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Shen S, Wang F, Cui Z, Yuan S, Meng L, Liu D, Ma L, Wang H. Puccinia triticina avirulence protein AvrLr21 directly interacts with wheat resistance protein Lr21 to activate wheat immune response. Commun Biol 2024; 7:1170. [PMID: 39294271 PMCID: PMC11410934 DOI: 10.1038/s42003-024-06881-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 09/11/2024] [Indexed: 09/20/2024] Open
Abstract
Wheat leaf rust, caused by Puccinia triticina (Pt), remains a constant threat to wheat production worldwide. Deployment of race-specific leaf rust (Lr) resistance genes in wheat provides effective protection against leaf rust, but often leads to selective pressures that drive the rapid emergence of new virulent Pt isolates in nature. However, the molecular mechanisms underlying the evasion of Lr-delivered resistance by leaf rust remain largely unknown. Here, we identify an avirulence gene AvrLr21 in Pt that triggers Lr21-dependent immune responses. BSMV (Barley stripe mosaic virus)-mediated host-induced gene silencing assay shows that silencing AvrLr21 compromises Lr21-mediated immunity. AvrLr21 interacts directly with Lr21 protein to induce a hypersensitive response in tobacco leaves. The evolved Lr21-breaking Pt isolates can suppress Lr21-mediated immunity. Our data provide a basis for studying the molecular determinants in Pt-wheat incompatible interaction and monitoring natural Pt populations to prioritize the deployment of Lr resistance genes in the field.
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Affiliation(s)
- Songsong Shen
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Fei Wang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Zhongchi Cui
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Shitao Yuan
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Linshuo Meng
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Daqun Liu
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Lisong Ma
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China.
- The State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural University, Baoding, China.
| | - Haiyan Wang
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China.
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Dulal N, Wilson RA. Paths of Least Resistance: Unconventional Effector Secretion by Fungal and Oomycete Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:653-661. [PMID: 38949402 DOI: 10.1094/mpmi-12-23-0212-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: 07/02/2024]
Abstract
Effector secretion by different routes mediates the molecular interplay between host plant and pathogen, but mechanistic details in eukaryotes are sparse. This may limit the discovery of new effectors that could be utilized for improving host plant disease resistance. In fungi and oomycetes, apoplastic effectors are secreted via the conventional endoplasmic reticulum (ER)-Golgi pathway, while cytoplasmic effectors are packaged into vesicles that bypass Golgi in an unconventional protein secretion (UPS) pathway. In Magnaporthe oryzae, the Golgi bypass UPS pathway incorporates components of the exocyst complex and a t-SNARE, presumably to fuse Golgi bypass vesicles to the fungal plasma membrane. Upstream, cytoplasmic effector mRNA translation in M. oryzae requires the efficient decoding of AA-ending codons. This involves the modification of wobble uridines in the anticodon loop of cognate tRNAs and fine-tunes cytoplasmic effector translation and secretion rates to maintain biotrophic interfacial complex integrity and permit host infection. Thus, plant-fungal interface integrity is intimately tied to effector codon usage, which is a surprising constraint on pathogenicity. Here, we discuss these findings within the context of fungal and oomycete effector discovery, delivery, and function in host cells. We show how cracking the codon code for unconventional cytoplasmic effector secretion in M. oryzae has revealed AA-ending codon usage bias in cytoplasmic effector mRNAs across kingdoms, including within the RxLR-dEER motif-encoding sequence of a bona fide Phytophthora infestans cytoplasmic effector, suggesting its subjection to translational speed control. By focusing on recent developments in understanding unconventional effector secretion, we draw attention to this important but understudied area of host-pathogen interactions. [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)
- Nawaraj Dulal
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, U.S.A
| | - Richard A Wilson
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE, U.S.A
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Dilla-Ermita CJ, Goldman P, Anchieta A, Feldmann MJ, Pincot DDA, Famula RA, Vachev M, Cole GS, Knapp SJ, Klosterman SJ, Henry PM. Secreted in Xylem 6 ( SIX6) Mediates Fusarium oxysporum f. sp. fragariae Race 1 Avirulence on FW1-Resistant Strawberry Cultivars. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:530-541. [PMID: 38552146 DOI: 10.1094/mpmi-02-24-0012-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: 06/25/2024]
Abstract
Fusarium oxysporum f. sp. fragariae (Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof race 2 is virulent on FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between a gene at the FW1 locus and an avirulence gene (AvrFW1) in Fof race 1. To identify a candidate AvrFW1, we compared genomes of 24 Fof race 1 and three Fof race 2 isolates. We found one candidate gene that was present in race 1, was absent in race 2, was highly expressed in planta, and was homologous to a known effector, secreted in xylem 6 (SIX6). We knocked out SIX6 in two Fof race 1 isolates by homologous recombination. All SIX6 knockout transformants (ΔSIX6) gained virulence on FW1/fw1 cultivars, whereas ectopic transformants and the wildtype isolates remained avirulent. ΔSIX6 isolates were quantitatively less virulent on FW1/fw1 cultivars Fronteras and San Andreas than fw1/fw1 cultivars. Seedlings from an FW1/fw1 × fw1/fw1 population were genotyped for FW1 and tested for susceptibility to a SIX6 knockout isolate. Results suggested that additional minor-effect quantitative resistance genes could be present at the FW1 locus. This work demonstrates that SIX6 acts as an avirulence factor interacting with a resistance gene at the FW1 locus. The identification of AvrFW1 enables surveillance for Fof race 2 and provides insight into the mechanisms of FW1-mediated resistance. [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)
- Christine Jade Dilla-Ermita
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Polly Goldman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Amy Anchieta
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Mishi Vachev
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Klosterman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Peter M Henry
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
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Rozano L, Jones DAB, Hane JK, Mancera RL. Template-Based Modelling of the Structure of Fungal Effector Proteins. Mol Biotechnol 2024; 66:784-813. [PMID: 36940017 PMCID: PMC11043172 DOI: 10.1007/s12033-023-00703-4] [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: 08/31/2022] [Accepted: 02/14/2023] [Indexed: 03/21/2023]
Abstract
The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs. The availability of experimentally determined three-dimensional (3D) structures of a number of effector proteins has recently highlighted structural similarities amongst groups of sequence-dissimilar fungal effectors, enabling the search for similar structural folds amongst effector sequence candidates. We have applied template-based modelling to predict the 3D structures of candidate effector sequences obtained from bioinformatics predictions and the PHI-BASE database. Structural matches were found not only with ToxA- and MAX-like effector candidates but also with non-fungal effector-like proteins-including plant defensins and animal venoms-suggesting the broad conservation of ancestral structural folds amongst cytotoxic peptides from a diverse range of distant species. Accurate modelling of fungal effectors were achieved using RaptorX. The utility of predicted structures of effector proteins lies in the prediction of their interactions with plant receptors through molecular docking, which will improve the understanding of effector-plant interactions.
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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 Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Darcy A B Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - James K Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, 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 Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia.
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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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Kariyawasam GK, Nelson AC, Williams SJ, Solomon PS, Faris JD, Friesen TL. The Necrotrophic Pathogen Parastagonospora nodorum Is a Master Manipulator of Wheat Defense. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:764-773. [PMID: 37581456 DOI: 10.1094/mpmi-05-23-0067-irw] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Parastagonospora nodorum is a necrotrophic pathogen of wheat that is particularly destructive in major wheat-growing regions of the United States, northern Europe, Australia, and South America. P. nodorum secretes necrotrophic effectors that target wheat susceptibility genes to induce programmed cell death (PCD), resulting in increased colonization of host tissue and, ultimately, sporulation to complete its pathogenic life cycle. Intensive research over the last two decades has led to the functional characterization of five proteinaceous necrotrophic effectors, SnTox1, SnToxA, SnTox267, SnTox3, and SnTox5, and three wheat susceptibility genes, Tsn1, Snn1, and Snn3D-1. Functional characterization has revealed that these effectors, in addition to inducing PCD, have additional roles in pathogenesis, including chitin binding that results in protection from wheat chitinases, blocking defense response signaling, and facilitating plant colonization. There are still large gaps in our understanding of how this necrotrophic pathogen is successfully manipulating wheat defense to complete its life cycle. This review summarizes our current knowledge, identifies knowledge gaps, and provides a summary of well-developed tools and resources currently available to study the P. nodorum-wheat interaction, which has become a model for necrotrophic specialist interactions. Further functional characterization of the effectors involved in this interaction and work toward a complete understanding of how P. nodorum manipulates wheat defense will provide fundamental knowledge about this and other necrotrophic interactions. Additionally, a broader understanding of this interaction will contribute to the successful management of Septoria nodorum blotch disease on wheat. [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)
- Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Ashley C Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Simon J Williams
- 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
| | - Justin D Faris
- Cereal Crops Research Unit, USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
- Cereal Crops Research Unit, USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
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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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8
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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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9
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Seong K, Krasileva KV. 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: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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Moolhuijzen PM, See PT, Shi G, Powell HR, Cockram J, Jørgensen LN, Benslimane H, Strelkov SE, Turner J, Liu Z, Moffat CS. A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology. Microb Genom 2022; 8:mgen000872. [PMID: 36214662 PMCID: PMC9676058 DOI: 10.1099/mgen.0.000872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, consisting of core and accessory genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for Pyrenophora tritici-repentis (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, 15 new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with 11 previously published Ptr genomes, a pangenome for 26 Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57 % and presents a new Ptr resource for searching natural homologues (orthologues not acquired by horizontal transfer from another species) using remote protein structural homology. Here, we identify for the first time a non-synonymous mutation in the Ptr necrotrophic effector gene ToxB, multiple copies of the inactive toxb within an isolate, a distant natural Pyrenophora homologue of a known Parastagonopora nodorum necrotrophic effector (SnTox3), and clear genomic break points for the ToxA effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity.
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Affiliation(s)
- Paula M. Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- *Correspondence: Paula M. Moolhuijzen,
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Harold R. Powell
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, England, UK
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Hamida Benslimane
- Département de Botanique, Ecole Nationale Supérieure Agronomique (ENSA), Hassan Badi, El-Harrach, Algiers, Algeria
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
- *Correspondence: Zhaohui Liu,
| | - Caroline S. Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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Zhang S, Li C, Si J, Han Z, Chen D. Action Mechanisms of Effectors in Plant-Pathogen Interaction. Int J Mol Sci 2022; 23:6758. [PMID: 35743201 PMCID: PMC9224169 DOI: 10.3390/ijms23126758] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 02/08/2023] Open
Abstract
Plant pathogens are one of the main factors hindering the breeding of cash crops. Pathogens, including oomycetes, fungus, and bacteria, secrete effectors as invasion weapons to successfully invade and propagate in host plants. Here, we review recent advances made in the field of plant-pathogen interaction models and the action mechanisms of phytopathogenic effectors. The review illustrates how effectors from different species use similar and distinct strategies to infect host plants. We classify the main action mechanisms of effectors in plant-pathogen interactions according to the infestation process: targeting physical barriers for disruption, creating conditions conducive to infestation, protecting or masking themselves, interfering with host cell physiological activity, and manipulating plant downstream immune responses. The investigation of the functioning of plant pathogen effectors contributes to improved understanding of the molecular mechanisms of plant-pathogen interactions. This understanding has important theoretical value and is of practical significance in plant pathology and disease resistance genetics and breeding.
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Affiliation(s)
| | | | | | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China; (S.Z.); (C.L.); (J.S.)
| | - Donghong Chen
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China; (S.Z.); (C.L.); (J.S.)
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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: 26] [Impact Index Per Article: 13.0] [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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Dagvadorj B, Outram MA, Williams SJ, Solomon PS. The necrotrophic effector ToxA from Parastagonospora nodorum interacts with wheat NHL proteins to facilitate Tsn1-mediated necrosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:407-418. [PMID: 35061310 DOI: 10.1111/tpj.15677] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
The plant pathogen Parastagonospora nodorum secretes necrotrophic effectors to promote disease. These effectors induce cell death on wheat cultivars carrying dominant susceptibility genes in an inverse gene-for-gene manner. However, the molecular mechanisms underpinning these interactions and resulting cell death remain unclear. Here, we used a yeast two-hybrid library approach to identify wheat proteins that interact with the necrotrophic effector ToxA. Using this strategy, we identified an interaction between ToxA and a wheat transmembrane NDR/HIN1-like protein (TaNHL10) and confirmed the interaction using in planta co-immunoprecipitation and confocal microscopy co-localization analysis. We showed that the C-terminus of TaNHL10 is extracellular whilst the N-terminus is localized in the cytoplasm. Further analyses using yeast two-hybrid and confocal microscopy co-localization showed that ToxA interacts with the C-terminal LEA2 extracellular domain of TaNHL10. Random mutagenesis was then used to identify a ToxA mutant, ToxAN109D , which was unable to interact with TaNHL10 in yeast two-hybrid assays. Subsequent heterologous expression and purification of ToxAN109D in Nicotiania benthamiana revealed that the mutated protein was unable to induce necrosis on Tsn1-dominant wheat cultivars, confirming that the interaction of ToxA with TaNHL10 is required to induce cell death. Collectively, these data advance our understanding on how ToxA induces cell death during infection and further highlight the importance of host cell surface interactions in necrotrophic pathosystems.
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Affiliation(s)
- Bayantes Dagvadorj
- 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
| | - Simon J Williams
- 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
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14
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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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15
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Kanyuka K, Igna AA, Solomon PS, Oliver RP. The rise of necrotrophic effectors. THE NEW PHYTOLOGIST 2022; 233:11-14. [PMID: 34723389 DOI: 10.1111/nph.17811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 JQ, UK
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alina A Igna
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 JQ, UK
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Richard P Oliver
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
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16
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Richards JK, Kariyawasam GK, Seneviratne S, Wyatt NA, Xu SS, Liu Z, Faris JD, Friesen TL. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. THE NEW PHYTOLOGIST 2022; 233:427-442. [PMID: 34227112 PMCID: PMC9292537 DOI: 10.1111/nph.17601] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Here we identify and functionally validate the effector targeting the host susceptibility genes Snn2, Snn6 and Snn7. We utilized whole-genome sequencing, association mapping, gene-disrupted mutants, gain-of-function transformants, virulence assays, bioinformatics and quantitative PCR to characterize these interactions. A single proteinaceous effector, SnTox267, targeted Snn2, Snn6 and Snn7 to trigger PCD. Snn2 and Snn6 functioned cooperatively to trigger PCD in a light-dependent pathway, whereas Snn7-mediated PCD functioned in a light-independent pathway. Isolates harboring 20 SnTox267 protein isoforms quantitatively varied in virulence. The diversity and distribution of isoforms varied between populations, indicating adaptation to local selection pressures. SnTox267 deletion resulted in the upregulation of effector genes SnToxA, SnTox1 and SnTox3. We validated a novel effector operating in an inverse-gene-for-gene manner to target three genetically distinct host susceptibility genes and elicit PCD. The discovery of the complementary gene action of Snn2 and Snn6 indicates their potential function in a guard or decoy model. Additionally, differences in light dependency in the elicited pathways and upregulation of unlinked effectors sheds new light onto a complex fungal necrotroph-host interaction.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | | | | | - Nathan A. Wyatt
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Steven S. Xu
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Justin D. Faris
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Timothy L. Friesen
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
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Outram MA, Solomon PS, Williams SJ. Pro-domain processing of fungal effector proteins from plant pathogens. PLoS Pathog 2021; 17:e1010000. [PMID: 34669754 PMCID: PMC8528282 DOI: 10.1371/journal.ppat.1010000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Megan A. Outram
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Peter S. Solomon
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Simon J. Williams
- Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
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Dagvadorj B, Solomon PS. Simple and efficient heterologous expression of necrosis-inducing effectors using the model plant Nicotiana benthamiana. PLANT DIRECT 2021; 5:e341. [PMID: 34466773 PMCID: PMC8381856 DOI: 10.1002/pld3.341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
Plant fungal pathogens cause devastating diseases on cereal plants and threaten global food security. During infection, these pathogens secrete proteinaceous effectors that promote disease. Some of these effectors from necrotrophic plant pathogens induce a cell death response (necrosis), which facilitates pathogen growth in planta. Characterization of these effectors typically requires heterologous expression, and microbial expression systems such as bacteria and yeast are the predominantly used. However, microbial expression systems often require optimization for any given effector and are, in general, not suitable for effectors involving cysteine bridges and posttranslational modifications for activity. Here, we describe a simple and efficient method for expressing such effectors in the model plant Nicotiana benthamiana. Briefly, an effector protein is transiently expressed and secreted into the apoplast of N. benthamiana by Agrobacterium-mediated infiltration. Two to three days subsequent to agroinfiltration, the apoplast from the infiltrated leaves is extracted and can be directly used for phenotyping on host plants. The efficacy of this approach was demonstrated by expressing the ToxA, Tox3, and Tox1 necrosis-inducing effectors from Parastagonospora nodorum. All three effectors produced in N. benthamiana were capable of inducing necrosis in wheat lines, and two of three showed visible bands on Coomassie-stained gel. These data suggest that N. benthamiana-agroinfiltration system is a feasible tool to obtain fungal effectors, especially those that require disulfide bonds and posttranslational modifications. Furthermore, due to the low number of proteins typically observed in the apoplast (compared with intracellular), this simple and high-throughput approach circumvents the requirement to lyse cells and further purifies the target proteins that are required in other heterologous systems. Because of its simplicity and potential for high-throughput, this method is highly amenable to the phenotyping of candidate protein effectors on host plants.
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Affiliation(s)
- Bayantes Dagvadorj
- Research School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Peter S. Solomon
- Research School of BiologyThe Australian National UniversityCanberraACTAustralia
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