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Alfaro M, Majcherczyk A, Kües U, Ramírez L, Pisabarro AG. Glucose counteracts wood-dependent induction of lignocellulolytic enzyme secretion in monokaryon and dikaryon submerged cultures of the white-rot basidiomycete Pleurotus ostreatus. Sci Rep 2020; 10:12421. [PMID: 32709970 PMCID: PMC7381666 DOI: 10.1038/s41598-020-68969-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
The secretome complexity and lignocellulose degrading capacity of Pleurotus ostreatus monokaryons mkPC9 and mkPC15 and mated dikaryon dkN001 were studied in submerged liquid cultures containing wood, glucose, and wood plus glucose as carbon sources. The study revealed that this white-rot basidiomycete attacks all the components of the plant cell wall. P. ostreatus secretes a variety of glycoside hydrolases, carbohydrate esterases, and polysaccharide lyases, especially when wood is the only carbon source. The presence of wood increased the secretome complexity, whereas glucose diminished the secretion of enzymes involved in cellulose, hemicellulose and pectin degradation. In contrast, the presence of glucose did not influence the secretion of redox enzymes or proteases, which shows the specificity of glucose on the secretion of cellulolytic enzymes. The comparison of the secretomes of monokaryons and dikaryons reveals that secretome complexity is unrelated to the nuclear composition of the strain.
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Affiliation(s)
- Manuel Alfaro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain
| | - Andrzej Majcherczyk
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
| | - Lucía Ramírez
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006, Pamplona, Spain.
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Oliveros CV, Chegwin Angarita C, Ardila Barrantes HD. Condiciones para el análisis de proteínas del micelio de Lentinula edodes obtenido por fermentación en estado líquido. REVISTA COLOMBIANA DE QUÍMICA 2019. [DOI: 10.15446/rev.colomb.quim.v48n3.74843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Lentinula edodes es una seta comestible con potencial para el desarrollo de nutraceúticos. Sin embargo, son incipientes los trabajos enfocados en su producción biotecnológica y el desarrollo de herramientas analíticas que permitan profundizar en su composición. En esta investigación se estudió la producción de biomasa del hongo en el tiempo mediante fermentación en estado líquido y se seleccionaron las condiciones que permiten la obtención de extractos para la aplicación de herramientas para análisis proteómicos. Los métodos de extracción de proteínas, ácido tricloroacético (TCA)-Acetona y TCA-Acetona-Fenol, fueron comparados en términos del rendimiento de extracción y los perfiles de separación usando electroforesis en 1D (SDS-PAGE) y 2D (IEF-SDS PAGE). Se determinó que a los 10 días de crecimiento se obtiene la mayor producción de biomasa y proteína total. La extracción con TCA-Acetona-Fenol presentó un mayor rendimiento, mayor resolución y número de bandas en la electroforesis 1D. En 2DE los dos métodos permitieron la extracción de proteínas con puntos isoeléctricos en el rango de pH 3-10, pero el método TCA-Acetona-Fenol conllevó a una extracción diferencial, favoreciendo el rango de 33 a 113 kDa. Estos resultados se constituyen en una primera aplicación de técnicas de separación electroforética para futuros estudios proteómicos
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Pandey V, Gupta AK, Singh M, Pandey D, Kumar A. Complementary Proteomics, Genomics approaches identifies potential pathogenicity/virulence factors in Tilletia indica induced under the influence of host factor. Sci Rep 2019; 9:553. [PMID: 30679765 PMCID: PMC6346058 DOI: 10.1038/s41598-018-37810-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
Karnal bunt disease of wheat is incited by quarantine fungal pathogen T. indica. Till date, there is little information on the pathogenic mechanisms involved in Karnal bunt. In order to understand the molecular mechanisms of disease pathogenesis, highly aggressive T. indica TiK isolate was cultured in the presence of host factor extracted from developing spikes of wheat variety WH-542. Modulation in protein profile of mycelial proteins and secretome from TiK cultured in the absence and presence of host factor was analyzed by 2-DE. Fifteen and twenty nine protein spots were up-regulated/differentially regulated in the proteome of mycelial and secreted proteins, respectively and identified using MALDI-TOF/TOF. Identified proteins are involved in suppression of host defense responses, lignin degradation of plant cell wall, penetration, adhesion of pathogen to host tissues, pathogen mediated reactive oxygen species generation, hydrolytic enzymes, detoxification of host generated reactive oxygen species. Further, integration of proteomic and genomic analysis has led to candidate pathogenicity/virulence factors identification. They were functionally annotated by sequence as well as structure based analysis. In this study, complementation of proteomics and genomics approaches resulted in novel pathogenicity/virulence factor(s) identification in T. indica.
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Affiliation(s)
- Vishakha Pandey
- Department of Molecular biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Atul Kumar Gupta
- Department of Molecular biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
| | - Manoj Singh
- Department of Molecular biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Dinesh Pandey
- Department of Molecular biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Anil Kumar
- Department of Molecular biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.
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Growth and protease secretion of Scedosporium aurantiacum under conditions of hypoxia. Microbiol Res 2018; 216:23-29. [PMID: 30269853 DOI: 10.1016/j.micres.2018.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 12/19/2022]
Abstract
One of the micro-environmental stresses that fungal pathogens, such as Scedosporium aurantiacum, colonising human lungs encounter in vivo is hypoxia, or deficiency of oxygen. In this work, we studied the impacts of a hypoxic micro-environment (oxygen levels ≤1%) on the growth of a clinical S. aurantiacum isolate (WM 06.482; CBS 136046) and an environmental strain (S. aurantiacum WM 10.136; CBS 136049) on mucin-containing synthetic cystic fibrosis sputum medium. Additionally, profiles of secreted proteases were compared between the two isolates and protease activity was assessed using class-specific substrates and inhibitors. Overall, both isolates grew slower and produced less biomass under hypoxia compared to normoxic conditions. The pH of the medium decreased to 4.0 over the cultivation time, indicating that S. aurantiacum released acidic compounds into the medium. Accordingly, secreted proteases of the two isolates were dominated by acidic proteases, including aspartic and cysteine proteases, with optimal protease activity at pH 4.0 and 6.0 respectively. The clinical isolate produced higher aspartic and cysteine protease activities. Conversely, all serine proteases, including elastase-like, trypsin-like, chymotrypsin-like and subtilisin-like proteases had higher activities in the environmental isolate. Sequence similarities to 13 secreted proteases were identified by mass spectrometry (MS) by searching against other fungal proteases in the NCBI database. Results from MS analysis were consistent with those from activity assays. The clinical highly-virulent, and environmental low-virulence S. aurantiacum isolates responded differently to hypoxia in terms of the type of proteases secreted, which may reflect their different virulence properties.
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Integrated proteomics, genomics, metabolomics approaches reveal oxalic acid as pathogenicity factor in Tilletia indica inciting Karnal bunt disease of wheat. Sci Rep 2018; 8:7826. [PMID: 29777151 PMCID: PMC5959904 DOI: 10.1038/s41598-018-26257-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/03/2018] [Indexed: 01/21/2023] Open
Abstract
Tilletia indica incites Karnal bunt (KB) disease in wheat. To date, no KB resistant wheat cultivar could be developed due to non-availability of potential biomarkers related to pathogenicity/virulence for screening of resistant wheat genotypes. The present study was carried out to compare the proteomes of T. indica highly (TiK) and low (TiP) virulent isolates. Twenty one protein spots consistently observed as up-regulated/differential in the TiK proteome were selected for identification by MALDI-TOF/TOF. Identified sequences showed homology with fungal proteins playing essential role in plant infection and pathogen survival, including stress response, adhesion, fungal penetration, invasion, colonization, degradation of host cell wall, signal transduction pathway. These results were integrated with T. indica genome sequence for identification of homologs of candidate pathogenicity/virulence related proteins. Protein identified in TiK isolate as malate dehydrogenase that converts malate to oxaloacetate which is precursor of oxalic acid. Oxalic acid is key pathogenicity factor in phytopathogenic fungi. These results were validated by GC-MS based metabolic profiling of T. indica isolates indicating that oxalic acid was exclusively identified in TiK isolate. Thus, integrated omics approaches leads to identification of pathogenicity/virulence factor(s) that would provide insights into pathogenic mechanisms of fungi and aid in devising effective disease management strategies.
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Sathesh-Prabu C, Lee YK. Genetic Variability and Proteome Profiling of a Radiation Induced Cellulase Mutant Mushroom Pleurotus florida. Pol J Microbiol 2018; 65:271-277. [PMID: 29334071 DOI: 10.5604/17331331.1215606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the genetic similarity changes between a mutant mushroom (Pleurotus florida, designated as PfCM4) having increased cellulolytic activity developed through radiation mutagenesis and its wild type by amplified fragment length polymorphism (AFLP). On average, 23 AFLP fragments were amplified per primer combination, and a total of 286 polymorphic fragments (78.57% polymorphism) with maximal fragment length of 1365 base pairs (bp) were obtained. The genetic similarity between wild type and PfCM4 was found to be 22.30%. In addition, mycelial and secreted protein profiling by 2D-PAGE showed at least three and five different protein spots in the range of 25 kD to 100 kD, respectively, in PfCM4. It seems that the variation in genetic similarity and different expression of both mycelial and secreted proteins in PfCM4 in comparison to the wild type could likely be correlated with its increased cellulolytic activity effected by the irradiation.
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Affiliation(s)
- Chandran Sathesh-Prabu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
| | - Young-Keun Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Korea
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Pandey V, Singh M, Pandey D, Marla S, Kumar A. Secretome Analysis Identifies Potential Pathogenicity/Virulence Factors of Tilletia indica, a Quarantined Fungal Pathogen Inciting Karnal Bunt Disease in Wheat. Proteomics 2018; 18:e1700473. [PMID: 29508525 DOI: 10.1002/pmic.201700473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/22/2018] [Indexed: 11/07/2022]
Abstract
Tilletia indica is a smut fungus that incites Karnal bunt in wheat. It has been considered as quarantine pest in more than 70 countries. Despite its quarantine significance, there is meager knowledge regarding the molecular mechanisms of disease pathogenesis. Moreover, various disease management strategies have proven futile. Development of effective disease management strategy requires identification of pathogenicity/virulence factors. With this aim, the present study was conducted to compare the secretomes of T. indica isolates, that is, highly (TiK) and low (TiP) virulent isolates. About 120 and 95 protein spots were detected reproducibly in TiK and TiP secretome gel images. Nineteen protein spots, which were consistently observed as upregulated/differential in the secretome of TiK isolate, were selected for their identification by MALDI-TOF/TOF. Identified proteins exhibited homology with fungal proteins playing important role in fungal adhesion, penetration, invasion, protection against host-derived reactive oxygen species, production of virulence factors, cellular signaling, and degradation of host cell wall proteins and antifungal proteins. These results were complemented with T. indica genome sequence leading to identification of candidate pathogenicity/virulence factors homologs that were further subjected to sequence- and structure-based functional annotation. Thus, present study reports the first comparative secretome analysis of T. indica for identification of pathogenicity/virulence factors. This would provide insights into pathogenic mechanisms of T. indica and aid in devising effective disease management strategies.
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Affiliation(s)
- Vishakha Pandey
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Uttarakhand, India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Uttarakhand, India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Uttarakhand, India
| | - Soma Marla
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Uttarakhand, India
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Watanabe T, Yoshioka K, Kido A, Lee J, Akiyoshi H, Watanabe T. Preparation of intracellular proteins from a white-rot fungus surrounded by polysaccharide sheath and optimization of their two-dimensional electrophoresis for proteomic studies. J Microbiol Methods 2017; 142:63-70. [PMID: 28916445 DOI: 10.1016/j.mimet.2017.09.009] [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: 07/21/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 11/26/2022]
Abstract
The functions and properties of fungal sheath, an extracellular polysaccharide produced by many white-rot fungi, have been studied. However, the strong adherence of the sheath to fungal hyphae had been a major impediment in preparing intracellular proteins from the fungi and analyzing their cellular responses. To overcome this issue, we developed a rapid and easy method to remove the polysaccharide sheath using a selective lignin degrader, Ceriporiopsis subvermispora, which produces large sheath amounts in the presence of a lignin-derived aromatic compound. Using this approach, we achieved thorough removal of sheath and cell disruption using beads and a solution with a high protein-solubilizing power, which enabled the efficient extraction of intracellular proteins from C. subvermispora surrounded by sheath. In addition, for proteomic analysis, we investigated whether these extracted proteins were compatible with two-dimensional electrophoresis. By efficiently concentrating on protein solubilization in the first dimension and using a stacking gel in the second dimension, we successfully obtained a high-resolution proteome map of C. subvermispora. We also used the same proteins for fluorescence two-dimensional difference gel electrophoresis to obtain the quantitative protein expression profiles. These steps demonstrated that two-dimensional electrophoresis-based proteomics can be used to clarify the composition of intracellular proteins from sheath-producing white-rot fungi.
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Affiliation(s)
- Takahito Watanabe
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan.
| | - Koichi Yoshioka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan; Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Ayako Kido
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Junseok Lee
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Hikari Akiyoshi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
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Vats A, Mishra S. Decolorization of complex dyes and textile effluent by extracellular enzymes of Cyathus bulleri cultivated on agro-residues/domestic wastes and proposed pathway of degradation of Kiton blue A and reactive orange 16. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:11650-11662. [PMID: 28324257 DOI: 10.1007/s11356-017-8802-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/10/2017] [Indexed: 06/06/2023]
Abstract
In this study, the white-rot fungus Cyathus bulleri was cultivated on low-cost agro-residues, namely wheat bran (WB), wheat straw (WS), and domestic waste orange peel (OP) for production of ligninolytic enzymes. Of the three substrates, WB and OP served as good materials for the production of laccase with no requirement of additional carbon or nitrogen source. Specific laccase activity of 94.4 U mg-1 extracellular protein and 21.01 U mg-1 protein was obtained on WB and OP, respectively. Maximum decolorization rate of 13.6 μmol h-1 U-1 laccase for reactive black 5 and 22.68 μmol h-1 U-1 laccase for reactive orange 16 (RO) was obtained with the WB culture filtrate, and 11.7 μmol h-1 U-1 laccase for reactive violet 5 was observed with OP culture filtrate. Importantly, Kiton blue A (KB), reported not to be amenable to enzymatic degradation, was degraded by culture filtrate borne activities. Products of degradation of KB and RO were identified by mass spectrometry, and a pathway of degradation proposed. WB-grown culture filtrate decolorized and detoxified real and simulated textile effluents by about 40%. The study highlights the use of inexpensive materials for the production of enzymes effective on dyes and effluents.
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Affiliation(s)
- Arpita Vats
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Barnabas L, Ashwin NMR, Kaverinathan K, Trentin AR, Pivato M, Sundar AR, Malathi P, Viswanathan R, Carletti P, Arrigoni G, Masi A, Agrawal GK, Rakwal R. In vitro secretomic analysis identifies putative pathogenicity-related proteins of Sporisorium scitamineum - The sugarcane smut fungus. Fungal Biol 2017; 121:199-211. [PMID: 28215348 DOI: 10.1016/j.funbio.2016.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 02/08/2023]
Abstract
Sporisorium scitamineum, the sugarcane smut pathogen, relies predominantly on its secretome to successfully colonise its host, in accordance with other related smut fungi. Considering the significance of deciphering its secretome, we have examined alterations in the in vitro secretome of S. scitamineum in response to synthetic and sugarcane meristem tissue-amended growth media, so as to identify host signal responsive secretory proteins. Secretory proteins that were differentially abundant and exclusively secreted in response to host extract media were identified by two-dimensional gel electrophoresis coupled with MALDI-TOF/TOF MS. Of the 16 differentially abundant and exclusively secreted proteins, nine proteins were identified. Among which, six were related to cell wall modification, morphogenesis, polysaccharide degradation, and carbohydrate metabolism. In planta gene expression profiling indicated that five in vitro secreted proteins were expressed in distinct patterns by S. scitamineum during different stages of infection with relatively higher expression at 1 day after inoculation, suggesting that these proteins could be aiding S. scitamineum at early time points in penetration and colonisation of sugarcane cells. The present study has provided insights into the alterations occurring in the secretome of S. scitamineum at in vitro conditions and has resulted in the identification of secretory proteins that are possibly associated with pathogenicity of the sugarcane smut fungus.
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Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, 641 007 Coimbatore, India
| | - N M R Ashwin
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, 641 007 Coimbatore, India
| | - Kalimuthu Kaverinathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, 641 007 Coimbatore, India
| | - Anna Rita Trentin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Via dell'Università 16, 35020 Legnaro, Padova, Italy
| | - Micaela Pivato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Via dell'Università 16, 35020 Legnaro, Padova, Italy
| | - Amalraj Ramesh Sundar
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, 641 007 Coimbatore, India.
| | - Palaniyandi Malathi
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, 641 007 Coimbatore, India
| | - Rasappa Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, 641 007 Coimbatore, India
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Via dell'Università 16, 35020 Legnaro, Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center of Padova University, Via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Via dell'Università 16, 35020 Legnaro, Padova, Italy
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE (Global Research Arch for Developing Education) Academy Private Limited, 44301 Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE (Global Research Arch for Developing Education) Academy Private Limited, 44301 Birgunj, Nepal; Faculty of Health and Sport Sciences & Tsukuba International Academy for Sport Studies (TIAS), University of Tsukuba, 305-8571 Ibaraki, Japan
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Han Z, Kautto L, Nevalainen H. Secretion of Proteases by an Opportunistic Fungal Pathogen Scedosporium aurantiacum. PLoS One 2017; 12:e0169403. [PMID: 28060882 PMCID: PMC5218550 DOI: 10.1371/journal.pone.0169403] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/16/2016] [Indexed: 01/31/2023] Open
Abstract
Scedosporium aurantiacum is an opportunistic filamentous fungus increasingly isolated from the sputum of cystic fibrosis patients, and is especially prevalent in Australia. At the moment, very little is known about the infection mechanism of this fungus. Secreted proteases have been shown to contribute to fungal virulence in several studies with other fungi. Here we have compared the profiles of proteases secreted by a clinical isolate Scedosporium aurantiacum (WM 06.482) and an environmental strain (WM 10.136) grown on a synthetic cystic fibrosis sputum medium supplemented with casein or mucin. Protease activity was assessed using class-specific substrates and inhibitors. Subtilisin-like and trypsin-like serine protease activity was detected in all cultures. The greatest difference in the secretion of proteases between the two strains occurred in mucin-supplemented medium, where the activities of the elastase-like, trypsin-like and aspartic proteases were, overall, 2.5–75 fold higher in the clinical strain compared to the environmental strain. Proteases secreted by the two strains in the mucin-supplemented medium were further analyzed by mass spectrometry. Six homologs of fungal proteases were identified from the clinical strain and five from the environmental strain. Of these, three were common for both strains including a subtilisin peptidase, a putative leucine aminopeptidase and a PA-SaNapH-like protease. Trypsin-like protease was identified by mass spectrometry only in the clinical isolate even though trypsin-like activity was present in all cultures. In contrast, high elastase-like activity was measured in the culture supernatant of the clinical strain but could not be identified by mass spectrometry searching against other fungi in the NCBI database. Future availability of an annotated genome will help finalise identification of the S. aurantiacum proteases.
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Affiliation(s)
- Zhiping Han
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia
- * E-mail:
| | - Liisa Kautto
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia
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Vasina DV, Pavlov AR, Koroleva OV. Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate. BMC Microbiol 2016; 16:106. [PMID: 27296712 PMCID: PMC4906887 DOI: 10.1186/s12866-016-0729-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 06/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fungi are organisms with the highest natural capacity to degrade lignocellulose substrates, which is enabled by complex systems of extracellular enzymes, whose expression and secretion depend on the characteristics of substrates and the environment. Results This study reports a secretome analysis for white-rot basidiomycete Trametes hirsuta cultivated on a synthetic media and a lignocellulose substrate. We demonstrate that T. hirsuta st. 072 produces multiple extracellular ligninolytic, cellulolytic, hemicellulolytic, peroxide generating, and proteolytic enzymes, as well as cerato-platanins. In contrast to other white rot species described earlier, which mostly secreted glucanases and mannosidases in response to the presence of the lignocellulose substrate, T. hirsuta expressed a spectrum of extracellular cellulolytic enzymes containing predominantly cellobiases and xylanases. As proteomic analysis could not detect lignin peroxidase (LiP) among the secreted lignin degrading enzymes, we attributed the observed extracellular LiP - like activity to the expressed versatile peroxidase (VP). An accessory enzyme, glyoxal oxidase, was found among the proteins secreted in the media during submerged cultivation of T. hirsuta both in the presence and in the absence of copper. However, aryl-alcohol oxidase (AAO) was not identified, despite the presence of AAO enzymatic activity secreted by the fungus. The spectra of the expressed enzymes dramatically changed depending on the growth conditions. Transfer from submerged cultivation to surface cultivation with the lignocellulose substrate switched off expression of exo-β-1,3-glucanase and α-amylase and turned on secretion of endo-β-1,3-glucanase and a range of glycosidases. In addition, an aspartic peptidase started being expressed instead of family S53 protease. For the first time, we report production of cerato-platanin proteins by Trametes species. The secretion of cerato-platanins was observed only in response to contact with lignocellulose, thus indicating a specific role of these proteins in degradation of the lignocellulose substrates. Conclusions Our results suggest a sequential mechanism of natural substrate degradation by T. hirsuta, in which the fungus produces different sets of enzymes to digest all main components of the substrate during cultivation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0729-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria V Vasina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia.
| | - Andrey R Pavlov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
| | - Olga V Koroleva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
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Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp. Protein J 2016; 35:100-6. [DOI: 10.1007/s10930-016-9656-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Bashir H, Gangwar R, Mishra S. Differential production of lignocellulolytic enzymes by a white rot fungus Termitomyces sp. OE147 on cellulose and lactose. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1290-9. [PMID: 26164778 DOI: 10.1016/j.bbapap.2015.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 01/10/2023]
Abstract
White-rot fungi are the only organisms known to degrade all basic wood polymers using different strategies of employing a variety of hydrolytic and oxidative enzymes. A comparative secretome analysis of Termitomyces sp. OE147 cultivated on cellulose and lactose was carried out by two-dimensional gel electrophoresis followed by MALDI-TOF/TOF-MS analysis to identify the enzymes coordinately expressed on cellulose. A total of 29 proteins, belonging to CAZy hydrolases (11), CAZy oxidoreductases (13) and some 'other' (5) proteins were identified. Among the CAZy hydrolases, a distinct repertoire of cellulolytic and hemicellulolytic enzymes were produced while among the CAZy oxidoreductases, cellobiose dehydrogenase and laccase were the predominant enzymes along with H2O2 dependent peroxidases. This coordinated expression indicated a unique and integrated system for degradation of not only crystalline cellulose but also other components of lignocellulolytic substrates, namely lignin and xylan. Activities of the identified proteins were confirmed by plate assays and activity measurements. Many of the enzyme activities were also correlated with reduction in the crystallinity index of cellulose. Based on the enhanced production of CDH, β-glucosidases and several oxidoreductases, a more prominent role of these enzymes is indicated in this fungus in cellulose breakdown.
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Affiliation(s)
- Humayra Bashir
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Rishabh Gangwar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Saroj Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
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15
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Petráčková D, Halada P, Bezoušková S, Křesinová Z, Svobodová K. A two-dimensional protein map of Pleurotus ostreatus microsomes-proteome dynamics. Folia Microbiol (Praha) 2015; 61:63-71. [DOI: 10.1007/s12223-015-0410-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/15/2015] [Indexed: 01/24/2023]
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16
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Bianco L, Perrotta G. Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis. Int J Mol Sci 2015; 16:5803-29. [PMID: 25775160 PMCID: PMC4394507 DOI: 10.3390/ijms16035803] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/17/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022] Open
Abstract
Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.
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Affiliation(s)
- Linda Bianco
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
| | - Gaetano Perrotta
- UTTRI-GENER Genetics and Genomics for Energy and Environment Laboratory-ENEA TRISAIA Research Center, 75025 Rotondella (Matera), Italy.
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17
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Comparative analysis of secretomes in basidiomycete fungi. J Proteomics 2014; 102:28-43. [DOI: 10.1016/j.jprot.2014.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/19/2014] [Accepted: 03/03/2014] [Indexed: 12/29/2022]
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18
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Fernández RG, Redondo I, Jorrin-Novo JV. Making a protein extract from plant pathogenic fungi for gel- and LC-based proteomics. Methods Mol Biol 2014; 1072:93-109. [PMID: 24136517 DOI: 10.1007/978-1-62703-631-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Proteomic technologies have become a successful tool to provide relevant information on fungal biology. In the case of plant pathogenic fungi, this approach would allow a deeper knowledge of the interaction and the biological cycle of the pathogen, as well as the identification of pathogenicity and virulence factors. These two elements open up new possibilities for crop disease diagnosis and environment-friendly crop protection. Phytopathogenic fungi, due to its particular cellular characteristics, can be considered as a recalcitrant biological material, which makes it difficult to obtain quality protein samples for proteomic analysis. This chapter focuses on protein extraction for gel- and LC-based proteomics with specific protocols of our current research with Botrytis cinerea.
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Affiliation(s)
- Raquel González Fernández
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Agrifood Campus of International Excellence, Córdoba, Spain
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19
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Chen G, Zhou Y, Zeng G, Liu H, Yan M, Chen A, Guan S, Shang C, Li H, He J. Alteration of culture fluid proteins by cadmium induction inPhanerochaete chrysosporium. J Basic Microbiol 2013; 55:141-7. [DOI: 10.1002/jobm.201300398] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 09/14/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Guiqiu Chen
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Ying Zhou
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Hongyu Liu
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Ming Yan
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Anwei Chen
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Song Guan
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Cui Shang
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Huanke Li
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
| | - Jianmin He
- College of Environmental Science and Engineering; Hunan University; Changsha P. R. China
- Key Laboratory of Environmental Biology and Pollution Control; Hunan University, Ministry of Education; Changsha P. R. China
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20
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González-Fernández R, Aloria K, Valero-Galván J, Redondo I, Arizmendi JM, Jorrín-Novo JV. Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains. J Proteomics 2013; 97:195-221. [PMID: 23811051 DOI: 10.1016/j.jprot.2013.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 06/10/2013] [Accepted: 06/13/2013] [Indexed: 01/14/2023]
Abstract
UNLABELLED The necrotrophic fungus Botrytis cinerea is a very damaging phytopathogen of wide host range and environmental persistence. It is difficult to control because of its genetic versatility, expressed in the many phenotypical differences among isolates. The genomes of the B. cinerea B05.10 and T4 strains have been recently sequenced, becoming a model system for necrotrophic pathogens, and thus opening new alternatives for functional genomics analysis. In this work, the mycelium and secreted proteome of six wild-type strains with different host range, and grown in liquid minimal medium, have been analyzed by using complementary gel-based (1-DE and 2-DE) and gel-free/label-free (nUPLC-MS(E)) approaches. We found differences in the protein profiles among strains belonging to both the mycelium and the secretome. A total of 47 and 51 variable proteins were identified in the mycelium and the secretome, respectively. Some of them, such as malate dehydrogenase or peptidyl-prolyl cis-trans isomerase from the mycelium, and endopolygalacturonase, aspartic protease or cerato-platanin protein from the secretome have been reported as virulence factors, which are involved in host-tissue invasion, pathogenicity or fungal development. BIOLOGICAL SIGNIFICANCE The necrotrophic fungus Botrytis cinerea is an important phytopathogen of wide host range and environmental persistence, causing substantial economic losses worldwide. In this work, the mycelium and secreted proteome of six B. cinerea wild-type strains with different host range have been analyzed by using complementary gel-based and gel-free/label-free approaches. Fungal genetic versatility was confirmed at the proteome level for both mycelium proteome and secreted proteins. A high number of hypothetical proteins with conserved domains related to toxin compounds or to unknown functions were identified, having qualitative differences among strains. The identification of hypothetical proteins suggests that the B. cinerea strains differ mostly in processes involved in adaptation to a particular environment or a growth condition, rather than in essential metabolic reactions. Proteomics can help in the identification of variable proteins related to the infection and colonization of host plant tissues, as well as of virulence and aggressiveness factors among different B. cinerea wild-type strains. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Raquel González-Fernández
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Dpt. of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence (ceiA3), 14071 Córdoba, Spain.
| | - Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - José Valero-Galván
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Dpt. of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence (ceiA3), 14071 Córdoba, Spain; Dpt. of Chemistry-Biology, Biomedical Sciences Institute, Autonomous University of Ciudad Juárez, 32300 Ciudad Juárez, Chihuahua, Mexico. http://www.uco.es/botrytis/
| | - Inmaculada Redondo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Dpt. of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence (ceiA3), 14071 Córdoba, Spain. http://www.uco.es/botrytis/
| | - Jesús M Arizmendi
- Dpt. of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Jesús V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Dpt. of Biochemistry and Molecular Biology, University of Cordoba, Agrifood Campus of International Excellence (ceiA3), 14071 Córdoba, Spain. http://www.uco.es/botrytis/
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21
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Collins C, Keane TM, Turner DJ, O'Keeffe G, Fitzpatrick DA, Doyle S. Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. J Proteome Res 2013; 12:2552-70. [PMID: 23656496 PMCID: PMC3679558 DOI: 10.1021/pr301131t] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Armillaria mellea is a major plant
pathogen. Yet, no large-scale “-omics” data are available
to enable new studies, and limited experimental models are available
to investigate basidiomycete pathogenicity. Here we reveal that the A. mellea genome comprises 58.35 Mb, contains 14473 gene
models, of average length 1575 bp (4.72 introns/gene). Tandem mass
spectrometry identified 921 mycelial (n = 629 unique)
and secreted (n = 183 unique) proteins. Almost 100
mycelial proteins were either species-specific or previously unidentified
at the protein level. A number of proteins (n = 111)
was detected in both mycelia and culture supernatant extracts. Signal
sequence occurrence was 4-fold greater for secreted (50.2%) compared
to mycelial (12%) proteins. Analyses revealed a rich reservoir of
carbohydrate degrading enzymes, laccases, and lignin peroxidases in
the A. mellea proteome, reminiscent of both basidiomycete
and ascomycete glycodegradative arsenals. We discovered that A. mellea exhibits a specific killing effect against Candida albicans during coculture. Proteomic investigation
of this interaction revealed the unique expression of defensive and
potentially offensive A. mellea proteins (n = 30). Overall, our data reveal new insights into the
origin of basidiomycete virulence and we present a new model system
for further studies aimed at deciphering fungal pathogenic mechanisms.
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Affiliation(s)
- Cassandra Collins
- Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare, Ireland
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22
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Girard V, Dieryckx C, Job C, Job D. Secretomes: The fungal strike force. Proteomics 2013; 13:597-608. [DOI: 10.1002/pmic.201200282] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Vincent Girard
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Cindy Dieryckx
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Claudette Job
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Dominique Job
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
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23
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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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24
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Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC. The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 2011; 333:762-5. [PMID: 21764756 DOI: 10.1126/science.1205411] [Citation(s) in RCA: 354] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry rot" fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.
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Affiliation(s)
- Daniel C Eastwood
- College of Science, University of Swansea, Singleton Park, Swansea SA2 8PP, UK.
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25
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Deng X, Schröder S, Redweik S, Wätzig H. Quantitative gel electrophoresis: new records in precision by elaborated staining and detection protocols. Electrophoresis 2011; 32:1667-74. [PMID: 21557259 DOI: 10.1002/elps.201000525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/07/2010] [Accepted: 10/25/2010] [Indexed: 11/08/2022]
Abstract
Gel electrophoresis (GE) is a very common analytical technique for proteome research and protein analysis. Despite being developed decades ago, there is still a considerable need to improve its precision. Using the fluorescence of Colloidal Coomassie Blue -stained proteins in near-infrared (NIR), the major error source caused by the unpredictable background staining is strongly reduced. This result was generalized for various types of detectors. Since GE is a multi-step procedure, standardization of every single step is required. After detailed analysis of all steps, the staining and destaining were identified as the major source of the remaining variation. By employing standardized protocols, pooled percent relative standard deviations of 1.2-3.1% for band intensities were achieved for one-dimensional separations in repetitive experiments. The analysis of variance suggests that the same batch of staining solution should be used for gels of one experimental series to minimize day-to-day variation and to obtain high precision.
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Affiliation(s)
- Xi Deng
- Institute of Pharmaceutical Chemistry, Technical University of Braunschweig, Braunschweig, Germany
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26
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Kües U, Rühl M. Multiple multi-copper oxidase gene families in basidiomycetes - what for? Curr Genomics 2011; 12:72-94. [PMID: 21966246 PMCID: PMC3129051 DOI: 10.2174/138920211795564377] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 11/22/2022] Open
Abstract
Genome analyses revealed in various basidiomycetes the existence of multiple genes for blue multi-copper oxidases (MCOs). Whole genomes are now available from saprotrophs, white rot and brown rot species, plant and animal pathogens and ectomycorrhizal species. Total numbers (from 1 to 17) and types of mco genes differ between analyzed species with no easy to recognize connection of gene distribution to fungal life styles. Types of mco genes might be present in one and absent in another fungus. Distinct types of genes have been multiplied at speciation in different organisms. Phylogenetic analysis defined different subfamilies of laccases sensu stricto (specific to Agaricomycetes), classical Fe2+-oxidizing Fet3-like ferroxidases, potential ferroxidases/laccases exhibiting either one or both of these enzymatic functions, enzymes clustering with pigment MCOs and putative ascorbate oxidases. Biochemically best described are laccases sensu stricto due to their proposed roles in degradation of wood, straw and plant litter and due to the large interest in these enzymes in biotechnology. However, biological functions of laccases and other MCOs are generally little addressed. Functions in substrate degradation, symbiontic and pathogenic intercations, development, pigmentation and copper homeostasis have been put forward. Evidences for biological functions are in most instances rather circumstantial by correlations of expression. Multiple factors impede research on biological functions such as difficulties of defining suitable biological systems for molecular research, the broad and overlapping substrate spectrum multi-copper oxidases usually possess, the low existent knowledge on their natural substrates, difficulties imposed by low expression or expression of multiple enzymes, and difficulties in expressing enzymes heterologously.
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Affiliation(s)
- Ursula Kües
- University of Goettingen, Büsgen-Institute, Division of Molecular Wood Biotechnology and Technical Mycology, Büsgenweg 2, 37077 Goettingen, Germany
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27
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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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