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Yang F, Jacobsen S, Jørgensen HJL, Collinge DB, Svensson B, Finnie C. Fusarium graminearum and Its Interactions with Cereal Heads: Studies in the Proteomics Era. FRONTIERS IN PLANT SCIENCE 2013; 4:37. [PMID: 23450732 PMCID: PMC3584246 DOI: 10.3389/fpls.2013.00037] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/12/2013] [Indexed: 05/18/2023]
Abstract
The ascomycete fungal pathogen Fusarium graminearum (teleomorph stage: Gibberella zeae) is the causal agent of Fusarium head blight in wheat and barley. This disease leads to significant losses of crop yield, and especially quality through the contamination by diverse fungal mycotoxins, which constitute a significant threat to the health of humans and animals. In recent years, high-throughput proteomics, aiming at identifying a broad spectrum of proteins with a potential role in the pathogenicity and host resistance, has become a very useful tool in plant-fungus interaction research. In this review, we describe the progress in proteomics applications toward a better understanding of F. graminearum pathogenesis, virulence, and host defense mechanisms. The contribution of proteomics to the development of crop protection strategies against this pathogen is also discussed briefly.
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Affiliation(s)
- Fen Yang
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
- Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenFrederiksberg C, Denmark
- *Correspondence: Fen Yang, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark. e-mail:
| | - Susanne Jacobsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenFrederiksberg C, Denmark
| | - Hans J. L. Jørgensen
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | - David B. Collinge
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of DenmarkLyngby, Denmark
| | - Birte Svensson
- Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenFrederiksberg C, Denmark
| | - Christine Finnie
- Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenFrederiksberg C, Denmark
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Gottwald S, Samans B, Lück S, Friedt W. Jasmonate and ethylene dependent defence gene expression and suppression of fungal virulence factors: two essential mechanisms of Fusarium head blight resistance in wheat? BMC Genomics 2012; 13:369. [PMID: 22857656 PMCID: PMC3533685 DOI: 10.1186/1471-2164-13-369] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 06/21/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Fusarium head blight (FHB) caused by Fusarium species like F. graminearum is a devastating disease of wheat (Triticum aestivum) worldwide. Mycotoxins such as deoxynivalenol produced by the fungus affect plant and animal health, and cause significant reductions of grain yield and quality. Resistant varieties are the only effective way to control this disease, but the molecular events leading to FHB resistance are still poorly understood. Transcriptional profiling was conducted for the winter wheat cultivars Dream (moderately resistant) and Lynx (susceptible). The gene expressions at 32 and 72 h after inoculation with Fusarium were used to trace possible defence mechanisms and associated genes. A comparative qPCR was carried out for selected genes to analyse the respective expression patterns in the resistant cultivars Dream and Sumai 3 (Chinese spring wheat). RESULTS Among 2,169 differentially expressed genes, two putative main defence mechanisms were found in the FHB-resistant Dream cultivar. Both are defined base on their specific mode of resistance. A non-specific mechanism was based on several defence genes probably induced by jasmonate and ethylene signalling, including lipid-transfer protein, thionin, defensin and GDSL-like lipase genes. Additionally, defence-related genes encoding jasmonate-regulated proteins were up-regulated in response to FHB. Another mechanism based on the targeted suppression of essential Fusarium virulence factors comprising proteases and mycotoxins was found to be an essential, induced defence of general relevance in wheat. Moreover, similar inductions upon fungal infection were frequently observed among FHB-responsive genes of both mechanisms in the cultivars Dream and Sumai 3. CONCLUSIONS Especially ABC transporter, UDP-glucosyltransferase, protease and protease inhibitor genes associated with the defence mechanism against fungal virulence factors are apparently active in different resistant genetic backgrounds, according to reports on other wheat cultivars and barley. This was further supported in our qPCR experiments on seven genes originating from this mechanism which revealed similar activities in the resistant cultivars Dream and Sumai 3. Finally, the combination of early-stage and steady-state induction was associated with resistance, while transcript induction generally occurred later and temporarily in the susceptible cultivars. The respective mechanisms are attractive for advanced studies aiming at new resistance and toxin management strategies.
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Affiliation(s)
- Sven Gottwald
- Department of Plant Breeding, Justus-Liebig University, Institute of Agronomy and Plant Breeding I, Heinrich-Buff-Ring 26-32, Giessen, D-35392, Germany
| | - Birgit Samans
- Biometry and Population Genetics, Justus-Liebig University, Institute of Agronomy and Plant Breeding II, Heinrich-Buff-Ring 26-32, Giessen, D-35392, Germany
| | - Stefanie Lück
- Department of Plant Breeding, Justus-Liebig University, Institute of Agronomy and Plant Breeding I, Heinrich-Buff-Ring 26-32, Giessen, D-35392, Germany
| | - Wolfgang Friedt
- Department of Plant Breeding, Justus-Liebig University, Institute of Agronomy and Plant Breeding I, Heinrich-Buff-Ring 26-32, Giessen, D-35392, Germany
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Yang F, Jensen JD, Svensson B, Jørgensen HJL, Collinge DB, Finnie C. Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat. MOLECULAR PLANT PATHOLOGY 2012; 13:445-53. [PMID: 22044785 PMCID: PMC6638632 DOI: 10.1111/j.1364-3703.2011.00759.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fusarium graminearum is a phytopathogenic fungus primarily infecting small grain cereals, including barley and wheat. Secreted enzymes play important roles in the pathogenicity of many fungi. In order to access the secretome of F. graminearum, the fungus was grown in liquid culture with barley or wheat flour as the sole nutrient source to mimic the host-pathogen interaction. A gel-based proteomics approach was employed to identify the proteins secreted into the culture medium. Sixty-nine unique fungal proteins were identified in 154 protein spots, including enzymes involved in the degradation of cell walls, starch and proteins. Of these proteins, 35% had not been identified in previous in planta or in vitro studies, 70% were predicted to contain signal peptides and a further 16% may be secreted in a nonclassical manner. Proteins identified in the 72 spots showing differential appearance between wheat and barley flour medium were mainly involved in fungal cell wall remodelling and the degradation of plant cell walls, starch and proteins. The in planta expression of corresponding F. graminearum genes was confirmed by quantitative reverse transcriptase-polymerase chain reaction in barley and wheat spikelets harvested at 2-6 days after inoculation. In addition, a clear difference in the accumulation of fungal biomass and the extent of fungal-induced proteolysis of plant β-amylase was observed in barley and wheat. The present study considerably expands the current database of F. graminearum secreted proteins which may be involved in Fusarium head blight.
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Affiliation(s)
- Fen Yang
- Department of Systems Biology, Enzyme and Protein Chemistry, Technical University of Denmark, 2800-Kongens Lyngby, Denmark
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Ravalason H, Grisel S, Chevret D, Favel A, Berrin JG, Sigoillot JC, Herpoël-Gimbert I. Fusarium verticillioides secretome as a source of auxiliary enzymes to enhance saccharification of wheat straw. BIORESOURCE TECHNOLOGY 2012; 114:589-96. [PMID: 22459963 DOI: 10.1016/j.biortech.2012.03.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/13/2012] [Accepted: 03/02/2012] [Indexed: 05/25/2023]
Abstract
Fusarium verticillioides secretes enzymes (secretome), some of which might be potentially useful for saccharification of lignocellulosic biomass since supplementation of commercial cellulases from Trichoderma reesei with the F. verticillioides secretome improved the enzymatic release of glucose, xylose and arabinose from wheat straw by 24%, 88% and 68%, respectively. Determination of enzymatic activities revealed a broad range of hemicellulases and pectinases poorly represented in commercial cocktails. Proteomics approaches identified 57 proteins potentially involved in lignocellulose breakdown among a total of 166 secreted proteins. This analysis highlighted the presence of carbohydrate-active enzymes (CAZymes) targeting pectin (from glycoside hydrolase families GH5, GH27, GH28, GH43, GH51, GH54, GH62, GH88 and GH93, polysaccharide lyase family PL4 and carbohydrate esterase family CE8) and hemicelluloses (from glycoside hydrolase families GH3, GH10, GH11, GH30, GH39, GH43 and GH67). These data provide a first step towards the identification of candidates to supplement T. reesei enzyme preparations for lignocellulose hydrolysis.
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Affiliation(s)
- Holy Ravalason
- INRA, UMR 1163 Biotechnologie des Champignons Filamenteux, 13288 Marseille, France.
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55
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Vincent D, Tan KC, Cassidy L, Solomon PS, Oliver RP. Proteomic techniques for plant-fungal interactions. Methods Mol Biol 2012; 835:75-96. [PMID: 22183648 DOI: 10.1007/978-1-61779-501-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Proteomics is a key technique that is helping elucidate many complex biological processes. The analysis of plant-pathogen interactions using proteomics is complicated by the presence of the proteomes of two species, but is benefiting from the developing maturity and power of these techniques. More and more pathogen genomes are being sequenced, so fungal proteomics is reaching its full potential and remains the chosen technology to unravel the molecular pathways of pathogenicity and resistance. In this chapter, we suggest proteomic strategies that have proved successful on various plant-interacting fungal species. Several protein extraction methods are described. For adequate quantitative analyses of protein abundances, we recommend either separation using two-dimensional gel electrophoresis or labelling with isobaric tags followed by two-dimensional HPLC separation. Proteins of interest are then identified using mass spectrometry. Identified proteins can assist in refining genome annotations, otherwise known as proteogenomics.
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Affiliation(s)
- Delphine Vincent
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
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56
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Dong X, Meinhardt SW, Schwarz PB. Isolation and characterization of two endoxylanases from Fusarium graminearum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:2538-2545. [PMID: 22313372 DOI: 10.1021/jf203407p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This paper reports the first isolation from cultures of two endoxylanases secreted by Fusarium graminearum Schwabe [teleomorph Gibberella zeae (Schweinitz) Petch]. When F. graminearum is grown on wheat bran hydrated with a modified synthetic medium, high xylanase activity can be extracted. The two endoxylanases were identified by LC-MS/MS as the products of genes FGSG_6445 (Genbank gene id 2788192 ) (xylanase 1) and FGSG_3624 (GenBank accession no. AJ863566 ) (xylanase 2) with 61 and 51% sequence coverage, respectively. Both enzymes showed a pH optimum at pH 6, with xylanase 1 exhibiting a wider active pH range (5.5-9) than xlylanase 2 (5.5-7.5). Their temperature dependences were similar, >60% between 35 and 60 °C, with optimal temperatures of 45 °C for xylanase 1 and 50 °C for xylanase 2. Kinetic studies found that both enzymes had a lower K(m) for linear beachwood xylan than arabinoxylan. For xylanase 2, the V(max) increased with arabinoxylan, but decreased for xylanase 1.
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Affiliation(s)
- Xinrong Dong
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108-6050, United States
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Couturier M, Navarro D, Olivé C, Chevret D, Haon M, Favel A, Lesage-Meessen L, Henrissat B, Coutinho PM, Berrin JG. Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis. BMC Genomics 2012; 13:57. [PMID: 22300648 PMCID: PMC3298532 DOI: 10.1186/1471-2164-13-57] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 02/02/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemi)cellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant information on the genes that are putatively involved in lignocellulose degradation. At present, additional experimental studies are essential to provide insights into the fungal secreted enzymatic pools involved in lignocellulose degradation. RESULTS In this study, we performed a wide analysis of 20 filamentous fungi for which genomic data are available to investigate their biomass-hydrolysis potential. A comparison of fungal genomes and secretomes using enzyme activity profiling revealed discrepancies in carbohydrate active enzymes (CAZymes) sets dedicated to plant cell wall. Investigation of the contribution made by each secretome to the saccharification of wheat straw demonstrated that most of them individually supplemented the industrial Trichoderma reesei CL847 enzymatic cocktail. Unexpectedly, the most striking effect was obtained with the phytopathogen Ustilago maydis that improved the release of total sugars by 57% and of glucose by 22%. Proteomic analyses of the best-performing secretomes indicated a specific enzymatic mechanism of U. maydis that is likely to involve oxido-reductases and hemicellulases. CONCLUSION This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process.
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58
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Plant Root Secretions and Their Interactions with Neighbors. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-23047-9_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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59
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Gonzalez-Fernandez R, Jorrin-Novo JV. Contribution of Proteomics to the Study of Plant Pathogenic Fungi. J Proteome Res 2011; 11:3-16. [DOI: 10.1021/pr200873p] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Raquel Gonzalez-Fernandez
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence, ceiA3, 14071 Cordoba, Spain
| | - Jesus V. Jorrin-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence, ceiA3, 14071 Cordoba, Spain
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60
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Glinka EM, Liao YC. Purification and partial characterisation of pectin methylesterase produced by Fusarium asiaticum. Fungal Biol 2011; 115:1112-21. [DOI: 10.1016/j.funbio.2011.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 07/07/2011] [Accepted: 07/11/2011] [Indexed: 11/25/2022]
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61
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62
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Phillips CM, Iavarone AT, Marletta MA. Quantitative Proteomic Approach for Cellulose Degradation by Neurospora crassa. J Proteome Res 2011; 10:4177-85. [DOI: 10.1021/pr200329b] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christopher M. Phillips
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, California 94720, United States
| | - Michael A. Marletta
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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63
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Wang Y, Wu J, Park ZY, Kim SG, Rakwal R, Agrawal GK, Kim ST, Kang KY. Comparative secretome investigation of Magnaporthe oryzae proteins responsive to nitrogen starvation. J Proteome Res 2011; 10:3136-48. [PMID: 21563842 DOI: 10.1021/pr200202m] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Magnaporthe oryzae is a fungal pathogen that causes blast disease in rice. During its early infection process, during which starvation of nutrients, including nitrogen, prevails before establishment of successful infection, the fungally secreted proteins play an important role in the pathogenicity and stress response. In this study, M. oryzae-secreted proteins were investigated in an N-deficient minimal medium using two-dimensional gel electrophoresis (2-DGE) coupled with mass spectrometry analysis (MALDI-TOF-MS and μLC-ESI-MS/MS). The 2-DGE analysis of secreted proteins detected 89 differentially expressed protein spots (14 downregulated and 75 upregulated) responsive to N starvation. Eighty five of the protein spots were identified by mass spectrometry analyses. Identified proteins were mainly cell wall hydrolase enzymes (22.4%), protein and lipid hydrolases (24.7%), reactive oxygen species detoxifying proteins (22.4%), and proteins with unknown function (14.1%), suggesting early production of prerequisite proteins for successful infection of the host. SignalP analysis predicted the presence of signal peptides in 67% of the identified proteins, suggesting that in addition to the classical Golgi/endoplasmic reticulum secretory pathway, M. oryzae might possess other, as yet undefined, secretory pathways. Those nonclassical or leaderless secretion proteins accounted for 25.9% of the total identified proteins by TatP and SecretomeP predictions. Semiquantitative reverse transcriptase polymerase chain reaction of seven randomly selected N-responsive secreted proteins also revealed a good correlation between RNA and protein levels. Taken together, the establishment of the M. oryzae secretome that is responsive to N starvation provides the first evidence of the secretion of 60 unreported and 25 previously known proteins. This developed protein inventory could be exploited to improve our understanding of the secretory mechanisms of M. oryzae and its invasive growth process in rice tissue.
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Affiliation(s)
- Yiming Wang
- Division of Applied Life Science (BK21 program), Gyeongsang National University, Jinju 660-701, South Korea
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64
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Gibson DM, King BC, Hayes ML, Bergstrom GC. Plant pathogens as a source of diverse enzymes for lignocellulose digestion. Curr Opin Microbiol 2011; 14:264-70. [DOI: 10.1016/j.mib.2011.04.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 04/07/2011] [Indexed: 01/09/2023]
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65
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Eggert K, Pawelzik E. Proteome analysis of Fusarium head blight in grains of naked barley (Hordeum vulgare
subsp. nudum
). Proteomics 2011; 11:972-85. [DOI: 10.1002/pmic.201000322] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 11/30/2010] [Accepted: 12/06/2010] [Indexed: 01/12/2023]
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66
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Abstract
Polysaccharide analysis using carbohydrate gel electrophoresis (PACE) relies on derivatization of the reducing ends of sugars with a fluorophore, followed by electrophoresis under optimized conditions in polyacrylamide gels. PACE is a sensitive and simple tool for studying polysaccharide structure or quantity and also has applications in the investigation of enzyme specificity.
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67
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Coumans JVF, Moens PDJ, Poljak A, Al-Jaaidi S, Pereg L, Raftery MJ. Plant-extract-induced changes in the proteome of the soil-borne pathogenic fungus Thielaviopsis basicola. Proteomics 2010; 10:1573-91. [PMID: 20186748 DOI: 10.1002/pmic.200900301] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Thielaviopsis basicola is a hemibiotroph fungus that causes black root rot disease in diverse plants with significant impact on cotton production in Australia. To elucidate how T. basicola growth and proteome are influenced by interactions with natural sources, this fungus was cultured in the presence of root extracts from non-host (wheat, hairy vetch) and susceptible host (cotton, lupin) plants. We found that T. basicola growth was significantly favored in the presence of host extracts, while hierarchical clustering analysis of 2-DE protein profiles of T. basicola showed plant species had a larger effect on the proteome than host/non-host status. Analysis by LC-MS/MS of unique and differentially expressed spots and identification using cross-species similarity searching and de novo sequencing allowed successful identification of 41 spots. These proteins were principally involved in primary metabolism with smaller numbers implicated in other diverse functions. Identification of several "morpho" proteins suggested morphological differences that were further microscopically investigated. Identification of several highly expressed spots suggested that vitamin B(6) is important in the T. basicola response to components present in hairy vetch extract, and finally, three spots, induced in the presence of lupin extract, may correspond to malic enzyme and be involved in lipid accumulation.
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Affiliation(s)
- Joëlle V F Coumans
- Molecular and Cellular Biology, School of Science and Technology, University of New England, Armidale, NSW, Australia.
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68
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Proteomics of plant pathogenic fungi. J Biomed Biotechnol 2010; 2010:932527. [PMID: 20589070 PMCID: PMC2878683 DOI: 10.1155/2010/932527] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 02/03/2010] [Accepted: 03/01/2010] [Indexed: 12/15/2022] Open
Abstract
Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.
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69
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Hong SY, So J, Lee J, Min K, Son H, Park C, Yun SH, Lee YW. Functional analyses of two syntaxin-like SNARE genes, GzSYN1 and GzSYN2, in the ascomycete Gibberella zeae. Fungal Genet Biol 2010; 47:364-72. [DOI: 10.1016/j.fgb.2010.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 12/24/2009] [Accepted: 01/20/2010] [Indexed: 10/19/2022]
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70
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The influence of Fusarium infection and growing location on the quantitative protein composition of (Part II) naked barley (Hordeum vulgare nudum). Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1234-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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71
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The influence of Fusarium infection and growing location on the quantitative protein composition of (part I) emmer (Triticum dicoccum). Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1229-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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72
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Vincent D, Balesdent MH, Gibon J, Claverol S, Lapaillerie D, Lomenech AM, Blaise F, Rouxel T, Martin F, Bonneu M, Amselem J, Dominguez V, Howlett BJ, Wincker P, Joets J, Lebrun MH, Plomion C. Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE. Electrophoresis 2010; 30:4118-36. [PMID: 19960477 DOI: 10.1002/elps.200900415] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, beta-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.
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73
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Tan KC, Ipcho SVS, Trengove RD, Oliver RP, Solomon PS. Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology. MOLECULAR PLANT PATHOLOGY 2009; 10:703-15. [PMID: 19694958 PMCID: PMC6640398 DOI: 10.1111/j.1364-3703.2009.00565.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
SUMMARY Peer-reviewed literature is today littered with exciting new tools and techniques that are being used in all areas of biology and medicine. Transcriptomics, proteomics and, more recently, metabolomics are three of these techniques that have impacted on fungal plant pathology. Used individually, each of these techniques can generate a plethora of data that could occupy a laboratory for years. When used in combination, they have the potential to comprehensively dissect a system at the transcriptional and translational level. Transcriptomics, or quantitative gene expression profiling, is arguably the most familiar to researchers in the field of fungal plant pathology. Microarrays have been the primary technique for the last decade, but others are now emerging. Proteomics has also been exploited by the fungal phytopathogen community, but perhaps not to its potential. A lack of genome sequence information has frustrated proteomics researchers and has largely contributed to this technique not fulfilling its potential. The coming of the genome sequencing era has partially alleviated this problem. Metabolomics is the most recent of these techniques to emerge and is concerned with the non-targeted profiling of all metabolites in a given system. Metabolomics studies on fungal plant pathogens are only just beginning to appear, although its potential to dissect many facets of the pathogen and disease will see its popularity increase quickly. This review assesses the impact of transcriptomics, proteomics and metabolomics on fungal plant pathology over the last decade and discusses their futures. Each of the techniques is described briefly with further reading recommended. Key examples highlighting the application of these technologies to fungal plant pathogens are also reviewed.
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Affiliation(s)
- Kar-Chun Tan
- Australian Centre for Necrotrophic Fungal Pathogens, SABC, Faculty of Health Sciences, Murdoch University, Murdoch 6150, Australia
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Dong H, Kemptner J, Marchetti-Deschmann M, Kubicek CP, Allmaier G. Development of a MALDI two-layer volume sample preparation technique for analysis of colored conidia spores of Fusarium by MALDI linear TOF mass spectrometry. Anal Bioanal Chem 2009; 395:1373-83. [DOI: 10.1007/s00216-009-3067-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 08/10/2009] [Accepted: 08/11/2009] [Indexed: 11/30/2022]
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Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, Phalip V. Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase. J Biol Chem 2009; 284:12285-96. [PMID: 19269961 PMCID: PMC2673297 DOI: 10.1074/jbc.m900439200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/19/2009] [Indexed: 11/06/2022] Open
Abstract
The phytopathogenic fungus Fusarium graminearum secretes a very diverse pool of glycoside hydrolases (GHs) aimed at degrading plant cell walls. alpha-l-Arabinanases are essential GHs participating in the complete hydrolysis of hemicellulose, a natural resource for various industrial processes, such as bioethanol or pharmaceuticals production. Arb93A, the exo-1,5-alpha-l-arabinanase of F. graminearum encoded by the gene fg03054.1, belongs to the GH93 family, for which no structural data exists. The enzyme is highly active (1065 units/mg) and displays a strict substrate specificity for linear alpha-1,5-l-arabinan. Biochemical assays and NMR experiments demonstrated that the enzyme releases alpha-1,5-l-arabinobiose from the nonreducing end of the polysaccharide. We determined the crystal structure of the native enzyme and its complex with alpha-1,5-l-arabinobiose, a degradation product of alpha-Me-1,5-l-arabinotetraose, at 1.85 and 2.05A resolution, respectively. Arb93A is a monomeric enzyme, which presents the six-bladed beta-propeller fold characteristic of sialidases of clan GHE. The configuration of the bound arabinobiose is consistent with the retaining mechanism proposed for the GH93 family. Catalytic residues were proposed from the structural analysis, and site-directed mutagenesis was used to validate their role. They are significantly different from those observed for GHE sialidases.
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Affiliation(s)
- Raphaël Carapito
- UMR 7175, Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg-CNRS, Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch-Graffenstaden, France
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76
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Fusarium graminearum xylanases show different functional stabilities, substrate specificities and inhibition sensitivities. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2008.12.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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King BC, Donnelly MK, Bergstrom GC, Walker LP, Gibson DM. An optimized microplate assay system for quantitative evaluation of plant cell wall-degrading enzyme activity of fungal culture extracts. Biotechnol Bioeng 2009; 102:1033-44. [PMID: 18973283 DOI: 10.1002/bit.22151] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Developing enzyme cocktails for cellulosic biomass hydrolysis complementary to current cellulase systems is a critical step needed for economically viable biofuels production. Recent genomic analysis indicates that some plant pathogenic fungi are likely a largely untapped resource in which to prospect for novel hydrolytic enzymes for biomass conversion. In order to develop high throughput screening assays for enzyme bioprospecting, a standardized microplate assay was developed for rapid analysis of polysaccharide hydrolysis by fungal extracts, incorporating biomass substrates. Fungi were grown for 10 days on cellulose- or switchgrass-containing media to produce enzyme extracts for analysis. Reducing sugar released from filter paper, Avicel, corn stalk, switchgrass, carboxymethylcellulose, and arabinoxylan was quantified using a miniaturized colorimetric assay based on 3,5-dinitrosalicylic acid. Significant interactions were identified among fungal species, growth media composition, assay substrate, and temperature. Within a small sampling of plant pathogenic fungi, some extracts had crude activities comparable to or greater than T. reesei, particularly when assayed at lower temperatures and on biomass substrates. This microplate assay system should prove useful for high-throughput bioprospecting for new sources of novel enzymes for biofuel production.
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Affiliation(s)
- Brian C King
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853, USA
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Vujanovic V, Vidovic S, Fernandez MR, Daida P, Korber D. Whole-cell protein and ITS rDNA profiles as diagnostic tools to discriminate Fusarium avenaceum intraspecific variability and associated virulence. Can J Microbiol 2009; 55:117-25. [DOI: 10.1139/w08-103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A total of 91 isolates of Fusarium avenaceum were regrouped into 15 phenotypes and 10 vegetative compatibility groups showing specific one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis (1-D SDS–PAGE) protein profiles and less-specific internal transcribed spacer rDNA profiles. Each isolate possessed reproducible signature protein bands. Indeed, the unweighted pair group method with arithmetic averages clustering revealed that the protein profile of each group of isolates correlated with fungus virulence. The use of SDS–PAGE offers a simple and sensitive technique for routine differentiation between pathogenic and nonpathogenic isolates within unknown F. avenaceum populations. The discovery has significant implications for risk assessment of cereal yield to ensure food and feed safety. This low-cost approach has the potential to be optimized and extended to a broad spectrum of Fusarium head blight pathogens.
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Affiliation(s)
- V. Vujanovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, Saskatoon, SK S9H 3X2, Canada
| | - S. Vidovic
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, Saskatoon, SK S9H 3X2, Canada
| | - M. R. Fernandez
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, Saskatoon, SK S9H 3X2, Canada
| | - P. Daida
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, Saskatoon, SK S9H 3X2, Canada
| | - D. Korber
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, P.O. Box 1030, Swift Current, Saskatoon, SK S9H 3X2, Canada
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Trail F. For blighted waves of grain: Fusarium graminearum in the postgenomics era. PLANT PHYSIOLOGY 2009; 149:103-10. [PMID: 19126701 PMCID: PMC2613717 DOI: 10.1104/pp.108.129684] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 11/06/2008] [Indexed: 05/22/2023]
Affiliation(s)
- Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824-1312, USA.
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Carapito R, Carapito C, Jeltsch JM, Phalip V. Efficient hydrolysis of hemicellulose by a Fusarium graminearum xylanase blend produced at high levels in Escherichia coli. BIORESOURCE TECHNOLOGY 2009; 100:845-850. [PMID: 18707875 DOI: 10.1016/j.biortech.2008.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 07/01/2008] [Accepted: 07/02/2008] [Indexed: 05/26/2023]
Abstract
A Fusarium graminearum-based enzyme blend for the efficient hydrolysis of hemicellulose, a crucial step for competitive bioethanol production, is described. The heretofore-uncharacterized endo-1,4-beta-xylanase (XylD), 1,4-beta-xylosidase (XyloA), and bifunctional xylosidase/arabinofuranosidase (Xylo/ArabA) were produced at high levels in Escherichia coli (10-38 mg/l). They displayed compatible pH and temperature-dependences, allowing their utilization for simultaneous substrate digestions. Monosaccharide analysis indicated a strong positive synergism between the enzymes during the degradation of oat spelt xylan. Two units of each protein catalyzed the release of 61% and 15% of the total amount of available d-xylose and l-arabinose, respectively, in only 4 h. The detailed cooperative mechanism of the three hydrolases was elucidated by polysaccharide analysis using carbohydrate gel electrophoresis (PACE) and the enzymes were shown to be suitable for the partial hydrolysis of pretreated crude plant biomass.
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Affiliation(s)
- Raphaël Carapito
- U.M.R. 7175, Ecole Supérieure de Biotechnologie de Strasbourg, Université Louis Pasteur-CNRS, Boulevard Sébastien Brandt, BP 10413, 67412 Illkirch-Graffenstaden, France
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81
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Kikot GE, Hours RA, Alconada TM. Contribution of cell wall degrading enzymes to pathogenesis of Fusarium graminearum
: a review. J Basic Microbiol 2008; 49:231-41. [DOI: 10.1002/jobm.200800231] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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82
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GzSNF1 is required for normal sexual and asexual development in the ascomycete Gibberella zeae. EUKARYOTIC CELL 2008; 8:116-27. [PMID: 19028993 DOI: 10.1128/ec.00176-08] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sucrose nonfermenting 1 (SNF1) protein kinase of yeast plays a central role in the transcription of glucose-repressible genes in response to glucose starvation. In this study, we deleted an ortholog of SNF1 from Gibberella zeae to characterize its functions by using a gene replacement strategy. The mycelial growth of deletion mutants (DeltaGzSNF1) was reduced by 21 to 74% on diverse carbon sources. The virulence of DeltaGzSNF1 mutants on barley decreased, and the expression of genes encoding cell-wall-degrading enzymes was reduced. The most distinct phenotypic changes were in sexual and asexual development. DeltaGzSNF1 mutants produced 30% fewer perithecia, which matured more slowly, and asci that contained one to eight abnormally shaped ascospores. Mutants in which only the GzSNF1 catalytic domain was deleted had the same phenotype changes as the DeltaGzSNF1 strains, but the phenotype was less extreme in the mutants with the regulatory domain deleted. In outcrosses between the DeltaGzSNF1 mutants, each perithecium contained approximately 70% of the abnormal ascospores, and approximately 50% of the asci showed unexpected segregation patterns in a single locus tested. The asexual spores of the DeltaGzSNF1 mutants were shorter and had fewer septa than those of the wild-type strain. The germination and nucleation of both ascospores and conidia were delayed in DeltaGzSNF1 mutants in comparison with those of the wild-type strain. GzSNF1 expression and localization depended on the developmental stage of the fungus. These results suggest that GzSNF1 is critical for normal sexual and asexual development in addition to virulence and the utilization of alternative carbon sources.
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83
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Tan KC, Heazlewood JL, Millar AH, Thomson G, Oliver RP, Solomon PS. A signaling-regulated, short-chain dehydrogenase of Stagonospora nodorum regulates asexual development. EUKARYOTIC CELL 2008; 7:1916-29. [PMID: 18776038 PMCID: PMC2583533 DOI: 10.1128/ec.00237-08] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 08/22/2008] [Indexed: 11/20/2022]
Abstract
The fungus Stagonospora nodorum is a causal agent of leaf and glume blotch disease of wheat. It has been previously shown that inactivation of heterotrimeric G protein signaling in Stagonospora nodorum caused development defects and reduced pathogenicity [P. S. Solomon et al., Mol. Plant-Microbe Interact. 17:456-466, 2004]. In this study, we sought to identify targets of the signaling pathway that may have contributed to phenotypic defects of the signaling mutants. A comparative analysis of Stagonospora nodorum wild-type and Galpha-defective mutant (gna1) intracellular proteomes was performed via two-dimensional polyacrylamide gel electrophoresis. Several proteins showed significantly altered abundances when comparing the two strains. One such protein, the short-chain dehydrogenase Sch1, was 18-fold less abundant in the gna1 strain, implying that it is positively regulated by Galpha signaling. Gene expression and transcriptional enhanced green fluorescent protein fusion analyses of Sch1 indicates strong expression during asexual development. Mutant strains of Stagonospora nodorum lacking Sch1 demonstrated poor growth on minimal media and exhibited a significant reduction in asexual sporulation on all growth media examined. Detailed histological experiments on sch1 pycnidia revealed that the gene is required for the differentiation of the subparietal layers of asexual pycnidia resulting in a significant reduction in both pycnidiospore size and numbers.
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Affiliation(s)
- Kar-Chun Tan
- Australian Centre for Necrotrophic Fungal Pathogens, Murdoch University, South Street, Murdoch 6150, Australia
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84
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Krijger JJ, Horbach R, Behr M, Schweizer P, Deising HB, Wirsel SGR. The yeast signal sequence trap identifies secreted proteins of the hemibiotrophic corn pathogen Colletotrichum graminicola. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:1325-1336. [PMID: 18785828 DOI: 10.1094/mpmi-21-10-1325] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The hemibiotroph Colletotrichum graminicola is the causal agent of stem rot and leaf anthracnose on Zea mays. Following penetration of epidermal cells, the fungus enters a short biotrophic phase, followed by a destructive necrotrophic phase of pathogenesis. During both phases, secreted fungal proteins are supposed to determine progress and success of the infection. To identify genes encoding such proteins, we constructed a yeast signal sequence trap (YSST) cDNA-library from RNA extracted from mycelium grown in vitro on corn cell walls and leaf extract. Of the 103 identified unigenes, 50 showed significant similarities to genes with a reported function, 25 sequences were similar to genes without a known function, and 28 sequences showed no similarity to entries in the databases. Macroarray hybridization and quantitative reverse-transcriptase polymerase chain reaction confirmed that most genes identified by the YSST screen are expressed in planta. Other than some genes that were constantly expressed, a larger set showed peaks of transcript abundances at specific phases of pathogenesis. Another set exhibited biphasic expression with peaks at the biotrophic and necrotrophic phase. Transcript analyses of in vitro-grown cultures revealed that several of the genes identified by the YSST screen were induced by the addition of corn leaf components, indicating that host-derived factors may have mimicked the host milieu.
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Affiliation(s)
- Jorrit-Jan Krijger
- Institut fur Agrar-und Ernahrungswissenschaften, Martin-Luther-Universitat Halle-Wittenberg, Halle, Germany
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85
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Kema GHJ, van der Lee TAJ, Mendes O, Verstappen ECP, Lankhorst RK, Sandbrink H, van der Burgt A, Zwiers LH, Csukai M, Waalwijk C. Large-scale gene discovery in the septoria tritici blotch fungus Mycosphaerella graminicola with a focus on in planta expression. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:1249-1260. [PMID: 18700829 DOI: 10.1094/mpmi-21-9-1249] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The foliar disease septoria tritici blotch, caused by the fungus Mycosphaerella graminicola, is currently the most important wheat disease in Europe. Gene expression was examined under highly different conditions, using 10 expressed sequence tag libraries generated from M. graminicola isolate IPO323 using seven in vitro and three in planta growth conditions. To identify fungal clones in the interaction libraries, we developed a selection method based on hybridization with the entire genomic DNA of M. graminicola, to selectively enrich these libraries for fungal genes. Assembly of the 27,007 expressed sequence tags resulted in 9,190 unigenes, representing 5.2 Mb of the estimated 39-Mb genome size of M. graminicola. All libraries contributed significantly to the number of unigenes, especially the in planta libraries representing different stages of pathogenesis, which covered 15% of the library-specific unigenes. Even under presymptomatic conditions (5 days postinoculation), when fungal biomass is less than 5%, this method enabled us to efficiently capture fungal genes expressed during pathogenesis. Many of these genes were uniquely expressed in planta, indicating that in planta gene expression significantly differed from in vitro expression. Examples of gene discovery included a number of cell wall-degrading enzymes, a broad set of genes involved in signal transduction (n=11) and a range of ATP-binding cassette (n=20) and major facilitator superfamily transporter genes (n=12) potentially involved in protection against antifungal compounds or the secretion of pathogenicity factors. In addition, evidence is provided for a mycovirus in M. graminicola that is highly expressed under various stress conditions, in particular, under nitrogen starvation. Our analyses provide a unique window on in vitro and in planta gene expression of M. graminicola.
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Affiliation(s)
- Gert H J Kema
- Plant Research International B.V., Wageningen, The Netherlands.
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86
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Guais O, Borderies G, Pichereaux C, Maestracci M, Neugnot V, Rossignol M, François JM. Proteomics analysis of "Rovabiot Excel", a secreted protein cocktail from the filamentous fungus Penicillium funiculosum grown under industrial process fermentation. J Ind Microbiol Biotechnol 2008; 35:1659-68. [PMID: 18696134 DOI: 10.1007/s10295-008-0430-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 07/30/2008] [Indexed: 11/25/2022]
Abstract
MS/MS techniques are well customized now for proteomic analysis, even for non-sequenced organisms, since peptide sequences obtained by these methods can be matched with those found in databases from closely related sequenced organisms. We used this approach to characterize the protein content of the "Rovabio Excel", an enzymatic cocktail produced by Penicillium funiculosum that is used as feed additive in animal nutrition. Protein separation by bi-dimensional electrophoresis yielded more than 100 spots, from which 37 proteins were unambiguously assigned from peptide sequences. By one-dimensional SDS-gel electrophoresis, 34 proteins were identified among which 8 were not found in the 2-DE analysis. A third method, termed 'peptidic shotgun', which consists in a direct treatment of the cocktail by trypsin followed by separation of the peptides on two-dimensional liquid chromatography, resulted in the identification of two additional proteins not found by the two other methods. Altogether, more than 50 proteins, among which several glycosylhydrolytic, hemicellulolytic and proteolytic enzymes, were identified by combining three separation methods in this enzymatic cocktail. This work confirmed the power of proteome analysis to explore the genome expression of a non-sequenced fungus by taking advantage of sequences from phylogenetically related filamentous fungi and pave the way for further functional analysis of P. funiculosum.
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Mehta A, Brasileiro ACM, Souza DSL, Romano E, Campos MA, Grossi-de-Sá MF, Silva MS, Franco OL, Fragoso RR, Bevitori R, Rocha TL. Plant-pathogen interactions: what is proteomics telling us? FEBS J 2008; 275:3731-46. [PMID: 18616468 DOI: 10.1111/j.1742-4658.2008.06528.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the years, several studies have been performed to analyse plant-pathogen interactions. Recently, functional genomic strategies, including proteomics and transcriptomics, have contributed to the effort of defining gene and protein function and expression profiles. Using these 'omic' approaches, pathogenicity- and defence-related genes and proteins expressed during phytopathogen infections have been identified and enormous datasets have been accumulated. However, the understanding of molecular plant-pathogen interactions is still an intriguing area of investigation. Proteomics has dramatically evolved in the pursuit of large-scale functional assignment of candidate proteins and, by using this approach, several proteins expressed during phytopathogenic interactions have been identified. In this review, we highlight the proteins expressed during plant-virus, plant-bacterium, plant-fungus and plant-nematode interactions reported in proteomic studies, and discuss these findings considering the advantages and limitations of current proteomic tools.
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Affiliation(s)
- Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil.
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88
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Rincones J, Scarpari LM, Carazzolle MF, Mondego JMC, Formighieri EF, Barau JG, Costa GGL, Carraro DM, Brentani HP, Vilas-Boas LA, de Oliveira BV, Sabha M, Dias R, Cascardo JM, Azevedo RA, Meinhardt LW, Pereira GAG. Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:891-908. [PMID: 18533830 DOI: 10.1094/mpmi-21-7-0891] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Moniliophthora perniciosa is a hemibiotrophic fungus that causes witches' broom disease (WBD) in cacao. Marked dimorphism characterizes this fungus, showing a monokaryotic or biotrophic phase that causes disease symptoms and a later dikaryotic or saprotrophic phase. A combined strategy of DNA microarray, expressed sequence tag, and real-time reverse-transcriptase polymerase chain reaction analyses was employed to analyze differences between these two fungal stages in vitro. In all, 1,131 putative genes were hybridized with cDNA from different phases, resulting in 189 differentially expressed genes, and 4,595 reads were clusterized, producing 1,534 unigenes. The analysis of these genes, which represent approximately 21% of the total genes, indicates that the biotrophic-like phase undergoes carbon and nitrogen catabolite repression that correlates to the expression of phytopathogenicity genes. Moreover, downregulation of mitochondrial oxidative phosphorylation and the presence of a putative ngr1 of Saccharomyces cerevisiae could help explain its lower growth rate. In contrast, the saprotrophic mycelium expresses genes related to the metabolism of hexoses, ammonia, and oxidative phosphorylation, which could explain its faster growth. Antifungal toxins were upregulated and could prevent the colonization by competing fungi. This work significantly contributes to our understanding of the molecular mechanisms of WBD and, to our knowledge, is the first to analyze differential gene expression of the different phases of a hemibiotrophic fungus.
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Affiliation(s)
- Johana Rincones
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, CP 6109, Campinas 13083-970, São Paulo, Brazil
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Carapito R, Hatsch D, Vorwerk S, Petkovski E, Jeltsch JM, Phalip V. Gene expression in Fusarium graminearum grown on plant cell wall. Fungal Genet Biol 2008; 45:738-48. [DOI: 10.1016/j.fgb.2007.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 12/03/2007] [Accepted: 12/03/2007] [Indexed: 10/22/2022]
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90
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Abstract
Filamentous fungi have been recognized as extraordinary producers of secreted proteins and are known to produce novel proteins and enzymes through dispensable metabolic pathways. Here, methods are described for the isolation and enrichment of samples of secreted proteins from cultures of filamentous fungi for analysis by gel electrophoresis and mass spectrometry techniques. These methods can be readily applied to the study of differential protein expression and secretion and metabolic pathways in filamentous fungi by proteomic approaches.
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91
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Development of a proteomic approach to monitor protein synthesis in mycotoxin producing moulds. Mycotoxin Res 2007; 23:161-5. [DOI: 10.1007/bf02946042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Accepted: 10/13/2007] [Indexed: 11/25/2022]
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92
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Xyr1 regulates xylanase but not cellulase formation in the head blight fungus Fusarium graminearum. Curr Genet 2007; 52:213-20. [PMID: 17924109 DOI: 10.1007/s00294-007-0154-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 08/31/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
Abstract
Fusarium graminearum is a plant pathogen that causes severe economical losses by infecting numerous agriculturally important plants and until now most culture plants have only low levels of Fusarium resistance. The plant cell wall can be assumed as the first target that has to be overcome by plant pathogens. Therefore pathogenic organisms are known to produce a complex cocktail of plant cell wall lytic enzymes. Xylanases are besides cellulases the most prominent enzymes secreted by Fusarium during growth on plant cell walls. We identified a putative regulator of xylanase production with high similarity to the Aspergillus niger XlnR and the Trichoderma reesei Xyr1 proteins. Disruptant strains of F. graminearum were heavily impaired in xylose utilization and xylanase production on wheat cell walls. In contrast to other filamentous fungi the lack of this transcriptional activator had no effect on the induction of cellulases.
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Paper JM, Scott-Craig JS, Adhikari ND, Cuomo CA, Walton JD. Comparative proteomics of extracellular proteinsin vitro andin planta from the pathogenic fungusFusarium graminearum. Proteomics 2007; 7:3171-83. [PMID: 17676664 DOI: 10.1002/pmic.200700184] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
High-throughput MS/MS was used to identify proteins secreted by Fusarium graminearum (Gibberella zeae) during growth on 13 media in vitro and in planta during infection of wheat heads. In vitro secreted proteins were collected from the culture filtrates, and in planta proteins were collected by vacuum infiltration. A total of 289 proteins (229 in vitro and 120 in planta) were identified with high statistical confidence. Forty-nine of the in planta proteins were not found in any of the in vitro conditions. The majority (91-100%) of the in vitro proteins had predicted signal peptides, but only 56% of the in planta proteins. At least 13 of the nonsecreted proteins found only in planta were single-copy housekeeping enzymes, including enolase, triose phosphate isomerase, phosphoglucomutase, calmodulin, aconitase, and malate dehydrogenase. The presence of these proteins in the in planta but not in vitro secretome might indicate that significant fungal lysis occurs during pathogenesis. On the other hand, several of the proteins lacking signal peptides that were found in planta have been reported to be potent immunogens secreted by animal pathogenic fungi, and therefore could be important in the interaction between F. graminearum and its host plants.
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Affiliation(s)
- Janet M Paper
- Department of Energy Plant Research Laboratory, Michigan State University, E. Lansing, MI 48824, USA
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94
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Juge N. Plant protein inhibitors of cell wall degrading enzymes. TRENDS IN PLANT SCIENCE 2006; 11:359-67. [PMID: 16774842 DOI: 10.1016/j.tplants.2006.05.006] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 05/04/2006] [Accepted: 05/25/2006] [Indexed: 05/10/2023]
Abstract
Plant cell walls, which consist mainly of polysaccharides (i.e. cellulose, hemicelluloses and pectins), play an important role in defending plants against pathogens. Most phytopathogenic microorganisms secrete an array of cell wall degrading enzymes (CWDEs) capable of depolymerizing the polysaccharides in the plant host wall. In response, plants have evolved a diverse battery of defence responses including protein inhibitors of these enzymes. These include inhibitors of pectin degrading enzymes such as polygalacturonases, pectinmethyl esterases and pectin lyases, and hemicellulose degrading enzymes such as endoxylanases and xyloglucan endoglucanases. The discovery of these plant inhibitors and the recent resolution of their three-dimensional structures, free or in complex with their target enzymes, provide new lines of evidence regarding their function and evolution in plant-pathogen interactions.
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Affiliation(s)
- Nathalie Juge
- Institut Méditerranéen de Recherche en Nutrition, Faculté des Sciences de St Jérôme, F-13397 Marseilles Cedex 20, France.
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95
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Hatsch D, Phalip V, Petkovski E, Jeltsch JM. Fusarium graminearum on plant cell wall: no fewer than 30 xylanase genes transcribed. Biochem Biophys Res Commun 2006; 345:959-66. [PMID: 16707104 DOI: 10.1016/j.bbrc.2006.04.171] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 04/26/2006] [Indexed: 11/26/2022]
Abstract
The transcription of a set of 32 putative xylanase genes from Fusarium graminearum was examined by quantitative PCR after growth on different carbon sources (hop cell wall, xylan, xylose, or carboxymethylcellulose). Growing on plant cell wall medium, this fungus displays a great diversity of expression of xylan-related genes, with 30 being induced. A second level of diversity exists because expression patterns can be very different for loci encoding enzymes with the same activity (the same EC number). The wealth of xylan-degrading enzymes and the differential expression confer on the fungus a great flexibility of reaction to variation in its environment.
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Affiliation(s)
- Didier Hatsch
- Institut de Médecine Légale, Université Louis Pasteur, 11 rue Humann, 67085 Strasbourg Cedex, France
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96
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Phalip V, Hatsch D, Laugel B, Jeltsch JM. An overview of fungal community diversity in diseased hop plantations. FEMS Microbiol Ecol 2006; 56:321-9. [PMID: 16629761 DOI: 10.1111/j.1574-6941.2006.00102.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Samples were taken from several hop fields presenting various symptoms. Fifty-nine pure filamentous fungal strains were isolated and identified through genomic DNA preparations, PCR amplification of the ribosomal DNA internal transcribed spacer region and database interrogations. The most frequent genera were Alternaria (16 isolates) and Epicoccum (14 isolates). The ecosystem was shown to be very diverse, since as many as 27 species belonging to 17 genera were recovered. Furthermore, many of the isolated fungi are known to be involved in phytopathogenesis.
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Affiliation(s)
- Vincent Phalip
- Laboratoire de Phytopathologie, Ecole Supérieure de Biotechnologie de Strasbourg, Université Louis Pasteur, Illkirch-Graffenstaden Cedex, France.
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