importance in disease resistance breeding where allelic variants of resistance genes often confer resistance to distinct populations, or races, of a pathogen. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produce de-novo genome assemblies of ten rice accessions with various rice blast resistance associations. These genome assemblies facilitate the identification and functional validation of novel alleles of the rice blast resistance genes Ptr and Pia. We uncover an allelic series for the unusual Ptr rice blast resistance gene, and additional alleles of the Pia resistance genes RGA4 and RGA5. By linking these associations to three thousand rice genomes we provide a useful tool to inform future rice blast breeding efforts. Our work shows that GWAS in combination with whole-genome sequencing is a powerful tool for gene cloning and to facilitate selection of specific resistance alleles for plant breeding.
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Affiliation(s)
- Julian R Greenwood
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| | | | - Thomas Kroj
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jonas Padilla
- International Rice Research Institute, Los Baños, Philippines
| | | | - Anna N Glaus
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Anne Roulin
- Agroscope, Müller-Thurgau-Strasse 29, 8820, Wädenswil, Switzerland
| | - André Padilla
- Centre de Biologie Structurale, CBS, University of Montpellier, CNRS UMR 5048, INSERM U, 1054, Montpellier, France
| | - Bo Zhou
- International Rice Research Institute, Los Baños, Philippines.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Center for Desert Agriculture, KAUST, Thuwal, 23955-6900, Saudi Arabia.
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3
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Singh D, Mathur S, Ranjan R. Pattern recognition receptors as potential therapeutic targets for developing immunological engineered plants. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:525-555. [PMID: 38762279 DOI: 10.1016/bs.apcsb.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
There is an urgent need to combat pathogen infestations in crop plants to ensure food security worldwide. To counter this, plants have developed innate immunity mediated by Pattern Recognition Receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) and damage- associated molecular patterns (DAMPs). PRRs activate Pattern-Triggered Immunity (PTI), a defence mechanism involving intricate cell-surface and intracellular receptors. The diverse ligand-binding ectodomains of PRRs, including leucine-rich repeats (LRRs) and lectin domains, facilitate the recognition of MAMPs and DAMPs. Pathogen resistance is mediated by a variety of PTI responses, including membrane depolarization, ROS production, and the induction of defence genes. An integral part of intracellular immunity is the Nucleotide-binding Oligomerization Domain, Leucine-rich Repeat proteins (NLRs) which recognize and respond to effectors in a potent manner. Enhanced understanding of PRRs, their ligands, and downstream signalling pathways has contributed to the identification of potential targets for genetically modified plants. By transferring PRRs across plant species, it is possible to create broad-spectrum resistance, potentially offering innovative solutions for plant protection and global food security. The purpose of this chapter is to provide an update on PRRs involved in disease resistance, clarify the mechanisms by which PRRs recognize ligands to form active receptor complexes and present various applications of PRRs and PTI in disease resistance management for plants.
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Affiliation(s)
- Deeksha Singh
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Shivangi Mathur
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Rajiv Ranjan
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India.
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4
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Song L, Yang T, Wang X, Ye W, Lu G. Magnaporthe oryzae Effector AvrPik-D Targets Rice Rubisco Small Subunit OsRBCS4 to Suppress Immunity. PLANTS (BASEL, SWITZERLAND) 2024; 13:1214. [PMID: 38732428 PMCID: PMC11085154 DOI: 10.3390/plants13091214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Rice blast, caused by the fungal pathogen Magnaporthe oryzae (M. oryzae), is a highly destructive disease that significantly impacts rice yield and quality. During the infection, M. oryzae secretes effector proteins to subvert the host immune response. However, the interaction between the effector protein AvrPik-D and its target proteins in rice, and the mechanism by which AvrPik-D exacerbates disease severity to facilitate infection, remains poorly understood. In this study, we found that the M. oryzae effector AvrPik-D interacts with the Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) small subunit OsRBCS4. The overexpression of the OsRBCS4 gene in transgenic rice not only enhances resistance to M. oryzae but also induces more reactive oxygen species following chitin treatment. OsRBCS4 localizes to chloroplasts and co-localizes with AvrPik-D within these organelles. AvrPik-D suppresses the transcriptional expression of OsRBCS4 and inhibits Rubisco activity in rice. In conclusion, our results demonstrate that the M. oryzae effector AvrPik-D targets the Rubisco small subunit OsRBCS4 and inhibits its carboxylase and oxygenase activity, thereby suppressing rice innate immunity to facilitate infection. This provides a novel mechanism for the M. oryzae effector to subvert the host immunity to promote infection.
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Affiliation(s)
- Linlin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
| | - Tao Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
| | - Xinxiao Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
| | - Wenyu Ye
- China National Engineering Research Center of JUNCAO Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.S.); (T.Y.); (X.W.)
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5
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Hao Q, Yang H, Chen S, Zhang C, Chen L, Cao D, Yuan S, Guo W, Yang Z, Huang Y, Qu Y, Qin L, Sheng X, Wang X, Mitra C, Zhong H, Dawson J, Bumann E, Wang W, Jiang Y, Tang G, Carlin R, Chen H, Liu Q, Shan Z, Zhou X. An pair of an atypical NLR encoding genes confer Asian soybean rust resistance in soybean. Nat Commun 2024; 15:3310. [PMID: 38632249 PMCID: PMC11023949 DOI: 10.1038/s41467-024-47611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is a devastating disease that is present in all major soybean-producing regions. The limited availability of resistant germplasm has resulted in a scarcity of commercial soybean cultivars that are resistant to the disease. To date, only the Chinese soybean landrace SX6907 has demonstrated an immune response to ASR. In this study, we present the isolation and characterization of Rpp6907-7 and Rpp6907-4, a gene pair that confer broad-spectrum resistance to ASR. Rpp6907-7 and Rpp6907-4 encode atypic nucleotide-binding leucine-rich repeat (NLR) proteins that are found to be required for NLR-mediated immunity. Genetic analysis shows that only Rpp6907-7 confers resistance, while Rpp6907-4 regulates Rpp6907-7 signaling activity by acting as a repressor in the absence of recognized effectors. Our work highlights the potential value of using Rpp6907 in developing resistant soybean cultivars.
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Affiliation(s)
- Qingnan Hao
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Hongli Yang
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Shuilian Chen
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Chanjuan Zhang
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Limiao Chen
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Dong Cao
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Songli Yuan
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Wei Guo
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Zhonglu Yang
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yi Huang
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China
| | - Yanhui Qu
- The Graduate School of Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Lucy Qin
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Xiaoyan Sheng
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Xueyan Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Chandrani Mitra
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Heng Zhong
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - John Dawson
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Eric Bumann
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Wenling Wang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Yaping Jiang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Guozhu Tang
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Ryan Carlin
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA
| | - Haifeng Chen
- Soybean Collaborative Innovation Center, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
| | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, 27709, USA.
| | - Zhihui Shan
- Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
| | - Xinan Zhou
- Soybean Genetics and breeding team, Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan, 430062, China.
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6
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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7
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Zhang X, Liu Y, Yuan G, Wang S, Wang D, Zhu T, Wu X, Ma M, Guo L, Guo H, Bhadauria V, Liu J, Peng YL. The synthetic NLR RGA5 HMA5 requires multiple interfaces within and outside the integrated domain for effector recognition. Nat Commun 2024; 15:1104. [PMID: 38321036 PMCID: PMC10847126 DOI: 10.1038/s41467-024-45380-2] [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: 08/08/2022] [Accepted: 01/19/2024] [Indexed: 02/08/2024] Open
Abstract
Some plant sensor nucleotide-binding leucine-rich repeat (NLR) receptors detect pathogen effectors through their integrated domains (IDs). Rice RGA5 sensor NLR recognizes its corresponding effectors AVR-Pia and AVR1-CO39 from the blast fungus Magnaporthe oryzae through direct binding to its heavy metal-associated (HMA) ID to trigger the RGA4 helper NLR-dependent resistance in rice. Here, we report a mutant of RGA5 named RGA5HMA5 that confers complete resistance in transgenic rice plants to the M. oryzae strains expressing the noncorresponding effector AVR-PikD. RGA5HMA5 carries three engineered interfaces, two of which lie in the HMA ID and the other in the C-terminal Lys-rich stretch tailing the ID. However, RGA5 variants having one or two of the three interfaces, including replacing all the Lys residues with Glu residues in the Lys-rich stretch, failed to activate RGA4-dependent cell death of rice protoplasts. Altogether, this work demonstrates that sensor NLRs require a concerted action of multiple surfaces within and outside the IDs to both recognize effectors and activate helper NLR-mediated resistance, and has implications in structure-guided designing of sensor NLRs.
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Affiliation(s)
- Xin Zhang
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Yang Liu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Guixin Yuan
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Shiwei Wang
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China
| | - Dongli Wang
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Tongtong Zhu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Xuefeng Wu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Mengqi Ma
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China
| | - Liwei Guo
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, China
| | - Hailong Guo
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Vijai Bhadauria
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Junfeng Liu
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China.
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, 100193, Beijing, China.
| | - You-Liang Peng
- The State Key Laboratory of Maize Bio-breeding, Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Agriculture Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, 100193, Beijing, China.
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, 100193, Beijing, China.
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8
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Normantovich M, Amitzur A, Offri S, Pashkovsky E, Shnaider Y, Nizan S, Yogev O, Jacob A, Taylor CG, Desbiez C, Whitham SA, Bar-Ziv A, Perl-Treves R. The melon Fom-1-Prv resistance gene pair: Correlated spatial expression and interaction with a viral protein. PLANT DIRECT 2024; 8:e565. [PMID: 38389929 PMCID: PMC10883720 DOI: 10.1002/pld3.565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
The head-to-head oriented pair of melon resistance genes, Fom-1 and Prv, control resistance to Fusarium oxysporum races 0 and 2 and papaya ringspot virus (PRSV), respectively. They encode, via several RNA splice variants, TIR-NBS-LRR proteins, and Prv has a C-terminal extra domain with a second NBS homologous sequence. In other systems, paired R-proteins were shown to operate by "labor division," with one protein having an extra integrated domain that directly binds the pathogen's Avr factor, and the second protein executing the defense response. We report that the expression of the two genes in two pairs of near-isogenic lines was higher in the resistant isoline and inducible by F. oxysporum race 2 but not by PRSV. The intergenic DNA region separating the coding sequences of the two genes acted as a bi-directional promoter and drove GUS expression in transgenic melon roots and transgenic tobacco plants. Expression of both genes was strong in melon root tips, around the root vascular cylinder, and the phloem and xylem parenchyma of tobacco stems and petioles. The pattern of GUS expression suggests coordinated expression of the two genes. In agreement with the above model, Prv's extra domain was shown to interact with the cylindrical inclusion protein of PRSV both in yeast cells and in planta.
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Affiliation(s)
- Michael Normantovich
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Arie Amitzur
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Sharon Offri
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ekaterina Pashkovsky
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Yula Shnaider
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Shahar Nizan
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Ohad Yogev
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Avi Jacob
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | | | | | - Steven A Whitham
- Department of Plant Pathology and Microbiology Iowa State University Ames Iowa USA
| | - Amalia Bar-Ziv
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
| | - Rafael Perl-Treves
- The Mina and Everard Goodman Faculty of Life Sciences Bar Ilan University Ramat Gan Israel
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9
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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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10
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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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11
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Crean EE, Bilstein-Schloemer M, Maekawa T, Schulze-Lefert P, Saur IML. A dominant-negative avirulence effector of the barley powdery mildew fungus provides mechanistic insight into barley MLA immune receptor activation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5854-5869. [PMID: 37474129 PMCID: PMC10540733 DOI: 10.1093/jxb/erad285] [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: 01/16/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) recognize pathogen effectors to mediate plant disease resistance often involving host cell death. Effectors escape NLR recognition through polymorphisms, allowing the pathogen to proliferate on previously resistant host plants. The powdery mildew effector AVRA13-1 is recognized by the barley NLR MLA13 and activates host cell death. We demonstrate here that a virulent form of AVRA13, called AVRA13-V2, escapes MLA13 recognition by substituting a serine for a leucine residue at the C-terminus. Counterintuitively, this substitution in AVRA13-V2 resulted in an enhanced MLA13 association and prevented the detection of AVRA13-1 by MLA13. Therefore, AVRA13-V2 is a dominant-negative form of AVRA13 and has probably contributed to the breakdown of Mla13 resistance. Despite this dominant-negative activity, AVRA13-V2 failed to suppress host cell death mediated by the MLA13 autoactive MHD variant. Neither AVRA13-1 nor AVRA13-V2 interacted with the MLA13 autoactive variant, implying that the binding moiety in MLA13 that mediates association with AVRA13-1 is altered after receptor activation. We also show that mutations in the MLA13 coiled-coil domain, which were thought to impair Ca2+ channel activity and NLR function, instead resulted in MLA13 autoactive cell death. Our results constitute an important step to define intermediate receptor conformations during NLR activation.
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Affiliation(s)
- Emma E Crean
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
| | | | - Takaki Maekawa
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Department for Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Paul Schulze-Lefert
- Department for Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
| | - Isabel M L Saur
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Germany
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12
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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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13
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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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14
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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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15
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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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16
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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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17
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Greenwood JR, Zhang X, Rathjen JP. Precision genome editing of crops for improved disease resistance. Curr Biol 2023; 33:R650-R657. [PMID: 37279695 DOI: 10.1016/j.cub.2023.04.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genome editing (GE) technologies allow rapid trait manipulation in crop plants. Disease resistance is one of the best test cases for this technology because it is usually monogenic and under constant challenge by rapidly evolving pathogens. Classical methods suffer from severe bottlenecks in discovery of new resistance (R) genes and their incorporation into elite varieties, largely because they are identified in landraces and species with limited sexual compatibility, and may last only a few years before losing effectiveness. Most plant R genes encode receptors located externally on the plasma membrane (receptor proteins and receptor kinases) or internally as NOD-like receptors (NLR). Both have well defined molecular interactions with activating pathogen ligands which are virulence proteins known as effectors. As structural data for R-effector interactions accumulate, promising strategies for rational manipulation of binding specificities are emerging. This offers the potential to change elite varieties directly rather than through 10-20 years of crossing. Successful application of GE is already evident in mutation of susceptibility (S) genes required for infection. GE is in its infancy with only four modified organisms grown currently in the US. The Anglosphere and Japan seem more open to deployment of these technologies, with the European Union, Switzerland and New Zealand being notably more conservative. Consumers are not well informed on the differences between GE and classical genetic modification (GM). The possibility that minor GE changes will not be regulated as GM offers the hope that current bottlenecks to resistance breeding can be eased.
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Affiliation(s)
- Julian R Greenwood
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Xiaoxiao Zhang
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia.
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18
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Yan X, Tang B, Ryder LS, MacLean D, Were VM, Eseola AB, Cruz-Mireles N, Ma W, Foster AJ, Osés-Ruiz M, Talbot NJ. The transcriptional landscape of plant infection by the rice blast fungus Magnaporthe oryzae reveals distinct families of temporally co-regulated and structurally conserved effectors. THE PLANT CELL 2023; 35:1360-1385. [PMID: 36808541 PMCID: PMC10118281 DOI: 10.1093/plcell/koad036] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 05/04/2023]
Abstract
The rice blast fungus Magnaporthe oryzae causes a devastating disease that threatens global rice (Oryza sativa) production. Despite intense study, the biology of plant tissue invasion during blast disease remains poorly understood. Here we report a high-resolution transcriptional profiling study of the entire plant-associated development of the blast fungus. Our analysis revealed major temporal changes in fungal gene expression during plant infection. Pathogen gene expression could be classified into 10 modules of temporally co-expressed genes, providing evidence for the induction of pronounced shifts in primary and secondary metabolism, cell signaling, and transcriptional regulation. A set of 863 genes encoding secreted proteins are differentially expressed at specific stages of infection, and 546 genes named MEP (Magnaportheeffector protein) genes were predicted to encode effectors. Computational prediction of structurally related MEPs, including the MAX effector family, revealed their temporal co-regulation in the same co-expression modules. We characterized 32 MEP genes and demonstrate that Mep effectors are predominantly targeted to the cytoplasm of rice cells via the biotrophic interfacial complex and use a common unconventional secretory pathway. Taken together, our study reveals major changes in gene expression associated with blast disease and identifies a diverse repertoire of effectors critical for successful infection.
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Affiliation(s)
- Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Bozeng Tang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lauren S Ryder
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vincent M Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Alice Bisola Eseola
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Neftaly Cruz-Mireles
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Weibin Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Andrew J Foster
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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19
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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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20
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Rozano L, Mukuka YM, Hane JK, Mancera RL. Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins. Int J Mol Sci 2023; 24:ijms24076262. [PMID: 37047233 PMCID: PMC10094246 DOI: 10.3390/ijms24076262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Pathogenic fungal diseases in crops are mediated by the release of effector proteins that facilitate infection. Characterising the structure of these fungal effectors is vital to understanding their virulence mechanisms and interactions with their hosts, which is crucial in the breeding of plant cultivars for disease resistance. Several effectors have been identified and validated experimentally; however, their lack of sequence conservation often impedes the identification and prediction of their structure using sequence similarity approaches. Structural similarity has, nonetheless, been observed within fungal effector protein families, creating interest in validating the use of computational methods to predict their tertiary structure from their sequence. We used Rosetta ab initio modelling to predict the structures of members of the ToxA-like and MAX effector families for which experimental structures are known to validate this method. An optimised approach was then used to predict the structures of phenotypically validated effectors lacking known structures. Rosetta was found to successfully predict the structure of fungal effectors in the ToxA-like and MAX families, as well as phenotypically validated but structurally unconfirmed effector sequences. Interestingly, potential new effector structural families were identified on the basis of comparisons with structural homologues and the identification of associated protein domains.
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21
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Kourelis J, Marchal C, Posbeyikian A, Harant A, Kamoun S. NLR immune receptor-nanobody fusions confer plant disease resistance. Science 2023; 379:934-939. [PMID: 36862785 DOI: 10.1126/science.abn4116] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/01/2023] [Indexed: 03/04/2023]
Abstract
Plant pathogens cause recurrent epidemics, threatening crop yield and global food security. Efforts to retool the plant immune system have been limited to modifying natural components and can be nullified by the emergence of new pathogen strains. Made-to-order synthetic plant immune receptors provide an opportunity to tailor resistance to pathogen genotypes present in the field. In this work, we show that plant nucleotide-binding, leucine-rich repeat immune receptors (NLRs) can be used as scaffolds for nanobody (single-domain antibody fragment) fusions that bind fluorescent proteins (FPs). These fusions trigger immune responses in the presence of the corresponding FP and confer resistance against plant viruses expressing FPs. Because nanobodies can be raised against most molecules, immune receptor-nanobody fusions have the potential to generate resistance against plant pathogens and pests delivering effectors inside host cells.
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Affiliation(s)
- Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Andres Posbeyikian
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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22
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Xiao G, Wang W, Liu M, Li Y, Liu J, Franceschetti M, Yi Z, Zhu X, Zhang Z, Lu G, Banfield MJ, Wu J, Zhou B. The Piks allele of the NLR immune receptor Pik breaks the recognition of AvrPik effectors of rice blast fungus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:810-824. [PMID: 36178632 DOI: 10.1111/jipb.13375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Arms race co-evolution of plant-pathogen interactions evolved sophisticated recognition mechanisms between host immune receptors and pathogen effectors. Different allelic haplotypes of an immune receptor in the host mount distinct recognition against sequence or non-sequence related effectors in pathogens. We report the molecular characterization of the Piks allele of the rice immune receptor Pik against rice blast pathogen, which requires two head-to-head arrayed nucleotide-binding sites and leucine-rich repeat proteins. Like other Pik alleles, both Piks-1 and Piks-2 are necessary and sufficient for mediating resistance. However, unlike other Pik alleles, Piks does not recognize any known AvrPik variants of Magnaporthe oryzae. Sequence analysis of the genome of an avirulent isolate V86010 further revealed that its cognate avirulence (Avr) gene most likely has no significant sequence similarity to known AvrPik variants. Piks-1 and Pikm-1 have only two amino acid differences within the integrated heavy metal-associated (HMA) domain. Pikm-HMA interacts with AvrPik-A, -D, and -E in vitro and in vivo, whereas Piks-HMA does not bind any AvrPik variants. Characterization of two amino acid residues differing Piks-1 from Pikm-1 reveal that Piks-E229Q derived from the exchange of Glu229 to Gln229 in Piks-1 gains recognition specificity against AvrPik-D but not AvrPik-A or -E, indicating that Piks-E229Q partially restores the Pikm spectrum. By contrast, Piks-A261V derived from the exchange of Ala261 to Val261 in Piks-1 retains Piks recognition specificity. We conclude that Glu229 in Piks-1 is critical for Piks breaking the canonical Pik/AvrPik recognition pattern. Intriguingly, binding activity and ectopic cell death induction is maintained between Piks-A261V and AvrPik-D, implying that positive outcomes from ectopic assays might be insufficient to deduce its immune activity against the relevant effectors in rice and rice blast interaction.
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Affiliation(s)
- Gui Xiao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
- International Rice Research Institute, Metro Manila, 1301, Philippines
| | - Wenjuan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Ya Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianbin Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
| | - Marina Franceschetti
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zhaofeng Yi
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
| | - Xiaoyuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, 210095, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jun Wu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410128, China
| | - Bo Zhou
- International Rice Research Institute, Metro Manila, 1301, Philippines
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23
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Zampieri E, Volante A, Marè C, Orasen G, Desiderio F, Biselli C, Canella M, Carmagnola L, Milazzo J, Adreit H, Tharreau D, Poncelet N, Vaccino P, Valè G. Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection. PLANTS (BASEL, SWITZERLAND) 2023; 12:757. [PMID: 36840105 PMCID: PMC9963729 DOI: 10.3390/plants12040757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of an elite cultivar. In this work, MABC coupled to foreground and background selections based on KASP marker assays has been applied to introgress four Pi genes (Piz, Pib, Pita, and Pik) in a renowned japonica Italian rice variety, highly susceptible to blast. Molecular analyses on the backcross (BC) lines highlighted the presence of an additional blast-resistance gene, the Pita-linked Pita2/Ptr gene, therefore increasing the number of blast-resistance introgressed genes to five. The recurrent genome was recovered up to 95.65%. Several lines carrying four (including Pita2) Pi genes with high recovery percentage levels were also obtained. Phenotypic evaluations confirmed the effectiveness of the pyramided lines against multivirulent strains, which also had broad patterns of resistance in comparison to those expected based on the pyramided Pi genes. The developed blast-resistant japonica lines represent useful donors of multiple blast-resistance genes for future rice-breeding programs related to the japonica group.
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Affiliation(s)
- Elisa Zampieri
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
- Institute for Sustainable Plant Protection, National Research Council, Strada Delle Cacce 73, 10135 Turin, TO, Italy
| | - Andrea Volante
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
- Council for Agricultural Research and Economics—Research Centre for Vegetable and Ornamental Crops, Corso Inglesi 508, 18038 Sanremo, IM, Italy
| | - Caterina Marè
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy
| | - Gabriele Orasen
- Bertone Sementi S.P.A., Strada Cacciolo, 15030 Terruggia, AL, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics—Research Centre for Genomics and Bioinformatics, Via S. Protaso 302, 29017 Fiorenzuola d’Arda, PC, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics—Viticulture and Oenology, Viale Santa Margherita 80, 52100 Arezzo, AR, Italy
| | - Marco Canella
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
| | - Lorena Carmagnola
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
| | - Joëlle Milazzo
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Henri Adreit
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Didier Tharreau
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Nicolas Poncelet
- CIRAD, UMR PHIM TA A 120/K, Campus de Baillarguet, 34, CEDEX 5, 34398 Montpellier, France
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, 34, 34398 Montpellier, France
| | - Patrizia Vaccino
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, VC, Italy
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, VC, Italy
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24
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Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector. PLoS Biol 2023; 21:e3001945. [PMID: 36656825 PMCID: PMC9851567 DOI: 10.1371/journal.pbio.3001945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
Studies focused solely on single organisms can fail to identify the networks underlying host-pathogen gene-for-gene interactions. Here, we integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik. Rice Piks-1, encoded by an allele of Pik-1, recognizes a previously unidentified effector encoded by the M. oryzae avirulence gene AVR-Mgk1, which is found on a mini-chromosome. AVR-Mgk1 has no sequence similarity to known AVR-Pik effectors and is prone to deletion from the mini-chromosome mediated by repeated Inago2 retrotransposon sequences. AVR-Mgk1 is detected by Piks-1 and by other Pik-1 alleles known to recognize AVR-Pik effectors; recognition is mediated by AVR-Mgk1 binding to the integrated heavy metal-associated (HMA) domain of Piks-1 and other Pik-1 alleles. Our findings highlight how complex gene-for-gene interaction networks can be disentangled by applying forward genetics approaches simultaneously to the host and pathogen. We demonstrate dynamic coevolution between an NLR integrated domain and multiple families of effector proteins.
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25
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Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses. Nat Microbiol 2023; 8:174-187. [PMID: 36604508 PMCID: PMC9816061 DOI: 10.1038/s41564-022-01287-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/11/2022] [Indexed: 01/07/2023]
Abstract
Elucidating the similarity and diversity of pathogen effectors is critical to understand their evolution across fungal phytopathogens. However, rapid divergence that diminishes sequence similarities between putatively homologous effectors has largely concealed the roots of effector evolution. Here we modelled the structures of 26,653 secreted proteins from 14 agriculturally important fungal phytopathogens, six non-pathogenic fungi and one oomycete with AlphaFold 2. With 18,000 successfully predicted folds, we performed structure-guided comparative analyses on two aspects of effector evolution: uniquely expanded sequence-unrelated structurally similar (SUSS) effector families and common folds present across the fungal species. Extreme expansion of lineage-specific SUSS effector families was found only in several obligate biotrophs, Blumeria graminis and Puccinia graminis. The highly expanded effector families were the source of conserved sequence motifs, such as the Y/F/WxC motif. We identified new classes of SUSS effector families that include known virulence factors, such as AvrSr35, AvrSr50 and Tin2. Structural comparisons revealed that the expanded structural folds further diversify through domain duplications and fusion with disordered stretches. Putatively sub- and neo-functionalized SUSS effectors could reconverge on regulation, expanding the functional pools of effectors in the pathogen infection cycle. We also found evidence that many effector families could have originated from ancestral folds conserved across fungi. Collectively, our study highlights diverse effector evolution mechanisms and supports divergent evolution as a major force in driving SUSS effector evolution from ancestral proteins.
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26
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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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27
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Rocafort M, Bowen JK, Hassing B, Cox MP, McGreal B, de la Rosa S, Plummer KM, Bradshaw RE, Mesarich CH. The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi. BMC Biol 2022; 20:246. [PMID: 36329441 PMCID: PMC9632046 DOI: 10.1186/s12915-022-01442-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required. Results We generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi. Conclusions Our study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01442-9.
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Affiliation(s)
- Mercedes Rocafort
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Berit Hassing
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Murray P Cox
- Bioprotection Aotearoa, School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Brogan McGreal
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Rosie E Bradshaw
- Bioprotection Aotearoa, School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
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28
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Macquet J, Mounichetty S, Raffaele S. Genetic co-option into plant-filamentous pathogen interactions. TRENDS IN PLANT SCIENCE 2022; 27:1144-1158. [PMID: 35909010 DOI: 10.1016/j.tplants.2022.06.011] [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: 02/23/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.
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Affiliation(s)
- Joris Macquet
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Shantala Mounichetty
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France.
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29
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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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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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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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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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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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Zhang B, Liu M, Wang Y, Yuan W, Zhang H. Plant NLRs: Evolving with pathogen effectors and engineerable to improve resistance. Front Microbiol 2022; 13:1018504. [PMID: 36246279 PMCID: PMC9554439 DOI: 10.3389/fmicb.2022.1018504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Pathogens are important threats to many plants throughout their lifetimes. Plants have developed different strategies to overcome them. In the plant immunity system, nucleotide-binding domain and leucine-rich repeat-containing proteins (NLRs) are the most common components. And recent studies have greatly expanded our understanding of how NLRs function in plants. In this review, we summarize the studies on the mechanism of NLRs in the processes of effector recognition, resistosome formation, and defense activation. Typical NLRs are divided into three groups according to the different domains at their N termini and function in interrelated ways in immunity. Atypical NLRs contain additional integrated domains (IDs), some of which directly interact with pathogen effectors. Plant NLRs evolve with pathogen effectors and exhibit specific recognition. Meanwhile, some NLRs have been successfully engineered to confer resistance to new pathogens based on accumulated studies. In summary, some pioneering processes have been obtained in NLR researches, though more questions arise as a result of the huge number of NLRs. However, with a broadened understanding of the mechanism, NLRs will be important components for engineering in plant resistance improvement.
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Xi Y, Chalvon V, Padilla A, Cesari S, Kroj T. The activity of the RGA5 sensor NLR from rice requires binding of its integrated HMA domain to effectors but not HMA domain self-interaction. MOLECULAR PLANT PATHOLOGY 2022; 23:1320-1330. [PMID: 35766176 PMCID: PMC9366066 DOI: 10.1111/mpp.13236] [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: 03/11/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 05/25/2023]
Abstract
The rice nucleotide-binding (NB) and leucine-rich repeat (LRR) domain immune receptors (NLRs) RGA4 and RGA5 form a helper NLR/sensor NLR (hNLR/sNLR) pair that specifically recognizes the effectors AVR-Pia and AVR1-CO39 from the blast fungus Magnaporthe oryzae. While RGA4 contains only canonical NLR domains, RGA5 has an additional unconventional heavy metal-associated (HMA) domain integrated after its LRR domain. This RGA5HMA domain binds the effectors and is crucial for their recognition. Investigation of the three-dimensional structure of the AVR1-CO39/RGA5HMA complex by X-ray crystallography identified a candidate surface for effector binding in the HMA domain and showed that the HMA domain self-interacts in the absence of effector through the same surface. Here, we investigated the relevance of this HMA homodimerization for RGA5 function and the role of the RGA5HMA effector-binding and self-interaction surface in effector recognition. By analysing structure-informed point mutations in the RGA5HMA -binding surface in protein interaction studies and in Nicotiana benthamiana cell death assays, we found that HMA self-interaction does not contribute to RGA5 function. However, the effector-binding surface of RGA5HMA identified by X-ray crystallography is crucial for both in vitro and in vivo effector binding as well as effector recognition. These results support the current hypothesis that noncanonical integrated domains of NLRs act primarily as effector traps and deepen our understanding of the sNLRs' function within NLR pairs.
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Affiliation(s)
- Yuxuan Xi
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Véronique Chalvon
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - André Padilla
- CBS, Univ Montpellier, CNRS, INSERMMontpellierFrance
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
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36
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Hu J, Liu M, Zhang A, Dai Y, Chen W, Chen F, Wang W, Shen D, Telebanco-Yanoria MJ, Ren B, Zhang H, Zhou H, Zhou B, Wang P, Zhang Z. Co-evolved plant and blast fungus ascorbate oxidases orchestrate the redox state of host apoplast to modulate rice immunity. MOLECULAR PLANT 2022; 15:1347-1366. [PMID: 35799449 DOI: 10.1016/j.molp.2022.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Apoplastic ascorbate oxidases (AOs) play a critical role in reactive oxygen species (ROS)-mediated innate host immunity by regulating the apoplast redox state. To date, little is known about how apoplastic effectors of the rice blast fungus Magnaporthe oryzae modulate the apoplast redox state of rice to subvert plant immunity. In this study, we demonstrated that M. oryzae MoAo1 is an AO that plays a role in virulence by modulating the apoplast redox status of rice cells. We showed that MoAo1 inhibits the activity of rice OsAO3 and OsAO4, which also regulate the apoplast redox status and plant immunity. In addition, we found that MoAo1, OsAO3, and OsAO4 all exhibit polymorphic variations whose varied interactions orchestrate pathogen virulence and rice immunity. Taken together, our results reveal a critical role for extracellular redox enzymes during rice blast infection and shed light on the importance of the apoplast redox state and its regulation in plant-pathogen interactions.
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Affiliation(s)
- Jiexiong Hu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ao Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Ying Dai
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Weizhong Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Fang Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Wenya Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | | | - Bin Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bo Zhou
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna 4031, Philippines
| | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China.
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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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Liu X, Wan L. Molecular insights into the biochemical functions and signalling mechanisms of plant NLRs. MOLECULAR PLANT PATHOLOGY 2022; 23:772-780. [PMID: 35355394 PMCID: PMC9104254 DOI: 10.1111/mpp.13195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Plant intracellular immune receptors known as NLR (nucleotide-binding leucine-rich repeat) proteins confer immunity and cause cell death. Plant NLR proteins that directly or indirectly recognize pathogen effector proteins to initiate immune signalling are regarded as sensor NLRs. Some NLR protein families function downstream of sensor NLRs to transduce immune signalling and are known as helper NLRs. Recent breakthrough studies on plant NLR protein structures and biochemical functions greatly advanced our understanding of NLR biology. Comprehensive and detailed knowledge on NLR biology requires future efforts to solve more NLR protein structures and investigate the signalling events between sensor and helper NLRs, and downstream of helper NLRs.
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Affiliation(s)
- Xiaoxiao Liu
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
| | - Li Wan
- National Key Laboratory of Plant Molecular GeneticsCAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghaiChina
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39
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Evolution of resistance (R) gene specificity. Essays Biochem 2022; 66:551-560. [PMID: 35612398 DOI: 10.1042/ebc20210077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.
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40
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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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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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42
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Wang Y, Pruitt RN, Nürnberger T, Wang Y. Evasion of plant immunity by microbial pathogens. Nat Rev Microbiol 2022; 20:449-464. [PMID: 35296800 DOI: 10.1038/s41579-022-00710-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2022] [Indexed: 12/21/2022]
Abstract
Plant pathogenic viruses, bacteria, fungi and oomycetes cause destructive diseases in natural habitats and agricultural settings, thereby threatening plant biodiversity and global food security. The capability of plants to sense and respond to microbial infection determines the outcome of plant-microorganism interactions. Host-adapted microbial pathogens exploit various infection strategies to evade or counter plant immunity and eventually establish a replicative niche. Evasion of plant immunity through dampening host recognition or the subsequent immune signalling and defence execution is a crucial infection strategy used by different microbial pathogens to cause diseases, underpinning a substantial obstacle for efficient deployment of host genetic resistance genes for sustainable disease control. In this Review, we discuss current knowledge of the varied strategies microbial pathogens use to evade the complicated network of plant immunity for successful infection. In addition, we discuss how to exploit this knowledge to engineer crop resistance.
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Affiliation(s)
- Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Rory N Pruitt
- Centre for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, Germany
| | - Thorsten Nürnberger
- Centre for Molecular Biology of Plants (ZMBP), University of Tübingen, Tübingen, Germany.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China. .,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China.
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43
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Benzerara K, Duprat E, Tristan BF, Géraldine C, Corinne CC, Franck C, Manuela D, Issa DS, Geoffroy G, Sigrid G, Muriel G, Purificación LG, Maxime M, Fériel SP, David M, Isabelle C. A new gene family diagnostic for intracellular biomineralization of amorphous Ca-carbonates by cyanobacteria. Genome Biol Evol 2022; 14:6526398. [PMID: 35143662 PMCID: PMC8890360 DOI: 10.1093/gbe/evac026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating 4 major types among the 35 known calcyanin homologs. Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or co-localized with genes involved in Ca or HCO3- transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization. Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria.
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Affiliation(s)
- Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Bitard-Feildel Tristan
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Caumes Géraldine
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Cassier-Chauvat Corinne
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Chauvat Franck
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dezi Manuela
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Diop Seydina Issa
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Gaschignard Geoffroy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Görgen Sigrid
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Gugger Muriel
- Institut Pasteur, Université de Paris, Collection of Cyanobacteria, F-75015 Paris, France
| | - López-García Purificación
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Millet Maxime
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Skouri-Panet Fériel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
| | - Moreira David
- Unité d’Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Callebaut Isabelle
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), 4 Place Jussieu, 75005 Paris, France
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44
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Yu DS, Outram MA, Crean E, Smith A, Sung YC, Darma R, Sun X, Ma L, Jones DA, Solomon PS, Williams SJ. Optimized Production of Disulfide-Bonded Fungal Effectors in Escherichia coli Using CyDisCo and FunCyDisCo Coexpression Approaches. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:109-118. [PMID: 34672679 DOI: 10.1094/mpmi-08-21-0218-ta] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Effectors are a key part of the arsenal of plant-pathogenic fungi and promote pathogen virulence and disease. Effectors typically lack sequence similarity to proteins with known functional domains and motifs, limiting our ability to predict their functions and understand how they are recognized by plant hosts. As a result, cross-disciplinary approaches involving structural biology and protein biochemistry are often required to decipher and better characterize effector function. These approaches are reliant on high yields of relatively pure protein, which often requires protein production using a heterologous expression system. For some effectors, establishing an efficient production system can be difficult, particularly those that require multiple disulfide bonds to achieve their naturally folded structure. Here, we describe the use of a coexpression system within the heterologous host Escherichia coli, termed CyDisCo (cytoplasmic disulfide bond formation in E. coli) to produce disulfide bonded fungal effectors. We demonstrate that CyDisCo and a naturalized coexpression approach termed FunCyDisCo (Fungi CyDisCo) can significantly improve the production yields of numerous disulfide-bonded effectors from diverse fungal pathogens. The ability to produce large quantities of functional recombinant protein has facilitated functional studies and crystallization of several of these reported fungal effectors. We suggest this approach could be broadly useful in the investigation of the function and recognition of a broad range of disulfide bond-containing effectors.[Formula: see text] Copyright © 2022 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)
- Daniel S Yu
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Emma Crean
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ashley Smith
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Yi-Chang Sung
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Reynaldi Darma
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Xizhe Sun
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agriculture University, Baoding, China
| | - Lisong Ma
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - David A Jones
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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45
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NLRs guard metabolism to coordinate pattern- and effector-triggered immunity. Nature 2022; 601:245-251. [PMID: 34912119 DOI: 10.1038/s41586-021-04219-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/09/2021] [Indexed: 01/09/2023]
Abstract
Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in plants enable them to respond to pathogens by activating the production of defence metabolites that orchestrate immune responses1-4. How the production of defence metabolites is promoted by immune receptors and coordinated with broad-spectrum resistance remains elusive. Here we identify the deubiquitinase PICI1 as an immunity hub for PTI and ETI in rice (Oryza sativa). PICI1 deubiquitinates and stabilizes methionine synthetases to activate methionine-mediated immunity principally through biosynthesis of the phytohormone ethylene. PICI1 is targeted for degradation by blast fungal effectors, including AvrPi9, to dampen PTI. Nucleotide-binding domain, leucine-rich-repeat-containing receptors (NLRs) in the plant immune system, such as PigmR, protect PICI1 from effector-mediated degradation to reboot the methionine-ethylene cascade. Natural variation in the PICI1 gene contributes to divergence in basal blast resistance between the rice subspecies indica and japonica. Thus, NLRs govern an arms race with effectors, using a competitive mode that hinges on a critical defence metabolic pathway to synchronize PTI with ETI and ensure broad-spectrum resistance.
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46
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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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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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48
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Xi Y, Chochois V, Kroj T, Cesari S. A novel robust and high-throughput method to measure cell death in Nicotiana benthamiana leaves by fluorescence imaging. MOLECULAR PLANT PATHOLOGY 2021; 22:1688-1696. [PMID: 34427040 PMCID: PMC8578831 DOI: 10.1111/mpp.13129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/08/2021] [Accepted: 08/05/2021] [Indexed: 05/31/2023]
Abstract
Assessing immune responses and cell death in Nicotiana benthamiana leaf agro-infiltration assays is a powerful and widely used experimental approach in molecular plant pathology. Here, we describe a reliable high-throughput protocol to quantify strong, macroscopically visible cell death responses in N. benthamiana agro-infiltration assays. The method relies on measuring the reduction of leaf autofluorescence in the red spectrum upon cell death induction and provides quantitative data suitable for straightforward statistical analysis. Two different well-established model nucleotide-binding and leucine-rich repeat domain proteins (NLRs) were used to ensure the genericity of the approach. Its accuracy and versatility were compared to visual scoring of the cell death response and standard methods commonly used to characterize NLR activities in N. benthamiana. A discussion of the advantages and limitations of our method compared to other protocols demonstrates its robustness and versatility and provides an effective means to select the best-suited protocol for a defined experiment.
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Affiliation(s)
- Yuxuan Xi
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Vincent Chochois
- CIRADUMR QualisudMontpellierFrance
- Qualisud, Univ MontpellierAvignon UniversitéCIRADInstitut AgroUniversité de La RéunionMontpellierFrance
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
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49
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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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50
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A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors. Proc Natl Acad Sci U S A 2021; 118:2110751118. [PMID: 34702740 PMCID: PMC8612214 DOI: 10.1073/pnas.2110751118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/21/2022] Open
Abstract
In this study, we generated a mutant of the rice nucleotide-binding and leucine-rich repeat (NLR) immunity receptor RGA5 by engineering its heavy metal–associated domain that recognizes the noncorresponding Magnaporthe oryzae Avrs- and ToxB-like effector AvrPib and confers resistance in transgenic rice to the blast fungus isolates with AvrPib, which is known to trigger blast resistance in rice cultivars carrying the R gene Pib, albeit by unknown mechanisms. Thus, this work demonstrates that integrated domain-containing plant NLR receptors can be engineered to confer resistance to pathogens carrying avirulence effectors that trigger plant immunity by unknown mechanisms, thereby providing a practical approach for developing multilines and cultivars with broad race spectrum resistance. Plant nucleotide-binding and leucine-rich repeat (NLR) receptors recognize avirulence effectors directly through their integrated domains (IDs) or indirectly via the effector-targeted proteins. Previous studies have succeeded in generating designer NLR receptors with new recognition profiles by engineering IDs or targeted proteins based on prior knowledge of their interactions with the effectors. However, it is yet a challenge to design a new plant receptor capable of recognizing effectors that function by unknown mechanisms. Several rice NLR immune receptors, including RGA5, possess an integrated heavy metal–associated (HMA) domain that recognizes corresponding Magnaporthe oryzae Avrs and ToxB-like (MAX) effectors in the rice blast fungus. Here, we report a designer rice NLR receptor RGA5HMA2 carrying an engineered, integrated HMA domain (RGA5-HMA2) that can recognize the noncorresponding MAX effector AvrPib and confers the RGA4-dependent resistance to the M. oryzae isolates expressing AvrPib, which originally triggers the Pib-mediated blast resistance via unknown mechanisms. The RGA5-HMA2 domain is contrived based on the high structural similarity of AvrPib with two MAX effectors, AVR-Pia and AVR1-CO39, recognized by cognate RGA5-HMA, the binding interface between AVR1-CO39 and RGA5-HMA, and the distinct surface charge of AvrPib and RAG5-HMA. This work demonstrates that rice NLR receptors with the HMA domain can be engineered to confer resistance to the M. oryzae isolates noncorresponding but structurally similar MAX effectors, which manifest cognate NLR receptor–mediated resistance with unknown mechanisms. Our study also provides a practical approach for developing rice multilines and broad race spectrum–resistant cultivars by introducing a series of engineered NLR receptors.
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