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Jia M, Gong X, Fan M, Liu H, Zhou H, Gu S, Liu Y, Dong J. Identification and analysis of the secretome of plant pathogenic fungi reveals lifestyle adaptation. Front Microbiol 2023; 14:1171618. [PMID: 37152749 PMCID: PMC10156984 DOI: 10.3389/fmicb.2023.1171618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
The secretory proteome plays an important role in the pathogenesis of phytopathogenic fungi. However, the relationship between the large-scale secretome of phytopathogenic fungi and their lifestyle is not fully understood. In the present study, the secretomes of 150 plant pathogenic fungi were predicted and the characteristics associated with different lifestyles were investigated. In total, 94,974 secreted proteins (SPs) were predicted from these fungi. The number of the SPs ranged from 64 to 1,662. Among these fungi, hemibiotrophic fungi had the highest number (average of 970) and proportion (7.1%) of SPs. Functional annotation showed that hemibiotrophic and necrotroph fungi, differ from biotrophic and symbiotic fungi, contained much more carbohydrate enzymes, especially polysaccharide lyases and carbohydrate esterases. Furthermore, the core and lifestyle-specific SPs orthogroups were identified. Twenty-seven core orthogroups contained 16% of the total SPs and their motif function annotation was represented by serine carboxypeptidase, carboxylesterase and asparaginase. In contrast, 97 lifestyle-specific orthogroups contained only 1% of the total SPs, with diverse functions such as PAN_AP in hemibiotroph-specific and flavin monooxygenases in necrotroph-specific. Moreover, obligate biotrophic fungi had the largest number of effectors (average of 150), followed by hemibiotrophic fungi (average of 120). Among these effectors, 4,155 had known functional annotation and pectin lyase had the highest proportion in the functionally annotated effectors. In addition, 32 sets of RNA-Seq data on pathogen-host interactions were collected and the expression levels of SPs were higher than that of non-SPs, and the expression level of effector genes was higher in biotrophic and hemibiotrophic fungi than in necrotrophic fungi, while secretase genes were highly expressed in necrotrophic fungi. Finally, the secretory activity of five predicted SPs from Setosphearia turcica was experimentally verified. In conclusion, our results provide a foundation for the study of pathogen-host interaction and help us to understand the fungal lifestyle adaptation.
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Affiliation(s)
- Mingxuan Jia
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaodong Gong
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Baoding, China
| | - Mengmeng Fan
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Haoran Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - He Zhou
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shouqin Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Baoding, China
- *Correspondence: Shouqin Gu, ; Yuwei Liu, ; Jingao Dong,
| | - Yuwei Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Baoding, China
- *Correspondence: Shouqin Gu, ; Yuwei Liu, ; Jingao Dong,
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- College of Plant Protection, Hebei Agricultural University, Baoding, China
- *Correspondence: Shouqin Gu, ; Yuwei Liu, ; Jingao Dong,
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Mustafa Z, Ölmez F, Akkaya M. Inactivation of a candidate effector gene of Zymoseptoria tritici affects its sporulation. Mol Biol Rep 2022; 49:11563-11571. [PMID: 36097116 DOI: 10.1007/s11033-022-07879-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/24/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Wheat is one of the most important staple crops produced worldwide. Its susceptibility to plant diseases reduces its production significantly. One of the most important diseases of wheat is septoria tritici blotch, a devastating disease observed in fields with wet and temperate conditions. Z. tritici secretes effector proteins to influence the host's defense mechanisms, as is typical of plant pathogens. In this investigation, we evaluated the pathogenicity of some Zymoseptoria tritici effector candidate genes having a signal peptide for secretion with no known function. METHODS AND RESULTS Three genes named Mycgr3G104383, Mycgr3G104444 and Mycgr3G105826 were knocked out separately through homologous recombination, generating Z. tritici IPO323 mutants lacking the functional copy of the corresponding genes. While KO1 and KO3 mutants did not show any significant differences during phenotypic and virulence investigations, the KO2 mutant generated exclusively macropycnidiospores in artificial media, different from wild-type IPO323 which produce only micropycidiospores. The mycelial growth capability of KO2 was also severely attenuated in all of the investigated growth conditions. These changes were observed independent of growth media and growth temperatures, implying that changes were genetic and inherited through generations. Virulence of knockout mutants in wheat leaves was observed to be similar to the wild-type IPO323. CONCLUSION Understanding the biology of Z. tritici and its interactions with wheat will reveal new strategies to fight septoria tritici blotch, enabling breeding wheat cultivars resistant to a broader spectrum of Z. tritici strains. Furthermore, gene knockout via homologous recombination proved to be a powerful tool for discovering novel gene functions.
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Affiliation(s)
- Zemran Mustafa
- Department of Plant Production and Technologies, Faculty of Agricultural Science and Technologies, Sivas University of Science and Technology, Sivas, Turkey.
| | - Fatih Ölmez
- Department of Plant Protection, Faculty of Agricultural Science and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mahinur Akkaya
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, China
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Li X, Yang S, Zhang M, Yang Y, Peng L. Identification of Pathogenicity-Related Effector Proteins and the Role of Piwsc1 in the Virulence of Penicillium italicum on Citrus Fruits. J Fungi (Basel) 2022; 8:jof8060646. [PMID: 35736129 PMCID: PMC9224591 DOI: 10.3390/jof8060646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
Blue mold caused by Penicillium italicum is one of the two major postharvest diseases of citrus fruits. The interactions of pathogens with their hosts are complicated, and virulence factors that mediate pathogenicity have not yet been identified. In present study, a prediction pipeline approach based on bioinformatics and transcriptomic data is designed to determine the effector proteins of P. italicum. Three hundred and seventy-five secreted proteins of P. italicum were identified, many of which (29.07%) were enzymes for carbohydrate utilization. Twenty-nine candidates were further analyzed and the expression patterns of 12 randomly selected candidate effector genes were monitored during the early stages of growth on PDA and infection of Navel oranges for validation. Functional analysis of a cell wall integrity-related gene Piwsc1, a core candidate, was performed by gene knockout. The deletion of Piwsc1 resulted in reduced virulence on citrus fruits, as presented by an approximate 57% reduction in the diameter of lesions. In addition, the mycelial growth rate, spore germination rate, and sporulation of ΔPiwsc1 decreased. The findings provide us with new insights to understand the pathogenesis of P. italicum and develop an effective and sustainable control method for blue mold.
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Sinha N, Patra SK, Ghosh S. Secretome Analysis of Macrophomina phaseolina Identifies an Array of Putative Virulence Factors Responsible for Charcoal Rot Disease in Plants. Front Microbiol 2022; 13:847832. [PMID: 35479629 PMCID: PMC9037145 DOI: 10.3389/fmicb.2022.847832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
Macrophomina phaseolina is a global devastating necrotrophic fungal pathogen. It causes charcoal rot disease in more than 500 host plants including major food crops, pulse crops, fiber crops, and oil crops. Despite having the whole-genome sequence of M. phaseolina, understanding the M. phaseolina genome-based plant–pathogen interactions is limited in the absence of direct experimental proof of secretion. Thus, it is essential to understand the host–microbe interaction and the disease pathogenesis, which can ensure global agricultural crop production and security. An in silico–predicted secretome of M. phaseolina is unable to represent the actual secretome. We could identify 117 proteins present in the secretome of M. phaseolina using liquid chromatography–electrospray ionization–tandem mass spectrometry. Data are available via ProteomeXchange with identifier PXD032749. An array of putative virulence factors of M. phaseolina were identified in the present study using solid-state culture. Similar virulence factors have been reported in other plant pathogenic fungi also. Among the secretory fungal proteins with positive economic impacts, lignocellulolytic enzymes are of prime importance. Further, we validated our results by detecting the cell wall–degrading enzymes xylanase, endoglucanase, and amylase in the secretome of M. phaseolina. The present study may provide a better understanding about the necrotrophic fungi M. phaseolina, which modulate the host plant defense barriers using secretory proteins.
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Affiliation(s)
- Nilanjan Sinha
- Department of Biochemistry, University of Calcutta, Kolkata, India
| | | | - Sanjay Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata, India
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Cao Z, Banniza S. Cross-Kingdom Gene Coexpression Analysis Using a Stemphylium botryosum-Lens ervoides System Revealed Plasticity of Intercommunication Between the Pathogen Secretome and the Host Immune Systems. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1365-1377. [PMID: 34890251 DOI: 10.1094/mpmi-05-21-0112-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Necrotrophic pathogens are responsible for significant declines in crop yield and quality worldwide. During the infection process, a pathogen releases a series of secretory proteins to counteract the plant immune system, and this interaction of pathogen and host molecules determines whether the pathogen will successfully invade the host plant tissues. In this study, we adopted co-transcriptomic approaches to analyze the Lens ervoides-Stemphylium botryosum system, with a focus on 1,216 fungal genes coding for secretory proteins and 8,810 disease-responsive genes of the host 48, 96, and 144 h postinoculation, captured in two F9 recombinant inbred lines (RILs) displaying contrasting disease responses. By constructing in planta gene coexpression networks (GCNs) for S. botryosum, we found that the pathogen tended to co-upregulate genes regulating cell wall degradation enzymes, effectors, oxidoreductases, and peptidases to a much higher degree in the susceptible host LR-66-577 than in the resistant RIL LR-66-637, indicating that the promotion of these digestive enzymes and toxins increased S. botryosum virulence. Construction of cross-kingdom GCNs between pathogen and plant for the two RILs revealed that the co-upregulation of these fungal digestive enzymes and toxins simultaneously promoted a series of defense responses such as redox change, expression of membrane-related genes and serine/threonine kinase, and stress and disease responses in the susceptible RIL which was not observed in the resistant RIL, indicating that these activities exacerbated susceptibility to S. botryosum.[Formula: see text] Copyright © 2021 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)
- Zhe Cao
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Sabine Banniza
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
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In silico approach to predict pancreatic β-cells classically secreted proteins. Biosci Rep 2021; 40:222021. [PMID: 32003782 PMCID: PMC7024845 DOI: 10.1042/bsr20193708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Pancreatic β-cells, residents of the islets of Langerhans, are the unique insulin-producers in the body. Their physiology is a topic of intensive studies aiming to understand the biology of insulin production and its role in diabetes pathology. However, investigations about these cells' subset of secreted proteins, the secretome, are surprisingly scarce and a list describing islet/β-cell secretome upon glucose-stimulation is not yet available. In silico predictions of secretomes are an interesting approach that can be employed to forecast proteins likely to be secreted. In this context, using the rationale behind classical secretion of proteins through the secretory pathway, a Python tool capable of predicting classically secreted proteins was developed. This tool was applied to different available proteomic data (human and rodent islets, isolated β-cells, β-cell secretory granules, and β-cells supernatant), filtering them in order to selectively list only classically secreted proteins. The method presented here can retrieve, organize, search and filter proteomic lists using UniProtKB as a central database. It provides analysis by overlaying different sets of information, filtering out potential contaminants and clustering the identified proteins into functional groups. A range of 70-92% of the original proteomes analyzed was reduced generating predicted secretomes. Islet and β-cell signal peptide-containing proteins, and endoplasmic reticulum-resident proteins were identified and quantified. From the predicted secretomes, exemplary conservational patterns were inferred, as well as the signaling pathways enriched within them. Such a technique proves to be an effective approach to reduce the horizon of plausible targets for drug development or biomarkers identification.
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Comparative analysis of extracellular proteomes reveals putative effectors of the boxwood blight pathogens, Calonectria henricotiae and C. pseudonaviculata. Biosci Rep 2021; 41:227917. [PMID: 33619567 PMCID: PMC7937907 DOI: 10.1042/bsr20203544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 01/25/2023] Open
Abstract
Calonectria henricotiae (Che) and C. pseudonaviculata (Cps) are destructive fungal pathogens causing boxwood blight, a persistent threat to horticultural production, landscape industries, established gardens, and native ecosystems. Although extracellular proteins including effectors produced by fungal pathogens are known to play a fundamental role in pathogenesis, the composition of Che and Cps extracellular proteins has not been examined. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics prediction tools, 630 extracellular proteins and 251 cell membrane proteins of Che and Cps were identified in the classical secretion pathway in the present study. In the non-classical secretion pathway, 79 extracellular proteins were identified. The cohort of proteins belonged to 364 OrthoMCL clusters, with the majority (62%) present in both species, and a subset unique to Che (19%) and Cps (20%). These extracellular proteins were predicted to play important roles in cell structure, regulation, metabolism, and pathogenesis. A total of 124 proteins were identified as putative effectors. Many of them are orthologs of proteins with documented roles in suppressing host defense and facilitating infection processes in other pathosystems, such as SnodProt1-like proteins in the OrthoMCL cluster OG5_152723 and PhiA-like cell wall proteins in the cluster OG5_155754. This exploratory study provides a repository of secreted proteins and putative effectors that can provide insights into the virulence mechanisms of the boxwood blight pathogens.
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Karki SJ, Reilly A, Zhou B, Mascarello M, Burke J, Doohan F, Douchkov D, Schweizer P, Feechan A. A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease. JOURNAL OF EXPERIMENTAL BOTANY 2021. [PMID: 33095257 DOI: 10.5061/dryad.9w0vt4bcx] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
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Affiliation(s)
- Sujit Jung Karki
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Reilly
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Maurizio Mascarello
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 8 32, 3000 Leuven, Belgium
| | - James Burke
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fiona Doohan
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitar Douchkov
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Patrick Schweizer
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Angela Feechan
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Karki SJ, Reilly A, Zhou B, Mascarello M, Burke J, Doohan F, Douchkov D, Schweizer P, Feechan A. A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:733-746. [PMID: 33095257 PMCID: PMC7853600 DOI: 10.1093/jxb/eraa489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/15/2020] [Indexed: 05/05/2023]
Abstract
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
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Affiliation(s)
- Sujit Jung Karki
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Reilly
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Maurizio Mascarello
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 8 32, 3000 Leuven, Belgium
| | - James Burke
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fiona Doohan
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitar Douchkov
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Patrick Schweizer
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Angela Feechan
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Correspondence:
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Hill EH, Solomon PS. Extracellular vesicles from the apoplastic fungal wheat pathogen Zymoseptoria tritici. Fungal Biol Biotechnol 2020; 7:13. [PMID: 32968488 PMCID: PMC7501697 DOI: 10.1186/s40694-020-00103-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The fungal pathogen Zymoseptoria tritici is a significant constraint to wheat production in temperate cropping regions around the world. Despite its agronomic impacts, the mechanisms allowing the pathogen to asymptomatically invade and grow in the apoplast of wheat leaves before causing extensive host cell death remain elusive. Given recent evidence of extracellular vesicles (EVs)-secreted, membrane-bound nanoparticles containing molecular cargo-being implicated in extracellular communication between plants and fungal pathogen, we have initiated an in vitro investigation of EVs from this apoplastic fungal wheat pathogen. We aimed to isolate EVs from Z. tritici broth cultures and examine their protein composition in relation to the soluble protein in the culture filtrate and to existing fungal EV proteomes. RESULTS Zymoseptoria tritici EVs were isolated from broth culture filtrates using differential ultracentrifugation (DUC) and examined with transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Z. tritici EVs were observed as a heterogeneous population of particles, with most between 50 and 250 nm. These particles were found in abundance in the culture filtrates of viable Z. tritici cultures, but not heat-killed cultures incubated for an equivalent time and of comparable biomass. Bottom-up proteomic analysis using LC-MS/MS, followed by stringent filtering revealed 240 Z. tritici EV proteins. These proteins were distinct from soluble proteins identified in Z. tritici culture filtrates, but were similar to proteins identified in EVs from other fungi, based on sequence similarity analyses. Notably, a putative marker protein recently identified in Candida albicans EVs was also consistently detected in Z. tritici EVs. CONCLUSION We have shown EVs can be isolated from the devastating fungal wheat pathogen Z. tritici and are similar to protein composition to previously characterised fungal EVs. EVs from human pathogenic fungi are implicated in virulence, but the role of EVs in the interaction of phytopathogenic fungi and their hosts is unknown. These in vitro analyses provide a basis for expanding investigations of Z. tritici EVs in planta, to examine their involvement in the infection process of this apoplastic wheat pathogen and more broadly, advance understanding of noncanonical secretion in filamentous plant pathogens.
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Affiliation(s)
- Erin H. Hill
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601 Australia
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, 2601 Australia
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Zhou B, Benbow HR, Brennan CJ, Arunachalam C, Karki SJ, Mullins E, Feechan A, Burke JI, Doohan FM. Wheat Encodes Small, Secreted Proteins That Contribute to Resistance to Septoria Tritici Blotch. Front Genet 2020; 11:469. [PMID: 32477410 PMCID: PMC7235427 DOI: 10.3389/fgene.2020.00469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/16/2020] [Indexed: 11/23/2022] Open
Abstract
During plant-pathogen interactions, pathogens secrete many rapidly evolving, small secreted proteins (SSPs) that can modify plant defense and permit pathogens to colonize plant tissue. The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), one of the most important foliar diseases of wheat, globally. Z. tritici is a strictly apoplastic pathogen that can secrete numerous proteins into the apoplast of wheat leaves to promote infection. We sought to determine if, during STB infection, wheat also secretes small proteins into the apoplast to mediate the recognition of pathogen proteins and/or induce defense responses. To explore this, we developed an SSP-discovery pipeline to identify small, secreted proteins from wheat genomic data. Using this pipeline, we identified 6,998 SSPs, representing 2.3% of all proteins encoded by the wheat genome. We then mined a microarray dataset, detailing a resistant and susceptible host response to STB, and identified 141 Z. tritici- responsive SSPs, representing 4.7% of all proteins encoded by Z. tritici - responsive genes. We demonstrate that a subset of these SSPs have a functional signal peptide and can interact with Z. tritici SSPs. Transiently silencing two of these wheat SSPs using virus-induced gene silencing (VIGS) shows an increase in susceptibility to STB, confirming their role in defense against Z. tritici.
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Affiliation(s)
- Binbin Zhou
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Harriet R. Benbow
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Ciarán J. Brennan
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Chanemougasoundharam Arunachalam
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
| | - Sujit J. Karki
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Ewen Mullins
- Department of Crop Science, Teagasc, Carlow, Ireland
| | - Angela Feechan
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - James I. Burke
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Fiona M. Doohan
- UCD School of Biology and Environmental Science, UCD Earth Institute, UCD O’Brien Centre for Science (East), University College Dublin, Dublin, Ireland
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Carreón-Anguiano KG, Islas-Flores I, Vega-Arreguín J, Sáenz-Carbonell L, Canto-Canché B. EffHunter: A Tool for Prediction of Effector Protein Candidates in Fungal Proteomic Databases. Biomolecules 2020; 10:biom10050712. [PMID: 32375409 PMCID: PMC7277995 DOI: 10.3390/biom10050712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pathogens are able to deliver small-secreted, cysteine-rich proteins into plant cells to enable infection. The computational prediction of effector proteins remains one of the most challenging areas in the study of plant fungi interactions. At present, there are several bioinformatic programs that can help in the identification of these proteins; however, in most cases, these programs are managed independently. Here, we present EffHunter, an easy and fast bioinformatics tool for the identification of effectors. This predictor was used to identify putative effectors in 88 proteomes using characteristics such as size, cysteine residue content, secretion signal and transmembrane domains.
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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, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - 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, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Julio Vega-Arreguín
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores-UNAM, León, México
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
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Queiroz CBD, Santana MF. Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia 2020; 112:491-503. [PMID: 32286912 DOI: 10.1080/00275514.2020.1716566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Biologia Molecular, Embrapa Amazônia Ocidental , Rodovia AM 10, km 29, s/n, CEP: 69010-970, Manaus, Amazonas, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia (BIOAGRO), Universidade Federal de Viçosa , CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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15
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Denton‐Giles M, McCarthy H, Sehrish T, Dijkwel Y, Mesarich CH, Bradshaw RE, Cox MP, Dijkwel PP. Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae. MOLECULAR PLANT PATHOLOGY 2020; 21:512-526. [PMID: 32061186 PMCID: PMC7060139 DOI: 10.1111/mpp.12913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 05/02/2023]
Abstract
Fungal effector proteins facilitate host-plant colonization and have generally been characterized as small secreted proteins (SSPs). We classified and functionally tested SSPs from the secretomes of three closely related necrotrophic phytopathogens: Ciborinia camelliae, Botrytis cinerea, and Sclerotinia sclerotiorum. Alignment of predicted SSPs identified a large protein family that share greater than 41% amino acid identity and that have key characteristics of previously described microbe-associated molecular patterns (MAMPs). Strikingly, 73 of the 75 SSP family members were predicted within the secretome of the host-specialist C. camelliae with single-copy homologs identified in the secretomes of the host generalists S. sclerotiorum and B. cinerea. To explore the potential function of this family of SSPs, 10 of the 73 C. camelliae proteins, together with the single-copy homologs from S. sclerotiorum (SsSSP3) and B. cinerea (BcSSP2), were cloned and expressed as recombinant proteins. Infiltration of SsSSP3 and BcSSP2 into host tissue induced rapid necrosis. In contrast, only one of the 10 tested C. camelliae SSPs was able to induce a limited amount of necrosis. Analysis of chimeric proteins consisting of domains from both a necrosis-inducing and a non-necrosis-inducing SSP demonstrated that the C-terminus of the S. sclerotiorum SSP is essential for necrosis-inducing function. Deletion of the BcSSP2 homolog from B. cinerea did not affect growth or pathogenesis. Thus, this research uncovered a family of highly conserved SSPs present in diverse ascomycetes that exhibit contrasting necrosis-inducing functions.
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Affiliation(s)
- Matthew Denton‐Giles
- Centre for Crop and Disease ManagementCurtin UniversityPerthAustralia
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Hannah McCarthy
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Tina Sehrish
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Yasmin Dijkwel
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Carl H. Mesarich
- School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Rosie E. Bradshaw
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Murray P. Cox
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Paul P. Dijkwel
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
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16
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Challacombe JF, Hesse CN, Bramer LM, McCue LA, Lipton M, Purvine S, Nicora C, Gallegos-Graves LV, Porras-Alfaro A, Kuske CR. Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. BMC Genomics 2019; 20:976. [PMID: 31830917 PMCID: PMC6909477 DOI: 10.1186/s12864-019-6358-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 12/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized. RESULTS Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures. CONCLUSIONS This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.
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Affiliation(s)
- Jean F Challacombe
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Present address: Colorado State University, College of Agricultural Sciences, 301 University Ave, Fort Collins, CO, 80523, USA.
| | - Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Horticultural Crops Research, USDA ARS, Corvallis, OR, USA
| | - Lisa M Bramer
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Mary Lipton
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel Purvine
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie Nicora
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | | | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Haddad Momeni M, Bollella P, Ortiz R, Thormann E, Gorton L, Abou Hachem M. A novel starch-binding laccase from the wheat pathogen Zymoseptoria tritici highlights the functional diversity of ascomycete laccases. BMC Biotechnol 2019; 19:61. [PMID: 31426777 PMCID: PMC6700816 DOI: 10.1186/s12896-019-0552-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Laccases are multicopper oxidases, which are assigned into auxiliary activity family 1 (AA1) in the CAZy database. These enzymes, catalyzing the oxidation of phenolic and nonphenolic substrates coupled to reduction of O2 to H2O, are increasingly attractive as eco-friendly oxidation biocatalysts. Basidiomycota laccases are well characterized due to their potential in de-lignification of lignocellulose. By contrast, insight into the biochemical diversity of Ascomycota counterparts from saprophytes and plant pathogens is scarce. RESULTS Here, we report the properties of the laccase from the major wheat pathogen Zymoseptoria tritici (ZtrLac1A), distinguished from common plant fungal pathogens by an apoplastic infection strategy. We demonstrate that ZtrLac1A is appended to a functional starch-binding module and displays an activity signature disfavoring relatively apolar phenolic redox mediators as compared to the related biochemically characterized laccases. By contrast, the redox potential of ZtrLac1A (370 mV vs. SHE) is similar to ascomycetes counterparts. The atypical specificity is consistent with distinctive sequence substitutions and insertions in loops flanking the T1 site and the enzyme C-terminus compared to characterized laccases. CONCLUSIONS ZtrLac1A is the first reported modular laccase appended to a functional starch-specific carbohydrate binding module of family 20 (CBM20). The distinct specificity profile of ZtrLac1A correlates to structural differences in the active site region compared to previously described ascomycetes homologues. These differences are also highlighted by the clustering of the sequence of ZtrLac1A in a distinct clade populated predominantly by plant pathogens in the phylogenetic tree of AA1 laccases. The possible role of these laccases in vivo merits further investigations. These findings expand our toolbox of laccases for green oxidation and highlight the binding functionality of CBM-appended laccases as versatile immobilization tags.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
| | - Paolo Bollella
- Department of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
- Department of Chemistry and Drug Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Ortiz
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs, Lyngby, Denmark
| | - Esben Thormann
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs, Lyngby, Denmark
| | - Lo Gorton
- Department of Biochemistry and Structural Biology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
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Francisco CS, Ma X, Zwyssig MM, McDonald BA, Palma-Guerrero J. Morphological changes in response to environmental stresses in the fungal plant pathogen Zymoseptoria tritici. Sci Rep 2019; 9:9642. [PMID: 31270361 PMCID: PMC6610121 DOI: 10.1038/s41598-019-45994-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 06/20/2019] [Indexed: 01/15/2023] Open
Abstract
During their life cycles, pathogens have to adapt to many biotic and abiotic environmental stresses to maximize their overall fitness. Morphological transitions are one of the least understood of the many strategies employed by fungal plant pathogens to adapt to constantly changing environments, even though different morphotypes may play important biological roles. Here, we first show that blastospores (the "yeast-like" form of the pathogen typically known only under laboratory conditions) can form from germinated pycnidiospores (asexual spores) on the surface of wheat leaves, suggesting that this morphotype can play an important role in the natural history of Z. tritici. Next, we characterized the morphological responses of this fungus to a series of environmental stresses to understand the effects of changing environments on fungal morphology and adaptation. All tested stresses induced morphological changes, but different responses were found among four strains. We discovered that Z. tritici forms chlamydospores and demonstrated that these structures are better able to survive extreme cold, heat and drought than other cell types. Finally, a transcriptomic analysis showed that morphogenesis and the expression of virulence factors are co-regulated in this pathogen. Our findings illustrate how changing environmental conditions can affect cellular morphology and lead to the formation of new morphotypes, with each morphotype having a potential impact on both pathogen survival and disease epidemiology.
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Affiliation(s)
| | - Xin Ma
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Maria Manuela Zwyssig
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Javier Palma-Guerrero
- Plant Pathology Group, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
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19
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The repertoire of effector candidates in Colletotrichum lindemuthianum reveals important information about Colletotrichum genus lifestyle. Appl Microbiol Biotechnol 2019; 103:2295-2309. [DOI: 10.1007/s00253-019-09639-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/04/2023]
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20
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Ye X, Zhong Z, Liu H, Lin L, Guo M, Guo W, Wang Z, Zhang Q, Feng L, Lu G, Zhang F, Chen Q. Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus. BMC Genomics 2018; 19:358. [PMID: 29747580 PMCID: PMC5946483 DOI: 10.1186/s12864-018-4739-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/30/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Leaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabolites employed as defense-related phytoalexins. To unravel the fungal adaptive mechanisms to various phytoalexins, we examined the genome of C. pseudoreteaudii, which is one of the most aggressive pathogens in southeast Asia. RESULTS A 63.7 Mb genome with 14,355 coding genes of C. pseudoreteaudii were assembled. Genomic comparisons identified 1785 species-specific gene families in C. pseudoreteaudii. Most of them were not annotated and those annotated genes were enriched in peptidase activity, pathogenesis, oxidoreductase activity, etc. RNA-seq showed that 4425 genes were differentially expressed on the eucalyptus(the resistant cultivar E. grandis×E.camaldulensis M1) tissue induced medium. The annotation of GO term and KEGG pathway indicated that some of the differential expression genes were involved in detoxification and transportation, such as genes encoding ABC transporters, degrading enzymes of aromatic compounds and so on. CONCLUSIONS Potential genomic determinants of phytoalexin detoxification were identified in C. pseudoreteaudii by comparison with 13 other fungi. This pathogen seems to employ membrane transporters and degradation enzymes to detoxify Eucalyptus phytoalexins. Remarkably, the Calonectria genome possesses a surprising number of secondary metabolism backbone enzyme genes involving toxin biosynthesis. It is also especially suited for cutin and lignin degradation. This indicates that toxin and cell wall degrading enzymes may act important roles in the establishment of Calonectria leaf blight. This study provides further understanding on the mechanism of pathogenesis in Calonectria.
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Affiliation(s)
- Xiaozhen Ye
- 0000 0004 1760 2876grid.256111.0Jinshan College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhenhui Zhong
- 0000 0004 1760 2876grid.256111.0State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hongyi Liu
- 0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lianyu Lin
- 0000 0004 1760 2876grid.256111.0State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Mengmeng Guo
- 0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Wenshuo Guo
- 0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zonghua Wang
- 0000 0004 1760 2876grid.256111.0State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qinghua Zhang
- 0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lizhen Feng
- 0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Guodong Lu
- 0000 0004 1760 2876grid.256111.0State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feiping Zhang
- 0000 0004 1760 2876grid.256111.0Forestry College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Quanzhu Chen
- 0000 0004 1760 2876grid.256111.0Jinshan College, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Hartmann FE, Croll D. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen. Mol Biol Evol 2018; 34:2808-2822. [PMID: 28981698 PMCID: PMC5850472 DOI: 10.1093/molbev/msx208] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence–absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence–absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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22
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McGrann GRD, Brown JKM. The role of reactive oxygen in the development of Ramularia leaf spot disease in barley seedlings. ANNALS OF BOTANY 2018; 121:415-430. [PMID: 29309539 PMCID: PMC5838821 DOI: 10.1093/aob/mcx170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 11/07/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Ramularia collo-cygni is an ascomycete fungus that colonizes barley primarily as a benign endophyte, although this interaction can become pathogenic, causing the disease Ramularia leaf spot (RLS). Factors, particularly reactive oxygen species, that resulted in the transition of the fungus from endophyte to necrotrophic parasite and the development of disease symptoms were investigated. METHODS Disease development in artificially inoculated seedlings of barley varieties varying in partial resistance to RLS was related to exposure to abiotic stress prior to inoculation. Histochemical and molecular analysis determined the effect of R. collo-cygni colonization on accumulation of reactive oxygen species and antioxidant gene expression. Development of RLS on barley lines defective in antioxidant enzymes and with altered redox status or non-functional chloroplasts was compared with the accumulation of fungal biomass to determine how these factors affect disease symptom expression. KEY RESULTS Exposure to abiotic stress increased symptom development in all susceptible and most partially resistant barley varieties, in association with greater hydrogen peroxide (H2O2) levels in leaves. Decreased activity of the antioxidant enzymes superoxide dismutase and catalase in transgenic and mutant plants had no effect on the disease transition, whereas manipulation of H2O2 levels during asymptomatic growth of the fungus increased disease symptoms in most susceptible varieties but not in partially resistant plants. Barley mutants that undergo rapid loss of green leaf area when infected by R. collo-cygni or albino mutants with non-functional chloroplasts showed reduced development of RLS symptoms. CONCLUSIONS These results imply that in seedlings the pathogenic transition of the normally endophytic fungus R. collo-cygni does not result from senescence as such, but rather is promoted by factors that result in changes to host reactive oxygen species. Barley varieties vary in the extent to which these factors promote RLS disease.
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24
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Krishnan P, Ma X, McDonald BA, Brunner PC. Widespread signatures of selection for secreted peptidases in a fungal plant pathogen. BMC Evol Biol 2018; 18:7. [PMID: 29368587 PMCID: PMC5784588 DOI: 10.1186/s12862-018-1123-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal plant pathogens secrete a large arsenal of hydrolytic enzymes during the course of infection, including peptidases. Secreted peptidases have been extensively studied for their role as effectors. In this study, we combined transcriptomics, comparative genomics and evolutionary analyses to investigate all 39 secreted peptidases in the fungal wheat pathogen Zymoseptoria tritici and its close relatives Z. pseudotritici and Z. ardabiliae. RESULTS RNA-seq data revealed that a majority of the secreted peptidases displayed differential transcription during the course of Z. tritici infection, indicative of specialization for different stages in the life cycle. Evolutionary analyses detected widespread evidence of adaptive evolution acting on at least 28 of the peptidases. A few peptidases displayed lineage-specific rates of molecular evolution, suggesting altered selection pressure in Z. tritici following host specialization on domesticated wheat. The peptidases belonging to MEROPS families A1 and G1 emerged as a particularly interesting group that may play key roles in host-pathogen co-evolution, host adaptation and pathogenicity. Sister genes in the A1 and G1 families showed accelerated substitution rates after gene duplications. CONCLUSIONS These results suggest widespread evolution of secreted peptidases leading to novel gene functions, consistent with predicted models of "escape from adaptive conflict" and "neo-functionalization". Our analyses identified candidate genes worthy of functional analyses that may encode effector functions, for example by suppressing plant defenses during the biotrophic phase of infection.
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Affiliation(s)
- Parvathy Krishnan
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Patrick C Brunner
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland.
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25
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Hartmann FE, Sánchez-Vallet A, McDonald BA, Croll D. A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. THE ISME JOURNAL 2017; 11:1189-1204. [PMID: 28117833 PMCID: PMC5437930 DOI: 10.1038/ismej.2016.196] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/10/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022]
Abstract
Fungal pathogens can rapidly evolve virulence towards resistant crops in agricultural ecosystems. Gains in virulence are often mediated by the mutation or deletion of a gene encoding a protein recognized by the plant immune system. However, the loci and the mechanisms of genome evolution enabling rapid virulence evolution are poorly understood. We performed genome-wide association mapping on a global collection of 106 strains of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe, to identify polymorphisms linked to virulence on two wheat varieties. We found 25 distinct genomic loci associated with reproductive success of the pathogen. However, no locus was shared between the host genotypes, suggesting host specialization. The main locus associated with virulence encoded a highly expressed, small secreted protein. Population genomic analyses showed that the gain in virulence was explained by a segregating gene deletion polymorphism. The deletion was likely adaptive by preventing detection of the encoded protein. Comparative genomics of closely related species showed that the locus emerged de novo since speciation. A large cluster of transposable elements in direct proximity to the locus generated extensive rearrangements leading to multiple independent gene losses. Our study demonstrates that rapid turnover in the chromosomal structure of a pathogen can drive host specialization.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
| | | | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
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Dagvadorj B, Ozketen AC, Andac A, Duggan C, Bozkurt TO, Akkaya MS. A Puccinia striiformis f. sp. tritici secreted protein activates plant immunity at the cell surface. Sci Rep 2017; 7:1141. [PMID: 28442716 PMCID: PMC5430700 DOI: 10.1038/s41598-017-01100-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/24/2017] [Indexed: 01/02/2023] Open
Abstract
Pathogens secrete effector proteins to suppress host immunity, mediate nutrient uptake and subsequently enable parasitism. However, on non-adapted hosts, effectors can be detected as non-self by host immune receptors and activate non-host immunity. Nevertheless, the molecular mechanisms of effector triggered non-host resistance remain unknown. Here, we report that a small cysteine-rich protein PstSCR1 from the wheat rust pathogen Puccinia striiformis f. sp. tritici (Pst) activates immunity in the non-host solanaceous model plant Nicotiana benthamiana. PstSCR1 homologs were found to be conserved in Pst, and in its closest relatives, Puccinia graminis f. sp. tritici and Puccinia triticina. When PstSCR1 was expressed in N. benthamiana with its signal peptide, it provoked the plant immune system, whereas no stimulation was observed when it was expressed without its signal peptide. PstSCR1 expression in N. benthamiana significantly reduced infection capacity of the oomycete pathogens. Moreover, apoplast-targeted PstSCR1 triggered plant cell death in a dose dependent manner. However, in Brassinosteroid insensitive 1-Associated Kinase 1 (SERK3/BAK1) silenced N. benthamiana, cell death was remarkably decreased. Finally, purified PstSCR1 protein activated defence related gene expression in N. benthamiana. Our results show that a Pst-secreted protein, PstSCR1 can activate surface mediated immunity in non-adapted hosts and contribute to non-host resistance.
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Affiliation(s)
- Bayantes Dagvadorj
- Middle East Technical University, Biotechnology Program, Department of Chemistry, Dumlupinar Blvd., Cankaya, Ankara, TR-06800, Turkey
| | - Ahmet Caglar Ozketen
- Middle East Technical University, Biotechnology Program, Department of Chemistry, Dumlupinar Blvd., Cankaya, Ankara, TR-06800, Turkey
| | - Ayse Andac
- Middle East Technical University, Biotechnology Program, Department of Chemistry, Dumlupinar Blvd., Cankaya, Ankara, TR-06800, Turkey
| | - Cian Duggan
- Imperial College London, Department of Life Sciences, London, SW7 2AZ, UK
| | | | - Mahinur S Akkaya
- Middle East Technical University, Biotechnology Program, Department of Chemistry, Dumlupinar Blvd., Cankaya, Ankara, TR-06800, Turkey.
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Palma-Guerrero J, Ma X, Torriani SFF, Zala M, Francisco CS, Hartmann FE, Croll D, McDonald BA. Comparative Transcriptome Analyses in Zymoseptoria tritici Reveal Significant Differences in Gene Expression Among Strains During Plant Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:231-244. [PMID: 28121239 DOI: 10.1094/mpmi-07-16-0146-r] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Zymoseptoria tritici is an ascomycete fungus that causes Septoria tritici blotch, a globally distributed foliar disease on wheat. Z. tritici populations are highly polymorphic and exhibit significant quantitative variation for virulence. Despite its importance, the genes responsible for quantitative virulence in this pathogen remain largely unknown. We investigated the expression profiles of four Z. tritici strains differing in virulence in an experiment conducted under uniform environmental conditions. Transcriptomes were compared at four different infection stages to characterize the regulation of gene families thought to be involved in virulence and to identify new virulence factors. The major components of the fungal infection transcriptome showed consistent expression profiles across strains. However, strain-specific regulation was observed for many genes, including some encoding putative virulence factors. We postulate that strain-specific regulation of virulence factors can determine the outcome of Z. tritici infections. We show that differences in gene expression may be major determinants of virulence variation among Z. tritici strains, adding to the already known contributions to virulence variation based on differences in gene sequence and gene presence/absence polymorphisms.
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Affiliation(s)
- Javier Palma-Guerrero
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Xin Ma
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Stefano F F Torriani
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
- 2 Syngenta Crop Protection AG, Schaffhauserstrasse, 4332 Stein, Switzerland
| | - Marcello Zala
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Carolina S Francisco
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Fanny E Hartmann
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Daniel Croll
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Bruce A McDonald
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
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Derbyshire M, Denton-Giles M, Hegedus D, Seifbarghy S, Rollins J, van Kan J, Seidl MF, Faino L, Mbengue M, Navaud O, Raffaele S, Hammond-Kosack K, Heard S, Oliver R. The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol 2017; 9:593-618. [PMID: 28204478 PMCID: PMC5381539 DOI: 10.1093/gbe/evx030] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/16/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.
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Affiliation(s)
- Mark Derbyshire
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
| | - Dwayne Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | | | - Jeffrey Rollins
- Department of Plant Pathology, University of Florida, Gainesville, FL
| | - Jan van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Malick Mbengue
- LIPM Université de Toulouse INRA CNRS, Castanet-Tolosan, France
| | - Olivier Navaud
- LIPM Université de Toulouse INRA CNRS, Castanet-Tolosan, France
| | | | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Stephanie Heard
- Department of Plant Pathology, University of Florida, Gainesville, FL
- Department of Plant Biology and Crop Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Richard Oliver
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
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Kettles GJ, Bayon C, Canning G, Rudd JJ, Kanyuka K. Apoplastic recognition of multiple candidate effectors from the wheat pathogen Zymoseptoria tritici in the nonhost plant Nicotiana benthamiana. THE NEW PHYTOLOGIST 2017; 213:338-350. [PMID: 27696417 PMCID: PMC5132004 DOI: 10.1111/nph.14215] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 08/19/2016] [Indexed: 05/18/2023]
Abstract
The fungus Zymoseptoria tritici is a strictly apoplastic, host-specific pathogen of wheat leaves and causal agent of septoria tritici blotch (STB) disease. All other plants are considered nonhosts, but the mechanism of nonhost resistance (NHR) to Z. tritici has not been addressed previously. We sought to develop Nicotiana benthamiana as a system to study NHR against Z. tritici. Fluorescence microscopy and quantitative reverse transcription polymerase chain reactions were used to establish the interaction between Z. tritici and N. benthamiana. Agrobacterium-mediated transient expression was used to screen putative Z. tritici effector genes for recognition in N. benthamiana, and virus-induced gene silencing (VIGS) was employed to determine the role of two receptor-like kinases (RLKs), NbBAK1 and NbSOBIR1, in Z. tritici effector recognition. Numerous Z. tritici putative effectors (14 of 63 tested) induced cell death or chlorosis in N. benthamiana. For most, phenotypes were light-dependent and required effector secretion to the leaf apoplastic space. Moreover, effector-induced host cell death was dependent on NbBAK1 and NbSOBIR1. Our results indicate widespread recognition of apoplastic effectors from a wheat-infecting fungal pathogen in a taxonomically distant nonhost plant species presumably by cell surface immune receptors. This suggests that apoplastic recognition of multiple nonadapted pathogen effectors may contribute to NHR.
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Affiliation(s)
- Graeme J. Kettles
- Department of Plant Biology & Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Carlos Bayon
- Department of Plant Biology & Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Gail Canning
- Department of Plant Biology & Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Jason J. Rudd
- Department of Plant Biology & Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
| | - Kostya Kanyuka
- Department of Plant Biology & Crop ScienceRothamsted ResearchHarpendenHertfordshireAL5 2JQUK
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30
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Zhan F, Xie Y, Zhu W, Sun D, McDonald BA, Zhan J. Linear Correlation Analysis of Zymoseptoria tritici Aggressiveness with In Vitro Growth Rate. PHYTOPATHOLOGY® 2016; 106:1255-1261. [PMID: 27348342 DOI: 10.1094/phyto-12-15-0338-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Zymoseptoria tritici is a globally distributed plant-pathogenic fungus causing Septoria tritici blotch of wheat. In this study, the in vitro growth rates and aggressiveness of 141 genetically distinct isolates sampled from four wheat fields on three continents were assessed to determine the association of these two ecological parameters. Aggressiveness was assessed on two spring wheat cultivars (‘Toronit’ and ‘Greina’) in a greenhouse using percentages of leaf area covered by lesions and pycnidia. We found a positive correlation between aggressiveness of pathogen strains on the two cultivars, consistent with a quantitative and host-nonspecific interaction in this pathosystem. We also found a positive correlation between aggressiveness and average growth rate at two temperatures, suggesting that in vitro pathogen growth rate may make a significant contribution to pathogen aggressiveness.
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Affiliation(s)
- Fangfang Zhan
- First, second, third, and fourth authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; fifth author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; and sixth author: Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou
| | - Yiekun Xie
- First, second, third, and fourth authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; fifth author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; and sixth author: Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou
| | - Wen Zhu
- First, second, third, and fourth authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; fifth author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; and sixth author: Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou
| | - Danli Sun
- First, second, third, and fourth authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; fifth author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; and sixth author: Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou
| | - Bruce A. McDonald
- First, second, third, and fourth authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; fifth author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; and sixth author: Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou
| | - Jiasui Zhan
- First, second, third, and fourth authors: Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; fifth author: Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, LFW, Zurich, CH-8092, Switzerland; and sixth author: Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou
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Gehrmann T, Pelkmans JF, Lugones LG, Wösten HAB, Abeel T, Reinders MJT. Schizophyllum commune has an extensive and functional alternative splicing repertoire. Sci Rep 2016; 6:33640. [PMID: 27659065 PMCID: PMC5034255 DOI: 10.1038/srep33640] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/31/2016] [Indexed: 01/01/2023] Open
Abstract
Recent genome-wide studies have demonstrated that fungi possess the machinery to alternatively splice pre-mRNA. However, there has not been a systematic categorization of the functional impact of alternative splicing in a fungus. We investigate alternative splicing and its functional consequences in the model mushroom forming fungus Schizophyllum commune. Alternative splicing was demonstrated for 2,285 out of 12,988 expressed genes, resulting in 20% additional transcripts. Intron retentions were the most common alternative splicing events, accounting for 33% of all splicing events, and 43% of the events in coding regions. On the other hand, exon skipping events were rare in coding regions (1%) but enriched in UTRs where they accounted for 57% of the events. Specific functional groups, including transcription factors, contained alternatively spliced genes. Alternatively spliced transcripts were regulated differently throughout development in 19% of the 2,285 alternatively spliced genes. Notably, 69% of alternatively spliced genes have predicted alternative functionality by loss or gain of functional domains, or by acquiring alternative subcellular locations. S. commune exhibits more alternative splicing than any other studied fungus. Taken together, alternative splicing increases the complexity of the S. commune proteome considerably and provides it with a rich repertoire of alternative functionality that is exploited dynamically.
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Affiliation(s)
- Thies Gehrmann
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Zuid-Holland 2628 CD, The Netherlands
| | - Jordi F. Pelkmans
- Microbiology, Department of Biology, Utrecht University, Utrecht, Utrecht 3585 CH, The Netherlands
| | - Luis G. Lugones
- Microbiology, Department of Biology, Utrecht University, Utrecht, Utrecht 3585 CH, The Netherlands
| | - Han A. B. Wösten
- Microbiology, Department of Biology, Utrecht University, Utrecht, Utrecht 3585 CH, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Zuid-Holland 2628 CD, The Netherlands
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts MA02142, United States of America
| | - Marcel J. T. Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, Zuid-Holland 2628 CD, The Netherlands
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Ismail IA, Able AJ. Secretome analysis of virulent Pyrenophora teres f. teres isolates. Proteomics 2016; 16:2625-2636. [PMID: 27402336 DOI: 10.1002/pmic.201500498] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 06/24/2016] [Accepted: 07/07/2016] [Indexed: 11/11/2022]
Abstract
Pyrenophora teres f. teres (Ptt) causes net form net blotch disease of barley, partially by producing necrosis-inducing proteins. The protein profiles of the culture filtrates of 28 virulent isolates were compared by a combination of 2DE and 1D-PAGE with 105 spots and 51 bands chosen for analysis by liquid chromatography electrospray ionization tandem mass spectrometry. A total of 259 individual proteins were identified with 63 of these proteins being common to the selected virulent isolates. Ptt secretes a broad spectrum of proteins including cell wall degrading enzymes; virulence factors and effectors; proteins associated with fungal pathogenesis and development; and proteins related to oxidation-reduction processes. Potential virulence factors and effectors identified included proteins with glucosidase activity, ricin B and concanavalin A-like lectins, glucanases, spherulin, cutinase, pectin lyase, leucine-rich repeat protein, and ceratoplatanin. Small proteins with unknown function but cysteine-rich, common to effectors, were also identified. Differences in the secretion profile of the Ptt isolates have also provided important insight into the different mechanisms contributing to virulence and the development of net form net blotch symptoms.
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Affiliation(s)
- Ismail A Ismail
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, Australia
| | - Amanda J Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, Australia.
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Paolinelli-Alfonso M, Villalobos-Escobedo JM, Rolshausen P, Herrera-Estrella A, Galindo-Sánchez C, López-Hernández JF, Hernandez-Martinez R. Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response. BMC Genomics 2016; 17:615. [PMID: 27514986 PMCID: PMC4981995 DOI: 10.1186/s12864-016-2952-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/19/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lasiodiplodia theobromae is a fungus of the Botryosphaeriaceae that causes grapevine vascular disease, especially in regions with hot climates. Fungi in this group often remain latent within their host and become virulent under abiotic stress. Transcriptional regulation analysis of L. theobromae exposed to heat stress (HS) was first carried out in vitro in the presence of grapevine wood (GW) to identify potential pathogenicity genes that were later evaluated for in planta expression. RESULTS A total of 19,860 de novo assembled transcripts were obtained, forty-nine per cent of which showed homology to the Botryosphaeriaceae fungi, Neofusicoccum parvum or Macrophomina phaseolina. Three hundred ninety-nine have homology with genes involved in pathogenic processes and several belonged to expanded gene families in others fungal grapevine vascular pathogens. Gene expression analysis showed changes in fungal metabolism of phenolic compounds; where genes encoding for enzymes, with the ability to degrade salicylic acid (SA) and plant phenylpropanoid precursors, were up-regulated during in vitro HS response, in the presence of GW. These results suggest that the fungal L-tyrosine catabolism pathway could help the fungus to remove phenylpropanoid precursors thereby evading the host defense response. The in planta up-regulation of salicylate hydroxylase, intradiol ring cleavage dioxygenase and fumarylacetoacetase encoding genes, further supported this hypothesis. Those genes were even more up-regulated in HS-stressed plants, suggesting that fungus takes advantage of the increased phenylpropanoid precursors produced under stress. Pectate lyase was up-regulated while a putative amylase was down-regulated in planta, this could be associated with an intercellular growth strategy during the first stages of colonization. CONCLUSIONS L. theobromae transcriptome was established and validated. Its usefulness was demonstrated through the identification of genes expressed during the infection process. Our results support the hypothesis that heat stress facilitates fungal colonization, because of the fungus ability to use the phenylpropanoid precursors and SA, both compounds known to control host defense.
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Affiliation(s)
- Marcos Paolinelli-Alfonso
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, BC 22860 Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del I. P. N., Irapuato, Gto 36821 Mexico
| | - Philippe Rolshausen
- Department of Botany and Plant Sciences,University of California Riverside, Riverside, 92521 CA USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del I. P. N., Irapuato, Gto 36821 Mexico
| | - Clara Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, BC 22860 Mexico
| | - José Fabricio López-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del I. P. N., Irapuato, Gto 36821 Mexico
| | - Rufina Hernandez-Martinez
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, BC 22860 Mexico
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The genome of the emerging barley pathogen Ramularia collo-cygni. BMC Genomics 2016; 17:584. [PMID: 27506390 PMCID: PMC4979122 DOI: 10.1186/s12864-016-2928-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 07/12/2016] [Indexed: 12/24/2022] Open
Abstract
Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2928-3) contains supplementary material, which is available to authorized users.
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Palma-Guerrero J, Torriani SFF, Zala M, Carter D, Courbot M, Rudd JJ, McDonald BA, Croll D. Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles. MOLECULAR PLANT PATHOLOGY 2016; 17:845-59. [PMID: 26610174 PMCID: PMC6638511 DOI: 10.1111/mpp.12333] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 05/03/2023]
Abstract
Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. The disease interaction is characterized by clearly defined temporal phases of infection, ultimately resulting in the death of host tissue. Zymoseptoria tritici is a highly polymorphic species with significant intraspecific variation in virulence profiles. We generated a deep transcriptomic sequencing dataset spanning the entire time course of an infection using a previously uncharacterized, highly virulent Z. tritici strain isolated from a Swiss wheat field. We found that seven clusters of gene transcription profiles explained the progression of the infection. The earliest highly up-regulated genes included chloroperoxidases, which may help the fungus cope with plant defences. The onset of necrotrophy was characterized by a concerted up-regulation of proteases, plant cell wall-degrading enzymes and lipases. Functions related to nutrition and growth characterized late necrotrophy and the transition to saprotrophic growth on dead plant tissue. We found that the peak up-regulation of genes essential for mating coincided with the necrotrophic phase. We performed an intraspecies comparative transcriptomics analysis using a comparable time course infection experiment of the genome reference isolate IPO323. Major components of the fungal infection transcriptome were conserved between the two strains. However, individual small, secreted proteins, proteases and cell wall-degrading enzymes showed strongly differentiated transcriptional profiles between isolates. Our analyses illustrate that successful STB infections involve complex transcriptomic remodelling to up-regulate distinct gene functions. Heterogeneity in transcriptomes among isolates may explain some of the considerable variation in virulence and host specialization found within the species.
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Affiliation(s)
- Javier Palma-Guerrero
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Stefano F F Torriani
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
- Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, Switzerland
| | - Marcello Zala
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Dee Carter
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Mikaël Courbot
- Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, Switzerland
| | - Jason J Rudd
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
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Structure of a Berberine Bridge Enzyme-Like Enzyme with an Active Site Specific to the Plant Family Brassicaceae. PLoS One 2016; 11:e0156892. [PMID: 27276217 PMCID: PMC4898691 DOI: 10.1371/journal.pone.0156892] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/21/2016] [Indexed: 01/15/2023] Open
Abstract
Berberine bridge enzyme-like (BBE-like) proteins form a multigene family (pfam 08031), which is present in plants, fungi and bacteria. They adopt the vanillyl alcohol-oxidase fold and predominantly show bi-covalent tethering of the FAD cofactor to a cysteine and histidine residue, respectively. The Arabidopsis thaliana genome was recently shown to contain genes coding for 28 BBE-like proteins, while featuring four distinct active site compositions. We determined the structure of a member of the AtBBE-like protein family (termed AtBBE-like 28), which has an active site composition that has not been structurally and biochemically characterized thus far. The most salient and distinguishing features of the active site found in AtBBE-like 28 are a mono-covalent linkage of a histidine to the 8α-position of the flavin-isoalloxazine ring and the lack of a second covalent linkage to the 6-position, owing to the replacement of a cysteine with a histidine. In addition, the structure reveals the interaction of a glutamic acid (Glu426) with an aspartic acid (Asp369) at the active site, which appear to share a proton. This arrangement leads to the delocalization of a negative charge at the active site that may be exploited for catalysis. The structure also indicates a shift of the position of the isoalloxazine ring in comparison to other members of the BBE-like family. The dioxygen surrogate chloride was found near the C(4a) position of the isoalloxazine ring in the oxygen pocket, pointing to a rapid reoxidation of reduced enzyme by dioxygen. A T-DNA insertional mutant line for AtBBE-like 28 results in a phenotype, that is characterized by reduced biomass and lower salt stress tolerance. Multiple sequence analysis showed that the active site composition found in AtBBE-like 28 is only present in the Brassicaceae, suggesting that it plays a specific role in the metabolism of this plant family.
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Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici. G3-GENES GENOMES GENETICS 2016; 6:779-91. [PMID: 26837952 PMCID: PMC4825649 DOI: 10.1534/g3.115.025197] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts 2 wks, and is followed by extensive host cell death, and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates, for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ∼10% had an effect on the coding regions of the genome. Furthermore, we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method, we have identified < 100 candidate effector genes whose gene sequence correlates with virulence toward a wheat cultivar carrying a major resistance gene.
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Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici. Fungal Genet Biol 2016; 79:71-5. [PMID: 26092791 DOI: 10.1016/j.fgb.2015.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 01/06/2023]
Abstract
The wheat pathogen Zymoseptoria tritici possesses a large number of accessory chromosomes that may be present or absent in its genome. The genome of the reference isolate IPO323 has been assembled to a very high standard and contains 21 full length chromosome sequences, 8 of which represent accessory chromosomes. The IPO323 reference, when combined with low-cost next-generation sequencing and bioinformatics, can be used as a powerful tool to assess the presence or absence of accessory chromosomes. We present an outline of a range of bioinformatics techniques that can be applied to the analysis of presence-absence variation among accessory chromosomes across 13 novel isolates of Z. tritici.
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Cell biology of Zymoseptoria tritici: Pathogen cell organization and wheat infection. Fungal Genet Biol 2016; 79:17-23. [PMID: 26092785 PMCID: PMC4502449 DOI: 10.1016/j.fgb.2015.04.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/27/2015] [Accepted: 04/02/2015] [Indexed: 01/26/2023]
Abstract
Cell biology of the infection begins to shed light on the host–pathogen interaction. The cell biology of the fungal pathogen is highly understudied. Intensified cell biology research promises new fungicide targets and will help mode-of-action studies.
Cell biological research in the wheat pathogen Zymoseptoria tritici (formerly Mycosphaerella graminicola) has led to a good understanding of the histology of the infection process. Expression profiling and bioinformatic approaches, combined with molecular studies on signaling pathways, effectors and potential necrosis factors provides first insight into the complex interplay between the host and the pathogen. Cell biological studies will help to further our understanding of the infection strategy of the fungus. The cellular organization and intracellular dynamics of the fungus itself is largely unexplored. Insight into essential cellular processes within the pathogen will expand our knowledge of the basic biology of Z. tritici, thereby providing putative new anti-fungal targets.
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Testa A, Oliver R, Hane J. Overview of genomic and bioinformatic resources for Zymoseptoria tritici. Fungal Genet Biol 2016; 79:13-6. [PMID: 26092784 DOI: 10.1016/j.fgb.2015.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 11/17/2022]
Abstract
Zymoseptoria tritici (syn. Mycosphaerella graminicola, Septoria tritici) is a haploid fungus belonging to the class Dothideomycetes. It is the causal agent of septoria leaf blotch - one of the world's most significant diseases of wheat. Here we review the genomic and bioinformatic resources that have been generated for Z. tritici. These include the whole-genome reference assembly for isolate IPO323, genome resequencing of alternate isolates, mitochondrial genome sequences, transcriptome sequences and expression data, and annotations of gene structure and function. We also highlight important advances in our fundamental knowledge of genome evolution and its effects on adaptation and pathogenicity in Z. tritici that have been facilitated by these resources.
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Affiliation(s)
- Alison Testa
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
| | - Richard Oliver
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia
| | - James Hane
- Centre for Crop and Disease Management, Curtin University, Perth, WA, Australia; Curtin Institute for Computation, Curtin University, Perth, WA, Australia.
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41
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Kettles GJ, Kanyuka K. Dissecting the Molecular Interactions between Wheat and the Fungal Pathogen Zymoseptoria tritici. FRONTIERS IN PLANT SCIENCE 2016; 7:508. [PMID: 27148331 PMCID: PMC4832604 DOI: 10.3389/fpls.2016.00508] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/30/2016] [Indexed: 05/10/2023]
Abstract
The Dothideomycete fungus Zymoseptoria tritici (previously known as Mycosphaerella graminicola and Septoria tritici) is the causative agent of Septoria tritici leaf blotch (STB) disease of wheat (Triticum aestivum L.). In Europe, STB is the most economically damaging disease of wheat, with an estimated ∼€1 billion per year in fungicide expenditure directed toward its control. Here, an overview of our current understanding of the molecular events that occur during Z. tritici infection of wheat leaves is presented. On the host side, this includes the contribution of (1) the pathogen-associated molecular pattern-triggered immunity (PTI) layer of plant defense, and (2) major Stb loci for resistance against Z. tritici. On the pathogen side of the interaction, we consolidate evidence from recent bioinformatic, transcriptomic and proteomic studies that begin to explain the contribution of Z. tritici effector proteins to the biphasic lifestyle of the fungus. This includes the discovery of chitin-binding proteins in the Z. tritici secretome, which contribute to evasion of immune surveillance by this pathogen, and the possible existence of 'necrotrophic' effectors from Z. tritici, which may actively stimulate host recognition in a manner similar to related necrotrophic fungal pathogens. We finish by speculating on how some of these recent fundamental discoveries might be harnessed to help improve resistance to STB in the world's second largest food crop.
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Mirzadi Gohari A, Ware SB, Wittenberg AHJ, Mehrabi R, Ben M'Barek S, Verstappen ECP, van der Lee TAJ, Robert O, Schouten HJ, de Wit PPJGM, Kema GHJ. Effector discovery in the fungal wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2015; 16:931-45. [PMID: 25727413 PMCID: PMC6638447 DOI: 10.1111/mpp.12251] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Fungal plant pathogens, such as Zymoseptoria tritici (formerly known as Mycosphaerella graminicola), secrete repertoires of effectors to facilitate infection or trigger host defence mechanisms. The discovery and functional characterization of effectors provides valuable knowledge that can contribute to the design of new and effective disease management strategies. Here, we combined bioinformatics approaches with expression profiling during pathogenesis to identify candidate effectors of Z. tritici. In addition, a genetic approach was conducted to map quantitative trait loci (QTLs) carrying putative effectors, enabling the validation of both complementary strategies for effector discovery. In planta expression profiling revealed that candidate effectors were up-regulated in successive waves corresponding to consecutive stages of pathogenesis, contrary to candidates identified by QTL mapping that were, overall, expressed at low levels. Functional analyses of two top candidate effectors (SSP15 and SSP18) showed their dispensability for Z. tritici pathogenesis. These analyses reveal that generally adopted criteria, such as protein size, cysteine residues and expression during pathogenesis, may preclude an unbiased effector discovery. Indeed, genetic mapping of genomic regions involved in specificity render alternative effector candidates that do not match the aforementioned criteria, but should nevertheless be considered as promising new leads for effectors that are crucial for the Z. tritici-wheat pathosystem.
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Affiliation(s)
- Amir Mirzadi Gohari
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Department of Plant Protection, College of Agriculture, University of Tehran, Plant Pathology Building, Karaj, Iran
| | - Sarah B Ware
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Alexander H J Wittenberg
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Rahim Mehrabi
- Cereal Research Department, Seed and Plant Improvement Institute, PO Box 31585-4119, Karaj, Iran
| | - Sarrah Ben M'Barek
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif, 2050, Tunisia
| | - Els C P Verstappen
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Theo A J van der Lee
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Olivier Robert
- Bioplante, Florimond Desprez, BP41, 59242, Cappelle-en-Pévèle, France
| | - Henk J Schouten
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Pierre P J G M de Wit
- Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Gert H J Kema
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
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The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen. Genetics 2015; 201:1213-28. [PMID: 26392286 DOI: 10.1534/genetics.115.180968] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/17/2015] [Indexed: 12/30/2022] Open
Abstract
Recombination has an impact on genome evolution by maintaining chromosomal integrity, affecting the efficacy of selection, and increasing genetic variability in populations. Recombination rates are a key determinant of the coevolutionary dynamics between hosts and their pathogens. Historic recombination events created devastating new pathogens, but the impact of ongoing recombination in sexual pathogens is poorly understood. Many fungal pathogens of plants undergo regular sexual cycles, and sex is considered to be a major factor contributing to virulence. We generated a recombination map at kilobase-scale resolution for the haploid plant pathogenic fungus Zymoseptoria tritici. To account for intraspecific variation in recombination rates, we constructed genetic maps from two independent crosses. We localized a total of 10,287 crossover events in 441 progeny and found that recombination rates were highly heterogeneous within and among chromosomes. Recombination rates on large chromosomes were inversely correlated with chromosome length. Short accessory chromosomes often lacked evidence for crossovers between parental chromosomes. Recombination was concentrated in narrow hotspots that were preferentially located close to telomeres. Hotspots were only partially conserved between the two crosses, suggesting that hotspots are short-lived and may vary according to genomic background. Genes located in hotspot regions were enriched in genes encoding secreted proteins. Population resequencing showed that chromosomal regions with high recombination rates were strongly correlated with regions of low linkage disequilibrium. Hence, genes in pathogen recombination hotspots are likely to evolve faster in natural populations and may represent a greater threat to the host.
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Derbyshire MC, Michaelson L, Parker J, Kelly S, Thacker U, Powers SJ, Bailey A, Hammond-Kosack K, Courbot M, Rudd J. Analysis of cytochrome b(5) reductase-mediated metabolism in the phytopathogenic fungus Zymoseptoria tritici reveals novel functionalities implicated in virulence. Fungal Genet Biol 2015; 82:69-84. [PMID: 26074495 PMCID: PMC4557397 DOI: 10.1016/j.fgb.2015.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/15/2022]
Abstract
Septoria tritici blotch (STB) caused by the Ascomycete fungus Zymoseptoria tritici is one of the most economically damaging diseases of wheat worldwide. Z. tritici is currently a major target for agricultural fungicides, especially in temperate regions where it is most prevalent. Many fungicides target electron transfer enzymes because these are often important for cell function. Therefore characterisation of genes encoding such enzymes may be important for the development of novel disease intervention strategies. Microsomal cytochrome b5 reductases (CBRs) are an important family of electron transfer proteins which in eukaryotes are involved in the biosynthesis of fatty acids and complex lipids including sphingolipids and sterols. Unlike the model yeast Saccharomyces cerevisiae which possesses only one microsomal CBR, the fully sequenced genome of Z. tritici bears three possible microsomal CBRs. RNA sequencing analysis revealed that ZtCBR1 is the most highly expressed of these genes under all in vitro and in planta conditions tested, therefore ΔZtCBR1 mutant strains were generated through targeted gene disruption. These strains exhibited delayed disease symptoms on wheat leaves and severely limited asexual sporulation. ΔZtCBR1 strains also exhibited aberrant spore morphology and hyphal growth in vitro. These defects coincided with alterations in fatty acid, sphingolipid and sterol biosynthesis observed through GC-MS and HPLC analyses. Data is presented which suggests that Z. tritici may use ZtCBR1 as an additional electron donor for key steps in ergosterol biosynthesis, one of which is targeted by azole fungicides. Our study reports the first functional characterisation of CBR gene family members in a plant pathogenic filamentous fungus. This also represents the first direct observation of CBR functional ablation impacting upon fungal sterol biosynthesis.
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Affiliation(s)
- Mark C Derbyshire
- Department of Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.
| | - Louise Michaelson
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Josie Parker
- Centre for Cytochrome P450 Diversity, Institute of Life Science, College of Medicine, Swansea University Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Steven Kelly
- Centre for Cytochrome P450 Diversity, Institute of Life Science, College of Medicine, Swansea University Singleton Park, Swansea SA2 8PP, Wales, UK
| | | | - Stephen J Powers
- Department of Computational and Systems Biology, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Andy Bailey
- Bristol University, Senate House, Tyndall Avenue, Bristol BS8 1TH, UK
| | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Mikael Courbot
- Syngenta, Syngenta AG, Schaffhauserstrasse, CH-4332 Stein, Switzerland
| | - Jason Rudd
- Department of Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.
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45
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Ramesh P, Reena P, Amitbikram M, Chaitanya J, Anju K. Insight into the transcriptome of Arthrobotrys conoides using high throughput sequencing. J Basic Microbiol 2015; 55:1394-405. [PMID: 26301953 DOI: 10.1002/jobm.201500237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/20/2015] [Indexed: 11/09/2022]
Abstract
Arthrobotrys conoides is a nematode-trapping fungus belonging to Orbiliales, Ascomycota group, and traps prey nematodes by means of adhesive network. Fungus has a potential to be used as a biocontrol agent against plant parasitic nematodes. In the present study, we characterized the transcriptome of A. conoides using high-throughput sequencing technology and characterized its virulence unigenes. Total 7,255 cDNA contigs with an average length of 425 bp were generated and 6184 (61.81%) transcripts were functionally annotated and characterized. Majority of unigenes were found analogous to the genes of plant pathogenic fungi. A total of 1749 transcripts were found to be orthologous with eukaryotic proteins of KOG database. Several carbohydrate active enzymes and peptidases were identified. We also analyzed classically and nonclassically secreted proteins and confirmed by BLASTP against fungal secretome database. A total of 916 contigs were analogous to 556 unique proteins of Pathogen Host Interaction (PHI) database. Further, we identified 91 unigenes homologous to the database of fungal virulence factor (DFVF). A total of 104 putative protein kinases coding transcripts were identified by BLASTP against KinBase database, which are major players in signaling pathways. This study provides a comprehensive look at the transcriptome of A. conoides and the identified unigenes might have a role in catching and killing prey nematodes by A. conoides.
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Affiliation(s)
- Pandit Ramesh
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India.,Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Patel Reena
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India
| | - Mohapatra Amitbikram
- Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Joshi Chaitanya
- Department of Animal Biotechnology, College of Veterinary Science and A.H., Anand Agricultural University, Anand, Gujarat, India
| | - Kunjadia Anju
- Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, New V.V. Nagar, Anand, Gujarat, India
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Heard S, Brown NA, Hammond-Kosack K. An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS One 2015; 10:e0130534. [PMID: 26107498 PMCID: PMC4480369 DOI: 10.1371/journal.pone.0130534] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/22/2015] [Indexed: 11/25/2022] Open
Abstract
Phytopathogenic fungi form intimate associations with host plant species and cause disease. To be successful, fungal pathogens communicate with a susceptible host through the secretion of proteinaceous effectors, hydrolytic enzymes and metabolites. Sclerotinia sclerotiorum and Botrytis cinerea are economically important necrotrophic fungal pathogens that cause disease on numerous crop species. Here, a powerful bioinformatics pipeline was used to predict the refined S. sclerotiorum and B. cinerea secretomes, identifying 432 and 499 proteins respectively. Analyses focusing on S. sclerotiorum revealed that 16% of the secretome encoding genes resided in small, sequence heterogeneous, gene clusters that were distributed over 13 of the 16 predicted chromosomes. Functional analyses highlighted the importance of plant cell hydrolysis, oxidation-reduction processes and the redox state to the S. sclerotiorum and B. cinerea secretomes and potentially host infection. Only 8% of the predicted proteins were distinct between the two secretomes. In contrast to S. sclerotiorum, the B. cinerea secretome lacked CFEM- or LysM-containing proteins. The 115 fungal and oomycete genome comparison identified 30 proteins specific to S. sclerotiorum and B. cinerea, plus 11 proteins specific to S. sclerotiorum and 32 proteins specific to B. cinerea. Expressed sequence tag (EST) and proteomic analyses showed that 246 S. sclerotiorum secretome encoding genes had EST support, including 101 which were only expressed in vitro and 49 which were only expressed in planta, whilst 42 predicted proteins were experimentally proven to be secreted. These detailed in silico analyses of two important necrotrophic pathogens will permit informed choices to be made when candidate effector proteins are selected for function analyses in planta.
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Affiliation(s)
- Steph Heard
- Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
| | - Neil A. Brown
- Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
| | - Kim Hammond-Kosack
- Plant Biology and Crop Science, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
- * E-mail:
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47
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Rudd JJ. Previous bottlenecks and future solutions to dissecting the Zymoseptoria tritici-wheat host-pathogen interaction. Fungal Genet Biol 2015; 79:24-8. [PMID: 26092786 PMCID: PMC4502452 DOI: 10.1016/j.fgb.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 11/24/2022]
Abstract
Zymoseptoria tritici (previously Mycosphaerella graminicola, teleomorph, Septoria tritici, anamorph) causes Septoria tritici blotch, one of the most economically important diseases of wheat (Triticum aestivum). The host pathogenic interaction, as currently understood, is intriguing, and may distinguish Z. tritici from many of the current models for plant pathogenic fungi. Many important questions remain which require a deeper understanding including; the nature and biological significance of the characteristic long latent periods of symptomless plant infection; how/why the fungus then effectively transitions from this to cause disease and reproduce? Elements of this transition currently resemble a putative "hijack" on plant defence but how is Z. tritici able to do this without any form of plant cell penetration? This commentary provides a summary of the recent history of research into the host-pathogen interaction, whilst highlighting some of the challenges going forwards, which will be faced by improved technologies and a growing research community.
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Affiliation(s)
- Jason J Rudd
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK.
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48
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RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements. G3-GENES GENOMES GENETICS 2015; 5:1323-33. [PMID: 25917918 PMCID: PMC4502367 DOI: 10.1534/g3.115.017731] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The fungal pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a prominent pathogen of wheat. The reference genome of the isolate IPO323 is one of the best-assembled eukaryotic genomes and encodes more than 10,000 predicted genes. However, a large proportion of the previously annotated gene models are incomplete, with either no start or no stop codons. The availability of RNA-seq data allows better predictions of gene structure. We here used two different RNA-seq datasets, de novo transcriptome assemblies, homology-based comparisons, and trained ab initio gene callers to generate a new gene annotation of Z. tritici IPO323. The annotation pipeline was also applied to re-sequenced genomes of three closely related species of Z. tritici: Z. pseudotritici, Z. ardabiliae, and Z. brevis. Comparative analyses of the predicted gene models using the four Zymoseptoria species revealed sets of species-specific orphan genes enriched with putative pathogenicity-related genes encoding small secreted proteins that may play essential roles in virulence and host specificity. De novo repeat identification allowed us to show that few families of transposable elements are shared between Zymoseptoria species while we observe many species-specific invasions and expansions. The annotation data presented here provide a high-quality resource for future studies of Z. tritici and its sister species and provide detailed insight into gene and genome evolution of fungal plant pathogens.
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Rudd JJ, Kanyuka K, Hassani-Pak K, Derbyshire M, Andongabo A, Devonshire J, Lysenko A, Saqi M, Desai NM, Powers SJ, Hooper J, Ambroso L, Bharti A, Farmer A, Hammond-Kosack KE, Dietrich RA, Courbot M. Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition. PLANT PHYSIOLOGY 2015; 167:1158-85. [PMID: 25596183 PMCID: PMC4348787 DOI: 10.1104/pp.114.255927] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/16/2015] [Indexed: 05/17/2023]
Abstract
The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.
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Affiliation(s)
- Jason J Rudd
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Kostya Kanyuka
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Keywan Hassani-Pak
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Mark Derbyshire
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Ambrose Andongabo
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Jean Devonshire
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Artem Lysenko
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Mansoor Saqi
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Nalini M Desai
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Stephen J Powers
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Juliet Hooper
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Linda Ambroso
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Arvind Bharti
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Andrew Farmer
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Kim E Hammond-Kosack
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Robert A Dietrich
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
| | - Mikael Courbot
- Department of Plant Biology and Crop Science (J.J.R., K.K., M.D., J.D., J.H., K.E.H.-K.) and Department of Computational and Systems Biology (K.H.-P., A.A., A.L., M.S., S.J.P.), Rothamsted Research, Harpenden, Hertshire AL5 2JQ, United Kingdom;Metabolon, Inc., Durham, North Carolina 27713 (N.M.D.);Syngenta Biotechnology, Inc., Research Triangle Park, North Carolina 27709 (L.A., A.B., R.A.D.);National Center for Genome Resources, Santa Fe, New Mexico 87505 (A.F.); andSyngenta Crop Protection AG, Crop Protection Research, CH-4332 Stein, Switzerland (M.C.)
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Escobar-Tovar L, Guzmán-Quesada M, Sandoval-Fernández JA, Gómez-Lim MA. Comparative analysis of the in vitro and in planta secretomes from Mycosphaerella fijiensis isolates. Fungal Biol 2015; 119:447-70. [PMID: 25986542 DOI: 10.1016/j.funbio.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 01/09/2023]
Abstract
Black Sigatoka, a devastating disease of bananas and plantains worldwide, is caused by the fungus Mycosphaerella fijiensis. Several banana cultivars such as 'Yangambi Km 5' and Calcutta IV, have been known to be resistant to the fungus, but the resistance has been broken in 'Yangambi Km 5' in Costa Rica. Since the resistance of this variety still persists in Mexico, the aim of this study was to compare the in vitro and in planta secretomes from two avirulent and virulent M. fijiensis isolates using proteomics and bioinformatics approaches. We aimed to identify differentially expressed proteins in fungal isolates that differ in pathogenicity and that might be responsible for breaking the resistance in 'Yangambi Km 5'. We were able to identify 90 protein spots in the secretomes of fungal isolates encoding 42 unique proteins and 35 differential spots between them. Proteins involved in carbohydrate transport and metabolism were more prevalent. Several proteases, pathogenicity-related, ROS detoxification and unknown proteins were also highly or specifically expressed by the virulent isolate in vitro or during in planta infection. An unknown protein representing a virulence factor candidate was also identified. These results demonstrated that the secretome reflects major differences between both M. fijiensis isolates.
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Affiliation(s)
- Lina Escobar-Tovar
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, 36821, Irapuato, Guanajuato, Mexico
| | - Mauricio Guzmán-Quesada
- Dirección de Investigaciones, Sección de Fitopatología, Corporación Bananera Nacional, 390-7210, La Rita, Guápiles, Costa Rica
| | - Jorge A Sandoval-Fernández
- Dirección de Investigaciones, Sección de Fitopatología, Corporación Bananera Nacional, 390-7210, La Rita, Guápiles, Costa Rica
| | - Miguel A Gómez-Lim
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, 36821, Irapuato, Guanajuato, Mexico.
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