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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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Chen S, Fan L, Song J, Zhang H, Doucette C, Hughes T, Campbell L. Quantitative proteomic analysis of Neosartorya pseudofischeri ascospores subjected to heat treatment. J Proteomics 2022; 252:104446. [PMID: 34883268 DOI: 10.1016/j.jprot.2021.104446] [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: 04/23/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
Neosartorya pseudofischeri, a heat- resistant fungus, was isolated from contaminated blueberry juice in our laboratory. To obtain a better understanding of the cellular process of heat- resistant fungus, a quantitative proteomic investigation employing stable isotope labeling by peptide demethylation was conducted on changes in intracellular proteins of N. pseudofischeri ascospores subjected to heat treatment at 93 °C for 0, 1 or 8 min. In total, 811 proteins were identified and quantified. Using the normalized ratio of protein abundance, proteins that changed more than two- fold after heat treatment were identified as significantly increased or decreased proteins and grouped into four clusters based on their quantitative changes. Decreased proteins were found mainly involved in the central carbon metabolism, heat stress responses, reactive oxygen intermediates elimination and translation events. A group of proteins in relation to toxicant degradation and antibiotic neutralization linking to environmental adaptability and tolerance of heat- resistant, was also identified. These findings provide insights into protein changes of N. pseudofischeri ascospores and lay foundations for further investigations on heat- resistant molds using targeted quantitative approaches. SIGNIFICANCE OF THE RESEARCH: Heat- resistant fungi can survive pasteurization processes, and subsequently germinate and grow to cause spoilage of food products, leading to significant economic losses for the food industry and potential health risk for the consumers. To obtain a better understanding of the cellular process of heat- resistant fungi, a quantitative proteomic approach employing stable isotope labeling by peptide demethylation has been used to investigate the intracellular protein changes of N. pseudofischeri ascospores isolated from blueberry juice and subjected to heat treatment. 150 significantly changed proteins were grouped into four clusters based on their quantitative changes. The significant decrease in protein abundance in response to heat treatment revealed possible mechanism that N. pseudofischeri ascospores could survive the heat treatment. This is the first proteomic profile report for N. pseudofischeri. These findings provide insights into protein changes of N. pseudofischeri and lay foundations for further investigations on heat- resistant fungi using targeted quantitative approaches to evaluate the efficiency of thermal treatment for processed food products.
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Affiliation(s)
- Si Chen
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China; Laboratory of aquatic product processing and quality safety, Marine Fisheries Research Institute of Zhejiang Province, Zhejiang, China
| | - Lihua Fan
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada.
| | - Jun Song
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Hong Zhang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China.
| | - Craig Doucette
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Timothy Hughes
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
| | - Leslie Campbell
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, 32 Main Street, Kentville, NS B4N 1J5, Canada
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Cologna NDMD, Gómez-Mendoza DP, Zanoelo FF, Giannesi GC, Guimarães NCDA, Moreira LRDS, Filho EXF, Ricart CAO. Exploring Trichoderma and Aspergillus secretomes: Proteomics approaches for the identification of enzymes of biotechnological interest. Enzyme Microb Technol 2018; 109:1-10. [DOI: 10.1016/j.enzmictec.2017.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
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Nagrale DT, Sharma L, Kumar S, Gawande SP. Recent Diagnostics and Detection Tools: Implications for Plant Pathogenic Alternaria and Their Disease Management. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Horn F, Heinekamp T, Kniemeyer O, Pollmächer J, Valiante V, Brakhage AA. Systems biology of fungal infection. Front Microbiol 2012; 3:108. [PMID: 22485108 PMCID: PMC3317178 DOI: 10.3389/fmicb.2012.00108] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/05/2012] [Indexed: 12/26/2022] Open
Abstract
Elucidation of pathogenicity mechanisms of the most important human-pathogenic fungi, Aspergillus fumigatus and Candida albicans, has gained great interest in the light of the steadily increasing number of cases of invasive fungal infections. A key feature of these infections is the interaction of the different fungal morphotypes with epithelial and immune effector cells in the human host. Because of the high level of complexity, it is necessary to describe and understand invasive fungal infection by taking a systems biological approach, i.e., by a comprehensive quantitative analysis of the non-linear and selective interactions of a large number of functionally diverse, and frequently multifunctional, sets of elements, e.g., genes, proteins, metabolites, which produce coherent and emergent behaviors in time and space. The recent advances in systems biology will now make it possible to uncover the structure and dynamics of molecular and cellular cause-effect relationships within these pathogenic interactions. We review current efforts to integrate omics and image-based data of host-pathogen interactions into network and spatio-temporal models. The modeling will help to elucidate pathogenicity mechanisms and to identify diagnostic biomarkers and potential drug targets for therapy and could thus pave the way for novel intervention strategies based on novel antifungal drugs and cell therapy.
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Affiliation(s)
- Fabian Horn
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll InstituteJena, Germany
| | - Thorsten Heinekamp
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll InstituteJena, Germany
| | - Olaf Kniemeyer
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll InstituteJena, Germany
| | - Johannes Pollmächer
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll InstituteJena, Germany
| | - Vito Valiante
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll InstituteJena, Germany
| | - Axel A. Brakhage
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll InstituteJena, Germany
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller UniversityJena, Germany
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Gutiérrez-Correa M, Ludeña Y, Ramage G, Villena GK. Recent Advances on Filamentous Fungal Biofilms for Industrial Uses. Appl Biochem Biotechnol 2012; 167:1235-53. [DOI: 10.1007/s12010-012-9555-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/06/2012] [Indexed: 11/28/2022]
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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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Chen XZ, Shen W, Fan Y, Wang ZX. [Genomics and metabolic engineering of filamentous fungi in the post-genomics era]. YI CHUAN = HEREDITAS 2011; 33:1067-78. [PMID: 21993281 DOI: 10.3724/sp.j.1005.2011.01067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Filamentous fungi are used in a variety of industrial processes including the production of primary metabolites (e.g., organic acid, vitamins, and extracellular enzymes) and secondary metabolites (e.g., antibiotics, alkaloids, and gibberellins). Moreover, filamentous fungi have become preferred cell factories for production of foreign (heterologous) proteins in biotechnology in recent years. Compared to bacterial and yeast hosts, filamentous fungi showed predominant features such as the ability of growing on rather simple and inexpensive substrates, producing and secreting exceptionally large amounts of proteins, post-translational modifications, and GRAS (generally regarded as safe) approval. Therefore, the exploration of filamentous fungi has been attractive recently. This review summarizes the recent development in genomics, comparative genomics, transcriptomics, proteomics and metabolomics of filamentous fungi, and describes their applications and functions in reconstruction of metabolic network, discovery of novel proteins and genes, investigation of cell physiological and biochemical reactions, and strain breeding. This review also analyzes the bottlenecks of heterologous protein expression in filamentous fungi. Furthermore, special emphasis is given on the strategies for improving the protein production, including fusion expression of heterologous proteins, RNAi technology, manipulations of secretion pathways, codon optimization of foreign genes, and screening of protease mutants. Lastly, this review proposes the future direction of metabolic engineering of filamentous fungi.
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Pinel C, Arlotto M, Issartel JP, Berger F, Pelloux H, Grillot R, Symoens F. Comparative proteomic profiles of Aspergillus fumigatus and Aspergillus lentulus strains by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS). BMC Microbiol 2011; 11:172. [PMID: 21798007 PMCID: PMC3162871 DOI: 10.1186/1471-2180-11-172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 07/28/2011] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) was applied to analyze the protein profiles in both somatic and metabolic extracts of Aspergillus species. The study was carried out on some Aspergillus species within the Fumigati section (Aspergillus fumigatus wild-types and natural abnormally pigmented mutants, and Aspergillus lentulus). The aim was to validate whether mass spectrometry protein profiles can be used as specific signatures to discriminate different Aspergillus species or even mutants within the same species. RESULTS The growth conditions and the SELDI-TOF parameters were determined to generate characteristic protein profiles of somatic and metabolic extracts of Aspergillus fumigatus strains using five different ProteinChips®, eight growth conditions combining two temperatures, two media and two oxygenation conditions. Nine strains were investigated: three wild-types and four natural abnormally pigmented mutant strains of A. fumigatus and two strains of A. lentulus. A total of 242 fungal extracts were prepared. The spectra obtained are protein signatures linked to the physiological states of fungal strains depending on culture conditions. The best resolutions were obtained using the chromatographic surfaces CM10, NP20 and H50 with fractions of fungi grown on modified Sabouraud medium at 37 °C in static condition. Under these conditions, the SELDI-TOF analysis allowed A. fumigatus and A. lentulus strains to be grouped into distinct clusters. CONCLUSIONS SELDI-TOF analysis distinguishes A. fumigatus from A. lentulus strains and moreover, permits separate clusters of natural abnormally pigmented A. fumigatus strains to be obtained. In addition, this methodology allowed us to point out fungal components specifically produced by a wild-type strain or natural mutants. It offers attractive potential for further studies of the Aspergillus biology or pathogenesis.
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Affiliation(s)
- Claudine Pinel
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie et Pathologie (IBP), Centre Hospitalier Universitaire Albert Michallon, BP 217, Grenoble, 38043, France
| | - Marie Arlotto
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
| | - Jean-Paul Issartel
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
| | - François Berger
- Institut de Neurosciences « Plateforme de Transcriptomique et de Protéomique Cliniques », (INSERM U836), Université Joseph Fourier, rue de la Chantourne, Grenoble, 38043, France
| | - Hervé Pelloux
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie et Pathologie (IBP), Centre Hospitalier Universitaire Albert Michallon, BP 217, Grenoble, 38043, France
| | - Renée Grillot
- Laboratoire de Parasitologie-Mycologie, Institut de Biologie et Pathologie (IBP), Centre Hospitalier Universitaire Albert Michallon, BP 217, Grenoble, 38043, France
| | - Françoise Symoens
- Mycology & Aerobiology Section, Scientific Institute of Public Health, 14 rue Juliette Wytsmanstreet, Brussels, 1050, Belgium
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Kniemeyer O. Proteomics of eukaryotic microorganisms: The medically and biotechnologically important fungal genus Aspergillus. Proteomics 2011; 11:3232-43. [DOI: 10.1002/pmic.201100087] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/26/2011] [Accepted: 04/05/2011] [Indexed: 11/09/2022]
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Abstract
Some fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of 'unknown function protein' as opposed to 'hypothetical protein' - once any protein has been identified by protein mass spectrometry. A combination of approaches including comparative proteomics, pathogen-induced protein expression and immunoproteomics are outlined, which, when used in combination with a variety of other techniques (e.g. functional genomics, microarray analysis, immunochemical and infection model systems), appear to yield comprehensive and definitive information on protein function in fungi. The relative advantages of proteomic, as opposed to transcriptomic-only, analyses are also described. In the future, combined high-throughput, quantitative proteomics, allied to transcriptomic sequencing, are set to reveal much about protein function in fungi.
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Affiliation(s)
- Sean Doyle
- Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Kniemeyer O, Schmidt AD, Vödisch M, Wartenberg D, Brakhage AA. Identification of virulence determinants of the human pathogenic fungi Aspergillus fumigatus and Candida albicans by proteomics. Int J Med Microbiol 2011; 301:368-77. [PMID: 21565549 DOI: 10.1016/j.ijmm.2011.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Both fungi Candida albicans and Aspergillus fumigatus can cause a number of life-threatening systemic infections in humans. The commensal yeast C. albicans is one of the main causes of nosocomial fungal infectious diseases, whereas the filamentous fungus A. fumigatus has become one of the most prevalent airborne fungal pathogens. Early diagnosis of these fungal infections is challenging, only a limited number of antifungals for treatment are available, and the molecular details of pathogenicity are hardly understood. The completion of both the A. fumigatus and C. albicans genome sequence provides the opportunity to improve diagnosis, to define new drug targets, to understand the functions of many uncharacterised proteins, and to study protein regulation on a global scale. With the application of proteomic tools, particularly two-dimensional gel electrophoresis and LC/MS-based methods, a comprehensive overview about the proteins of A. fumigatus and C. albicans present or induced during environmental changes and stress conditions has been obtained in the past 5 years. However, for the discovery of further putative virulence determinants, more sensitive and targeted proteomic methods have to be applied. Here, we review the recent proteome data generated for A. fumigatus and C. albicans that are related to factors required for pathogenicity.
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Affiliation(s)
- Olaf Kniemeyer
- Dept. of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.
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Comparison of transcriptional and translational changes caused by long-term menadione exposure in Aspergillus nidulans. Fungal Genet Biol 2011; 48:92-103. [DOI: 10.1016/j.fgb.2010.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 06/08/2010] [Accepted: 08/19/2010] [Indexed: 01/14/2023]
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Teutschbein J, Albrecht D, Pötsch M, Guthke R, Aimanianda V, Clavaud C, Latgé JP, Brakhage AA, Kniemeyer O. Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic mold Aspergillus fumigatus. J Proteome Res 2010; 9:3427-42. [PMID: 20507060 DOI: 10.1021/pr9010684] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity having the initial contact with the host. Applying two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), we established a 2-D reference map of conidial proteins. By MALDI-TOF mass spectrometry, we identified a total number of 449 different proteins. We show that 57 proteins of our map are over-represented in resting conidia compared to mycelium. Enzymes involved in reactive oxygen intermediates (ROI) detoxification, pigment biosynthesis, and conidial rodlet layer formation were highly abundant in A. fumigatus spores and most probably account for their enormous stress resistance. Interestingly, pyruvate decarboxylase and alcohol dehydrogenase were detectable in dormant conidia, suggesting that alcoholic fermentation plays a role during dormancy or early germination. Moreover, we show that enzymes for rapid reactivation of protein biosynthesis and metabolic processes are preserved in resting conidia, which therefore feature the potential to immediately respond to an environmental stimulus by germination. The generated data lay the foundations for further proteomic analyses and a better understanding of fungal pathogenesis.
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Affiliation(s)
- Janka Teutschbein
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
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Expression and export: recombinant protein production systems for Aspergillus. Appl Microbiol Biotechnol 2010; 87:1255-70. [DOI: 10.1007/s00253-010-2672-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/07/2010] [Accepted: 05/08/2010] [Indexed: 11/26/2022]
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Barros BHR, da Silva SH, dos ReisMarques EDR, Rosa JC, Yatsuda AP, Roberts DW, Braga GUL. A proteomic approach to identifying proteins differentially expressed in conidia and mycelium of the entomopathogenic fungus Metarhizium acridum. Fungal Biol 2010; 114:572-9. [PMID: 20943168 DOI: 10.1016/j.funbio.2010.04.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 04/07/2010] [Accepted: 04/20/2010] [Indexed: 11/26/2022]
Abstract
Metarhizium spp. is an important worldwide group of entomopathogenic fungi used as an interesting alternative to chemical insecticides in programs of agricultural pest and disease vector control. Metarhizium conidia are important in fungal propagation and also are responsible for host infection. Despite their importance, several aspects of conidial biology, including their proteome, are still unknown. We have established conidial and mycelial proteome reference maps for Metarhizium acridum using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS). In all, 1130±102 and 1200±97 protein spots were detected in ungerminated conidia and fast-growing mycelia, respectively. Comparison of the two protein-expression profiles reveled that only 35% of the protein spots were common to both developmental stages. Out of 94 2-DE protein spots (65 from conidia, 25 from mycelia and two common to both) analyzed using mass spectrometry, seven proteins from conidia, 15 from mycelia and one common to both stages were identified. The identified protein spots exclusive to conidia contained sequences similar to known fungal stress-protector proteins (such as heat shock proteins (HSP) and 6-phosphogluconate dehydrogenase) plus the fungal allergen Alt a 7, actin and the enzyme cobalamin-independent methionine synthase. The identified protein spots exclusive to mycelia included proteins involved in several cell housekeeping biological processes. Three proteins (HSP 90, 6-phosphogluconate dehydrogenase and allergen Alt a 7) were present in spots in conidial and mycelial gels, but they differed in their locations on the two gels.
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Affiliation(s)
- Bruno H R Barros
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 14040-903, Brazil
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Sørensen LM, Lametsch R, Andersen MR, Nielsen PV, Frisvad JC. Proteome analysis of Aspergillus niger: lactate added in starch-containing medium can increase production of the mycotoxin fumonisin B2 by modifying acetyl-CoA metabolism. BMC Microbiol 2009; 9:255. [PMID: 20003296 PMCID: PMC2807875 DOI: 10.1186/1471-2180-9-255] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2009] [Accepted: 12/10/2009] [Indexed: 12/01/2022] Open
Abstract
Background Aspergillus niger is a filamentous fungus found in the environment, on foods and feeds and is used as host for production of organic acids, enzymes and proteins. The mycotoxin fumonisin B2 was recently found to be produced by A. niger and hence very little is known about production and regulation of this metabolite. Proteome analysis was used with the purpose to reveal how fumonisin B2 production by A. niger is influenced by starch and lactate in the medium. Results Fumonisin B2 production by A. niger was significantly increased when lactate and starch were combined in the medium. Production of a few other A. niger secondary metabolites was affected similarly by lactate and starch (fumonisin B4, orlandin, desmethylkotanin and pyranonigrin A), while production of others was not (ochratoxin A, ochratoxin alpha, malformin A, malformin C, kotanin, aurasperone B and tensidol B). The proteome of A. niger was clearly different during growth on media containing 3% starch, 3% starch + 3% lactate or 3% lactate. The identity of 59 spots was obtained, mainly those showing higher or lower expression levels on medium with starch and lactate. Many of them were enzymes in primary metabolism and other processes that affect the intracellular level of acetyl-CoA or NADPH. This included enzymes in the pentose phosphate pathway, pyruvate metabolism, the tricarboxylic acid cycle, ammonium assimilation, fatty acid biosynthesis and oxidative stress protection. Conclusions Lactate added in a medium containing nitrate and starch can increase fumonisin B2 production by A. niger as well as production of some other secondary metabolites. Changes in the balance of intracellular metabolites towards a higher level of carbon passing through acetyl-CoA and a high capacity to regenerate NADPH during growth on medium with starch and lactate were found to be the likely cause of this effect. The results lead to the hypothesis that fumonisin production by A. niger is regulated by acetyl-CoA.
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Affiliation(s)
- Louise M Sørensen
- Department of Systems Biology, Søltofts Plads, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.
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Vödisch M, Albrecht D, Leßing F, Schmidt AD, Winkler R, Guthke R, Brakhage AA, Kniemeyer O. Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus. Proteomics 2009; 9:1407-15. [DOI: 10.1002/pmic.200800394] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Analysis of extracellular proteins of Aspergillus oryzae grown on soy sauce koji. Biosci Biotechnol Biochem 2009; 73:192-5. [PMID: 19129648 DOI: 10.1271/bbb.80500] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aspergillus oryzae AS 3.951 is widely used in Chinese soy sauce manufacture, but little is known about the profiles of the extracellular proteins from the culture of soybean koji. In this study, we carried out MALDI-TOF/TOF MS analysis of extracellular proteins during koji culture. Besides well-known proteins (TAA and Oryzin), a variety of aminopeptidase and proteases were identical at the proteome level. This suggests that A. oryzae AS 3.951 has a powerful capacity to digest soybean protein.
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Fungal secretomes—nature’s toolbox for white biotechnology. Appl Microbiol Biotechnol 2008; 80:381-8. [DOI: 10.1007/s00253-008-1572-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 06/09/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
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Kniemeyer O, Lessing F, Brakhage AA. Proteome analysis for pathogenicity and new diagnostic markers for Aspergillus fumigatus. Med Mycol 2008; 47 Suppl 1:S248-54. [PMID: 18651311 DOI: 10.1080/13693780802169138] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
With the completion of the Aspergillus fumigatus genome it is now possible to study protein regulation on a global scale. One of the most suitable protein separation techniques is based on 2D-gel electrophoresis, which allows the separation of proteins based on their charge and size in a gel matrix. In addition, gel-free proteomics techniques based on liquid-chromatography coupled with mass spectrometry have gained importance. With the application of proteomic tools a comprehensive overview about the proteins of A. fumigatus present or induced during environmental changes and stress conditions can be obtained. For A. fumigatus, several proteomic studies have already been published including the response of the fungus to oxidative stress that induced the up-regulation of many proteins including catalases and thioredoxin peroxidase. Since many of the identified proteins/genes were apparently regulated by a putative Saccharomyces cerevisiae Yap1 homolog, the corresponding gene of A. fumigatus was identified, designated Afyap1 and further characterized. In addition, some of the gene products expressed under stress conditions are also known fungal antigens, such as the thioredoxin peroxidase AspF3. Thus, besides pathogenicity studies, proteomics also delivers the tools to screen for new antigens which could improve the diagnosis of diseases caused by A. fumigatus.
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Affiliation(s)
- Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute (HKI), Jena, Germany.
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