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Outram MA, Chen J, Broderick S, Li Z, Aditya S, Tasneem N, Arndell T, Blundell C, Ericsson DJ, Figueroa M, Sperschneider J, Dodds PN, Williams SJ. AvrSr27 is a zinc-bound effector with a modular structure important for immune recognition. THE NEW PHYTOLOGIST 2024; 243:314-329. [PMID: 38730532 DOI: 10.1111/nph.19801] [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: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Effector proteins are central to the success of plant pathogens, while immunity in host plants is driven by receptor-mediated recognition of these effectors. Understanding the molecular details of effector-receptor interactions is key for the engineering of novel immune receptors. Here, we experimentally determined the crystal structure of the Puccinia graminis f. sp. tritici (Pgt) effector AvrSr27, which was not accurately predicted using AlphaFold2. We characterised the role of the conserved cysteine residues in AvrSr27 using in vitro biochemical assays and examined Sr27-mediated recognition using transient expression in Nicotiana spp. and wheat protoplasts. The AvrSr27 structure contains a novel β-strand rich modular fold consisting of two structurally similar domains that bind to Zn2+ ions. The N-terminal domain of AvrSr27 is sufficient for interaction with Sr27 and triggering cell death. We identified two Pgt proteins structurally related to AvrSr27 but with low sequence identity that can also associate with Sr27, albeit more weakly. Though only the full-length proteins, trigger Sr27-dependent cell death in transient expression systems. Collectively, our findings have important implications for utilising protein prediction platforms for effector proteins, and those embarking on bespoke engineering of immunity receptors as solutions to plant disease.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Sean Broderick
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Zhao Li
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Shouvik Aditya
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nuren Tasneem
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Taj Arndell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Cheryl Blundell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3186, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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2
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Mukhopadhyay S, Garvetto A, Neuhauser S, Pérez-López E. Decoding the Arsenal: Protist Effectors and Their Impact on Photosynthetic Hosts. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:498-506. [PMID: 38551366 DOI: 10.1094/mpmi-11-23-0196-cr] [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: 06/22/2024]
Abstract
Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes, and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, which makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionizing the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools like AlphaFold2 enable structure-based function prediction of effector candidates with divergent protein sequences. In turn, this allows us to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Soham Mukhopadhyay
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- L'Institute EDS, Université Laval, Quebec City, Quebec, Canada
| | - Andrea Garvetto
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Edel Pérez-López
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- L'Institute EDS, Université Laval, Quebec City, Quebec, Canada
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3
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De la Concepcion JC, Langner T, Fujisaki K, Yan X, Were V, Lam AHC, Saado I, Brabham HJ, Win J, Yoshida K, Talbot NJ, Terauchi R, Kamoun S, Banfield MJ. Zinc-finger (ZiF) fold secreted effectors form a functionally diverse family across lineages of the blast fungus Magnaporthe oryzae. PLoS Pathog 2024; 20:e1012277. [PMID: 38885263 PMCID: PMC11213319 DOI: 10.1371/journal.ppat.1012277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 06/28/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024] Open
Abstract
Filamentous plant pathogens deliver effector proteins into host cells to suppress host defence responses and manipulate metabolic processes to support colonization. Understanding the evolution and molecular function of these effectors provides knowledge about pathogenesis and can suggest novel strategies to reduce damage caused by pathogens. However, effector proteins are highly variable, share weak sequence similarity and, although they can be grouped according to their structure, only a few structurally conserved effector families have been functionally characterized to date. Here, we demonstrate that Zinc-finger fold (ZiF) secreted proteins form a functionally diverse effector family in the blast fungus Magnaporthe oryzae. This family relies on the Zinc-finger motif for protein stability and is ubiquitously present in blast fungus lineages infecting 13 different host species, forming different effector tribes. Homologs of the canonical ZiF effector, AVR-Pii, from rice infecting isolates are present in multiple M. oryzae lineages. Wheat infecting strains of the fungus also possess an AVR-Pii like allele that binds host Exo70 proteins and activates the immune receptor Pii. Furthermore, ZiF tribes may vary in the proteins they bind to, indicating functional diversification and an intricate effector/host interactome. Altogether, we uncovered a new effector family with a common protein fold that has functionally diversified in lineages of M. oryzae. This work expands our understanding of the diversity of M. oryzae effectors, the molecular basis of plant pathogenesis and may ultimately facilitate the development of new sources for pathogen resistance.
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Affiliation(s)
- Juan Carlos De la Concepcion
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Koki Fujisaki
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, Japan
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Anson Ho Ching Lam
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Indira Saado
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Helen J. Brabham
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Kentaro Yoshida
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Mark J. Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Hou J, Xiao H, Yao P, Ma X, Shi Q, Yang J, Hou H, Li L. Unveiling the mechanism of broad-spectrum blast resistance in rice: The collaborative role of transcription factor OsGRAS30 and histone deacetylase OsHDAC1. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1740-1756. [PMID: 38294722 PMCID: PMC11123394 DOI: 10.1111/pbi.14299] [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: 08/31/2023] [Revised: 11/15/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Rice blast, caused by Magnaporthe oryzae, significantly impacts grain yield, necessitating the identification of broad-spectrum resistance genes and their functional mechanisms for disease-resistant crop breeding. Here, we report that rice with knockdown OsHDAC1 gene expression displays enhanced broad-spectrum blast resistance without effects on plant height and tiller numbers compared to wild-type rice, while rice overexpressing OsHDAC1 is more susceptible to M. oryzae. We identify a novel blast resistance transcription factor, OsGRAS30, which genetically acts upstream of OsHDAC1 and interacts with OsHDAC1 to suppress its enzymatic activity. This inhibition increases the histone H3K27ac level, thereby boosting broad-spectrum blast resistance. Integrating genome-wide mapping of OsHDAC1 and H3K27ac targets with RNA sequencing analysis unveils how OsHDAC1 mediates the expression of OsSSI2, OsF3H, OsRLR1 and OsRGA5 to regulate blast resistance. Our findings reveal that the OsGRAS30-OsHDAC1 module is critical to rice blast control. Therefore, targeting either OsHDAC1 or OsGRAS30 offers a promising approach for enhancing crop blast resistance.
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Affiliation(s)
- Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Huangzhuo Xiao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Peng Yao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Xiaoci Ma
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Qipeng Shi
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Jin Yang
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
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Lahfa M, Barthe P, de Guillen K, Cesari S, Raji M, Kroj T, Le Naour—Vernet M, Hoh F, Gladieux P, Roumestand C, Gracy J, Declerck N, Padilla A. The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited. PLoS Pathog 2024; 20:e1012176. [PMID: 38709846 PMCID: PMC11132498 DOI: 10.1371/journal.ppat.1012176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/28/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast disease on numerous cereals and grasses. In spite of high sequence divergence, MAX effectors share a common fold characterized by a ß-sandwich core stabilized by a conserved disulfide bond. In this study, we investigated the structural landscape and diversity within the MAX effector repertoire of P. oryzae. Combining experimental protein structure determination and in silico structure modeling we validated the presence of the conserved MAX effector core domain in 77 out of 94 groups of orthologs (OG) identified in a previous population genomic study. Four novel MAX effector structures determined by NMR were in remarkably good agreement with AlphaFold2 (AF2) predictions. Based on the comparison of the AF2-generated 3D models we propose a classification of the MAX effectors superfamily in 20 structural groups that vary in the canonical MAX fold, disulfide bond patterns, and additional secondary structures in N- and C-terminal extensions. About one-third of the MAX family members remain singletons, without strong structural relationship to other MAX effectors. Analysis of the surface properties of the AF2 MAX models also highlights the high variability within the MAX family at the structural level, potentially reflecting the wide diversity of their virulence functions and host targets.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Philippe Barthe
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Mouna Raji
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marie Le Naour—Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - François Hoh
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Jérôme Gracy
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Nathalie Declerck
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
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6
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Talbi N, Blekemolen MC, Janevska S, Zendler D, van Tilbeurgh H, Fudal I, Takken FLW. Facilitation of Symplastic Effector Protein Mobility by Paired Effectors Is Conserved in Different Classes of Fungal Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:304-314. [PMID: 37782126 DOI: 10.1094/mpmi-07-23-0103-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
It has been discovered that plant pathogens produce effectors that spread via plasmodesmata (PD) to allow modulation of host processes in distal uninfected cells. Fusarium oxysporum f. sp. lycopersici (Fol) facilitates effector translocation by expansion of the size-exclusion limit of PD using the Six5/Avr2 effector pair. How other fungal pathogens manipulate PD is unknown. We recently reported that many fungal pathogens belonging to different families carry effector pairs that resemble the SIX5/AVR2 gene pair from Fol. Here, we performed structural predictions of three of these effector pairs from Leptosphaeria maculans (Lm) and tested their ability to manipulate PD and to complement the virulence defect of a Fol SIX5 knockout mutant. We show that the AvrLm10A homologs are structurally related to FolSix5 and localize at PD when they are expressed with their paired effectors. Furthermore, these effectors were found to complement FolSix5 function in cell-to-cell mobility assays and in fungal virulence. We conclude that distantly related fungal species rely on structurally related paired effector proteins to manipulate PD and facilitate effector mobility. The wide distribution of these effector pairs implies Six5-mediated effector translocation to be a conserved propensity among fungal plant pathogens. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Mila C Blekemolen
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Slavica Janevska
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Daniel Zendler
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
| | - Herman van Tilbeurgh
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute of Life Science (SILS), University of Amsterdam, Amsterdam, the Netherlands
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7
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Waksman T, Astin E, Fisher SR, Hunter WN, Bos JIB. Computational Prediction of Structure, Function, and Interaction of Myzus persicae (Green Peach Aphid) Salivary Effector Proteins. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:338-346. [PMID: 38171380 DOI: 10.1094/mpmi-10-23-0154-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Similar to plant pathogens, phloem-feeding insects such as aphids deliver effector proteins inside their hosts that act to promote host susceptibility and enable feeding and infestation. Despite exciting progress toward identifying and characterizing effector proteins from these insects, their functions remain largely unknown. The recent groundbreaking development in protein structure prediction algorithms, combined with the availability of proteomics and transcriptomic datasets for agriculturally important pests, provides new opportunities to explore the structural and functional diversity of effector repertoires. In this study, we sought to gain insight into the infection strategy used by the Myzus persicae (green peach aphid) by predicting and analyzing the structures of a set of 71 effector candidate proteins. We used two protein structure prediction methods, AlphaFold and OmegaFold, that produced mutually consistent results. We observed a wide continuous spectrum of structures among the effector candidates, from disordered proteins to globular enzymes. We made use of the structural information and state-of-the-art computational methods to predict M. persicae effector protein properties, including function and interaction with host plant proteins. Overall, our investigation provides novel insights into prediction of structure, function, and interaction of M. persicae effector proteins and will guide the necessary experimental characterization to address new hypotheses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Thomas Waksman
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - Edmund Astin
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - S Ronan Fisher
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - William N Hunter
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
| | - Jorunn I B Bos
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, U.K
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, U.K
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8
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John E, Chau MQ, Hoang CV, Chandrasekharan N, Bhaskar C, Ma LS. Fungal Cell Wall-Associated Effectors: Sensing, Integration, Suppression, and Protection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:196-210. [PMID: 37955547 DOI: 10.1094/mpmi-09-23-0142-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The cell wall (CW) of plant-interacting fungi, as the direct interface with host plants, plays a crucial role in fungal development. A number of secreted proteins are directly associated with the fungal CW, either through covalent or non-covalent interactions, and serve a range of important functions. In the context of plant-fungal interactions many are important for fungal development in the host environment and may therefore be considered fungal CW-associated effectors (CWAEs). Key CWAE functions include integrating chemical/physical signals to direct hyphal growth, interfering with plant immunity, and providing protection against plant defenses. In recent years, a diverse range of mechanisms have been reported that underpin their roles, with some CWAEs harboring conserved motifs or functional domains, while others are reported to have novel features. As such, the current understanding regarding fungal CWAEs is systematically presented here from the perspective of their biological functions in plant-fungal interactions. An overview of the fungal CW architecture and the mechanisms by which proteins are secreted, modified, and incorporated into the CW is first presented to provide context for their biological roles. Some CWAE functions are reported across a broad range of pathosystems or symbiotic/mutualistic associations. Prominent are the chitin interacting-effectors that facilitate fungal CW modification, protection, or suppression of host immune responses. However, several alternative functions are now reported and are presented and discussed. CWAEs can play diverse roles, some possibly unique to fungal lineages and others conserved across a broad range of plant-interacting fungi. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Evan John
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Minh-Quang Chau
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Cuong V Hoang
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo UPM, 28223 Pozuelo de Alarcón, Spain
| | | | - Chibbhi Bhaskar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Lay-Sun Ma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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9
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Yu DS, Outram MA, Smith A, McCombe CL, Khambalkar PB, Rima SA, Sun X, Ma L, Ericsson DJ, Jones DA, Williams SJ. The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies. eLife 2024; 12:RP89280. [PMID: 38411527 PMCID: PMC10942635 DOI: 10.7554/elife.89280] [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] [Indexed: 02/28/2024] Open
Abstract
Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant-fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.
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Affiliation(s)
- Daniel S Yu
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Megan A Outram
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Ashley Smith
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Carl L McCombe
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Pravin B Khambalkar
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Sharmin A Rima
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Xizhe Sun
- Research School of Biology, The Australian National UniversityCanberraAustralia
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agriculture UniversityBaodingChina
| | - Lisong Ma
- Research School of Biology, The Australian National UniversityCanberraAustralia
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural UniversityBaodingChina
| | - Daniel J Ericsson
- Research School of Biology, The Australian National UniversityCanberraAustralia
- The Australian Nuclear Science and Technology Organisation, Australian SynchrotronClaytonAustralia
| | - David A Jones
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Simon J Williams
- Research School of Biology, The Australian National UniversityCanberraAustralia
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10
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Carreón-Anguiano KG, Gómez-Tah R, Pech-Balan E, Ek-Hernández GE, De los Santos-Briones C, Islas-Flores I, Canto-Canché B. Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors. J Fungi (Basel) 2023; 9:970. [PMID: 37888226 PMCID: PMC10607838 DOI: 10.3390/jof9100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.
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Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Efren Pech-Balan
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Gemaly Elisama Ek-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - César De los Santos-Briones
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico;
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
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11
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Derbyshire MC, Raffaele S. Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors. Nat Commun 2023; 14:5244. [PMID: 37640704 PMCID: PMC10462633 DOI: 10.1038/s41467-023-40949-9] [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: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Micro-organismes Environnement (LIPME), INRAE, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France.
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12
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Cao Y, Kümmel F, Logemann E, Gebauer JM, Lawson AW, Yu D, Uthoff M, Keller B, Jirschitzka J, Baumann U, Tsuda K, Chai J, Schulze-Lefert P. Structural polymorphisms within a common powdery mildew effector scaffold as a driver of coevolution with cereal immune receptors. Proc Natl Acad Sci U S A 2023; 120:e2307604120. [PMID: 37523523 PMCID: PMC10410722 DOI: 10.1073/pnas.2307604120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
In plants, host-pathogen coevolution often manifests in reciprocal, adaptive genetic changes through variations in host nucleotide-binding leucine-rich repeat immune receptors (NLRs) and virulence-promoting pathogen effectors. In grass powdery mildew (PM) fungi, an extreme expansion of a RNase-like effector family, termed RALPH, dominates the effector repertoire, with some members recognized as avirulence (AVR) effectors by cereal NLR receptors. We report the structures of the sequence-unrelated barley PM effectors AVRA6, AVRA7, and allelic AVRA10/AVRA22 variants, which are detected by highly sequence-related barley NLRs MLA6, MLA7, MLA10, and MLA22 and of wheat PM AVRPM2 detected by the unrelated wheat NLR PM2. The AVR effectors adopt a common scaffold, which is shared with the RNase T1/F1 family. We found striking variations in the number, position, and length of individual structural elements between RALPH AVRs, which is associated with a differentiation of RALPH effector subfamilies. We show that all RALPH AVRs tested have lost nuclease and synthetase activities of the RNase T1/F1 family and lack significant binding to RNA, implying that their virulence activities are associated with neo-functionalization events. Structure-guided mutagenesis identified six AVRA6 residues that are sufficient to turn a sequence-diverged member of the same RALPH subfamily into an effector specifically detected by MLA6. Similar structure-guided information for AVRA10 and AVRA22 indicates that MLA receptors detect largely distinct effector surface patches. Thus, coupling of sequence and structural polymorphisms within the RALPH scaffold of PMs facilitated escape from NLR recognition and potential acquisition of diverse virulence functions.
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Affiliation(s)
- Yu Cao
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Florian Kümmel
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Elke Logemann
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Jan M. Gebauer
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Aaron W. Lawson
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
| | - Dongli Yu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Matthias Uthoff
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich8008, Switzerland
| | - Jan Jirschitzka
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Jijie Chai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne50674, Germany
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou310024, China
- Beijing Frontier Research Center for Biological Structure, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research, Cologne50829, Germany
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13
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Talbi N, Fokkens L, Audran C, Petit‐Houdenot Y, Pouzet C, Blaise F, Gay EJ, Rouxel T, Balesdent M, Rep M, Fudal I. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes. MOLECULAR PLANT PATHOLOGY 2023; 24:914-931. [PMID: 37128172 PMCID: PMC10346447 DOI: 10.1111/mpp.13338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Fungal effectors (small-secreted proteins) have long been considered as species or even subpopulation-specific. The increasing availability of high-quality fungal genomes and annotations has allowed the identification of trans-species or trans-genera families of effectors. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus causing stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighbouring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome showed that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes, in a pair, always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and/or petioles and stems. Of the two protein pairs further investigated, AvrLm10A_like1/AvrLm10B_like1 and AvrLm10A_like2/AvrLm10B_like2, the second one had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair, and cross-interactions were also detected for two pairs. AvrLm10A homologues were identified in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi. One of them, SIX5, is an effector from Fusarium oxysporum f. sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A/SIX5 homologues were associated with at least eight distinct putative effector families, suggesting that AvrLm10A/SIX5 is able to cooperate with different effectors. These results point to a general role of the AvrLm10A/SIX5 proteins as "cooperating proteins", able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighbouring AvrLm10A homologue.
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Affiliation(s)
- Nacera Talbi
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | - Like Fokkens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
- Present address:
Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
| | - Corinne Audran
- UMR LIPMEUniversité de Toulouse, INRAE, CNRSCastanet‐TolosanFrance
| | | | - Cécile Pouzet
- FRAIB‐TRI Imaging Platform Facilities, FR AIBUniversité de Toulouse, CNRSCastanet‐TolosanFrance
| | | | - Elise J. Gay
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | | | | | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
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14
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Gautier A, Laval V, Faure S, Rouxel T, Balesdent MH. Polymorphism of Avirulence Genes and Adaptation to Brassica Resistance Genes Is Gene-Dependent in the Phytopathogenic Fungus Leptosphaeria maculans. PHYTOPATHOLOGY 2023; 113:1222-1232. [PMID: 36802873 DOI: 10.1094/phyto-12-22-0466-r] [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: 06/18/2023]
Abstract
The fungal phytopathogen Leptosphaeria maculans, which causes stem canker (blackleg) of rapeseed (Brassica napus), is mainly controlled worldwide by genetic resistance, which includes major resistance genes (Rlm). This model is one of those for which the highest number of avirulence genes (AvrLm) has been cloned. In many systems, including the L. maculans-B. napus interaction, intense use of resistance genes exerts strong selection pressure on the corresponding avirulent isolates, and the fungi may rapidly escape resistance through various molecular events which modify the avirulence genes. In the literature, the study of polymorphism at avirulence loci is often focused on single genes under selection pressure. In this study, we investigate allelic polymorphism at 11 avirulence loci in a French population of 89 L. maculans isolates collected on a trap cultivar in four geographic locations in the 2017-2018 cropping season. The corresponding Rlm genes have been (i) used for a long time, (ii) recently used, or (iii) unused in agricultural practice. The sequence data generated indicate an extreme diversity of situations. For example, genes submitted to an ancient selection may have either been deleted in populations (AvrLm1) or replaced by a single-nucleotide mutated virulent version (AvrLm2, AvrLm5-9). Genes that have never been under selection may either be nearly invariant (AvrLm6, AvrLm10A, AvrLm10B), exhibit rare deletions (AvrLm11, AvrLm14), or display a high diversity of alleles and isoforms (AvrLmS-Lep2). These data suggest that the evolutionary trajectory of avirulence/virulence alleles is gene-dependent and independent of selection pressure in L. maculans. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Angélique Gautier
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | - Valérie Laval
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | | | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, UR BIOGER, Bâtiment F, 22 Place de l'Agronomie, CS 80022, 91120 Palaiseau Cedex, France
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15
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Fernandez J. The Phantom Menace: latest findings on effector biology in the rice blast fungus. ABIOTECH 2023; 4:140-154. [PMID: 37581025 PMCID: PMC10423181 DOI: 10.1007/s42994-023-00099-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/11/2023] [Indexed: 08/16/2023]
Abstract
Magnaporthe oryzae is a hemibiotrophic fungus responsible for the economically devastating and recalcitrant rice blast disease. However, the blast fungus is not only restricted to rice plants as it can also infect wheat, millet, and other crops. Despite previous outstanding discoveries aimed to understand and control the disease, the fungus remains one of the most important pathogens that threatens global food security. To cause disease, M. oryzae initiates morphological changes to attach, penetrate, and colonize rice cells, all while suppressing plant immune defenses that would otherwise hinder its proliferation. As such, M. oryzae actively secretes a battery of small proteins called "effectors" to manipulate host machinery. In this review, we summarize the latest findings in effector identification, expression, regulation, and functionality. We review the most studied effectors and their roles in pathogenesis. Additionally, we discern the current methodologies to structurally catalog effectors, and we highlight the importance of climate change and its impact on the future of rice blast disease.
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Affiliation(s)
- Jessie Fernandez
- Department of Microbiology and Cell Science at University of Florida-Institute of Food and Agricultural Science, Gainesville, FL 32611 USA
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16
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Teulet A, Quan C, Evangelisti E, Wanke A, Yang W, Schornack S. A pathogen effector FOLD diversified in symbiotic fungi. THE NEW PHYTOLOGIST 2023. [PMID: 37257494 DOI: 10.1111/nph.18996] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Pathogenic fungi use secreted effector proteins to suppress immunity and support their infection, but effectors have also been reported from fungi that engage in nutritional symbioses with plants. Sequence-based effector comparisons between pathogens and symbiotic arbuscular mycorrhizal (AM) fungi are hampered by the huge diversity of effector sequences even within closely related microbes. To find sequence-divergent but structurally similar effectors shared between symbiotic and pathogenic fungi, we compared secreted protein structure models of the AM fungus Rhizophagus irregularis to known pathogen effectors. We identified proteins with structural similarity to known Fusarium oxysporum f. sp. lycopersici dual domain (FOLD) effectors, which occur in low numbers in several fungal pathogens. Contrastingly, FOLD genes from AM fungi (MycFOLDs) are found in enlarged and diversified gene families with higher levels of positive selection in their C-terminal domains. Our structure model comparison suggests that MycFOLDs are similar to carbohydrate-binding motifs. Different MycFOLD genes are expressed during colonisation of different hosts and MycFOLD-17 transcripts accumulate in plant intracellular arbuscules. The exclusive presence of MycFOLDs across unrelated plant-colonising fungi, their inducible expression, lineage-specific sequence diversification and transcripts in arbuscules suggest that FOLD proteins act as effectors during plant colonisation of symbiotic and pathogenic fungi.
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Affiliation(s)
- Albin Teulet
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Clément Quan
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | | | - Alan Wanke
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
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17
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Amezrou R, Audéon C, Compain J, Gélisse S, Ducasse A, Saintenac C, Lapalu N, Louet C, Orford S, Croll D, Amselem J, Fillinger S, Marcel TC. A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat. PLoS Pathog 2023; 19:e1011376. [PMID: 37172036 DOI: 10.1371/journal.ppat.1011376] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/24/2023] [Accepted: 04/19/2023] [Indexed: 05/14/2023] Open
Abstract
Zymoseptoria tritici is the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping AvrStb9 transgenic strains on Stb9 cultivars, near isogenic lines and wheat mapping populations, showed that AvrStb9 interacts with Stb9 resistance gene, triggering an immune response. AvrStb9 encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector. AvrStb9 is also conserved among a global Z. tritici population and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an 'atypical' conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.
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Affiliation(s)
- Reda Amezrou
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Colette Audéon
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Jérôme Compain
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | | | - Aurélie Ducasse
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | | | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | | | - Simon Orford
- Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Daniel Croll
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
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18
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Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Guo Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. MOLECULAR PLANT PATHOLOGY 2023; 24:474-494. [PMID: 36790136 PMCID: PMC10098069 DOI: 10.1111/mpp.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.
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Affiliation(s)
- Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | | | - Yanan Guo
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | - Richard C. Hamelin
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | | | - Mengmeng Lu
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Hannah M. McCarthy
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Christiaan R. Schol
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
- Plant BreedingWageningen University & ResearchWageningenNetherlands
| | | | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Alex Z. Zaccaron
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Rosie E. Bradshaw
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
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Lovelace AH, Dorhmi S, Hulin MT, Li Y, Mansfield JW, Ma W. Effector Identification in Plant Pathogens. PHYTOPATHOLOGY 2023; 113:637-650. [PMID: 37126080 DOI: 10.1094/phyto-09-22-0337-kd] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effectors play a central role in determining the outcome of plant-pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host-pathogen interactions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Sara Dorhmi
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
- Department of Microbiology and Plant Pathology, University of California Riverside, CA 92521, U.S.A
| | | | - Yufei Li
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
| | - John W Mansfield
- Faculty of Natural Sciences, Imperial College London, London, SW7 2BX, U.K
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
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Gao J, Zhang Y, Yu L, Li Y, Liao S, Wang J, Guan L. Identification of Enolase 1 as a Potential Target for Magnaporthe oryzae: Integrated Proteomic and Molecular Dynamics Simulation. J Chem Inf Model 2023; 63:619-632. [PMID: 36580498 DOI: 10.1021/acs.jcim.2c01265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rice blast is an essential factor affecting rice yield and quality, which is caused by Magnaporthe oryzae (M. oryzae). Isobavachalcone (IBC) is a botanical fungicide derived from the seed extract of the Leguminosae plant Psoralea corylifolia L. and has shown an excellent rice blast control effect in field applications. To explore the potential targets of rice blast control, the analysis of the differentially expressed proteins (DEPs) between the liquid culture medium of mycelium treated by 10 mg/L of IBC for 2 h and the control group indicated that Enolase 1 (ENO1) was the most significantly down-regulated DEP with a fold change value of 0.305. In vitro experiments showed that after treating liquid culture mycelium with 10 mg/L of IBC for 0.5, 1, 2, 4, and 8 h, the enzymatic activity of ENO1 in the IBC experimental groups was 0.97, 0.75, 0.52, 0.44, and 0.39 times as much as in the control groups, respectively. To further explore the molecular interaction and binding mode between IBC and ENO1, the three-dimensional structure of ENO1 was established based on homology modeling. Molecular docking and molecular dynamics simulation showed that IBC had a pi-pi stacking effect with the residue TYR_365, a hydrogen bond interaction with the residue ARG_393, and hydrophobic interactions with non-polar residues ALA_361, LYS_362, and VAL_371 of ENO1. These findings indicated that ENO1 is a potential target of M. oryzae, which would pave the way for screening novel effective fungicides targeting ENO1.
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Affiliation(s)
- Jie Gao
- Department of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang110142, China
| | - Yaoliang Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Lin Yu
- Applied Biology Laboratory, Shenyang University of Chemical Technology, Shenyang110142, China
| | - Yuejuan Li
- Department of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang110142, China
| | - Shumin Liao
- Department of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang110142, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang110016, China
| | - Lijie Guan
- Department of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang110142, China
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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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Todd JNA, Carreón-Anguiano KG, Islas-Flores I, Canto-Canché B. Fungal Effectoromics: A World in Constant Evolution. Int J Mol Sci 2022; 23:13433. [PMID: 36362218 PMCID: PMC9656242 DOI: 10.3390/ijms232113433] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 10/28/2023] Open
Abstract
Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.
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Affiliation(s)
- Jewel Nicole Anna Todd
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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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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