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Gautam I, Yarava JR, Xu Y, Li R, Scott FJ, Mentink-Vigier F, Momany M, Latgé JP, Wang T. Comparative Analysis of Polysaccharide and Cell Wall Structure in Aspergillus nidulans and Aspergillus fumigatus by Solid-State NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607833. [PMID: 39185159 PMCID: PMC11343165 DOI: 10.1101/2024.08.13.607833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Invasive aspergillosis poses a significant threat to immunocompromised patients, leading to high mortality rates associated with these infections. Targeting the biosynthesis of cell wall carbohydrates is a promising strategy for antifungal drug development and will be advanced by a molecular-level understanding of the native structures of polysaccharides within their cellular context. Solid-state NMR spectroscopy has recently provided detailed insights into the cell wall organization of Aspergillus fumigatus, but genetic and biochemical evidence highlights species-specific differences among Aspergillus species. In this study, we employed a combination of 13C, 15N, and 1H-detection solid-state NMR, supplemented by Dynamic Nuclear Polarization (DNP), to compare the structural organization of cell wall polymers and their assembly in the cell walls of A. fumigatus and A. nidulans, both of which are key model organisms and human pathogens. The two species exhibited a similar rigid core architecture, consisting of chitin, α-glucan, and β-glucan, which contributed to comparable cell wall properties, including polymer dynamics, water retention, and supramolecular organization. However, differences were observed in the chitin, galactosaminogalactan, protein, and lipid content, as well as in the dynamics of galactomannan and the structure of the glucan matrix.
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Affiliation(s)
- Isha Gautam
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | | | - Yifan Xu
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Reina Li
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Faith J. Scott
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | | | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology, University of Crete, Heraklion, Greece
- Fungal Respiratory Infections Research Unit and SFR ICAT, University of Angers, France
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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Wang ZD, Wang BT, Jin L, Ruan HH, Jin FJ. Implications of carbon catabolite repression for Aspergillus-based cell factories: A review. Biotechnol J 2024; 19:e2300551. [PMID: 38403447 DOI: 10.1002/biot.202300551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 02/27/2024]
Abstract
Carbon catabolite repression (CCR) is a global regulatory mechanism that allows organisms to preferentially utilize a preferred carbon source (usually glucose) by suppressing the expression of genes associated with the utilization of nonpreferred carbon sources. Aspergillus is a large genus of filamentous fungi, some species of which have been used as microbial cell factories for the production of organic acids, industrial enzymes, pharmaceuticals, and other fermented products due to their safety, substrate convenience, and well-established post-translational modifications. Many recent studies have verified that CCR-related genetic alterations can boost the yield of various carbohydrate-active enzymes (CAZymes), even under CCR conditions. Based on these findings, we emphasize that appropriate regulation of the CCR pathway, especially the expression of the key transcription factor CreA gene, has great potential for further expanding the application of Aspergillus cell factories to develop strains for industrial CAZymes production. Further, the genetically modified CCR strains (chassis hosts) can also be used for the production of other useful natural products and recombinant proteins, among others. We here review the regulatory mechanisms of CCR in Aspergillus and its direct application in enzyme production, as well as its potential application in organic acid and pharmaceutical production to illustrate the effects of CCR on Aspergillus cell factories.
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Affiliation(s)
- Zhen-Dong Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Bao-Teng Wang
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Long Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Hong-Hua Ruan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Feng-Jie Jin
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
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Zheng L, Wang R, Fei Y, Pan Y, Zhou P, Shen R, Lan P. Fungal Secretomics Through iTRAQ-Based Analysis. Methods Mol Biol 2024; 2820:139-153. [PMID: 38941021 DOI: 10.1007/978-1-0716-3910-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Our understanding of how fungi respond and adapt to external environments can be increased by the comprehensive data sets of fungal-secreted proteins. Fungi produce a variety of secreted proteins, and environmental conditions can easily influence the fungal secretome. However, the low abundance of secreted proteins and their post-translational modifications make protein extraction more challenging. Hence, the enrichment of secreted proteins is a crucial procedure for secretome analysis. This chapter illustrates a protocol for iTRAQ-based quantitative secretome analysis describing the example of fungi exposed to different environmental conditions. The fungal-secreted proteins can be extracted by combining ultrafiltration and TCA-acetone precipitation. Subsequently, the secreted proteins can be identified and quantified by the iTRAQ-based quantitative proteomics approach.
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Affiliation(s)
- Lu Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ruonan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuchen Fei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yilin Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peijun Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ping Lan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- University of Chinese Academy of Sciences, Nanjing, China.
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Proteomic analysis of Aspergillus flavus reveals the antifungal action of Perilla frutescens essential oil by interfering with energy metabolism and defense function. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112660] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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6
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Abstract
Aspergillus fumigatus is a saprotrophic fungus; its primary habitat is the soil. In its ecological niche, the fungus has learned how to adapt and proliferate in hostile environments. This capacity has helped the fungus to resist and survive against human host defenses and, further, to be responsible for one of the most devastating lung infections in terms of morbidity and mortality. In this review, we will provide (i) a description of the biological cycle of A. fumigatus; (ii) a historical perspective of the spectrum of aspergillus disease and the current epidemiological status of these infections; (iii) an analysis of the modes of immune response against Aspergillus in immunocompetent and immunocompromised patients; (iv) an understanding of the pathways responsible for fungal virulence and their host molecular targets, with a specific focus on the cell wall; (v) the current status of the diagnosis of different clinical syndromes; and (vi) an overview of the available antifungal armamentarium and the therapeutic strategies in the clinical context. In addition, the emergence of new concepts, such as nutritional immunity and the integration and rewiring of multiple fungal metabolic activities occurring during lung invasion, has helped us to redefine the opportunistic pathogenesis of A. fumigatus.
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Affiliation(s)
- Jean-Paul Latgé
- School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Georgios Chamilos
- School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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Teixeira TR, Santos GSD, Armstrong L, Colepicolo P, Debonsi HM. Antitumor Potential of Seaweed Derived-Endophytic Fungi. Antibiotics (Basel) 2019; 8:E205. [PMID: 31683523 PMCID: PMC6963884 DOI: 10.3390/antibiotics8040205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/30/2022] Open
Abstract
The marine environment presents a high biodiversity and a valuable source of bioactive compounds with therapeutic and biotechnological potential. Among the organisms present in marine environment, the endophytic fungi isolated from seaweed stand out. These microorganisms have aroused interest in the scientific community regarding its various activities such as antiviral, antimicrobial, antioxidant, photoprotective, cytotoxic, genotoxic, anti-inflammatory, and anticancer, besides establishing important ecological relations with its hosts. Anticancer molecules derived from marine natural sources are a promising target against different types of cancer. The disease's high rates of morbidity and mortality affect millions of people world wild and the search for new therapeutic alternatives is needed. Thus, this review partially summarizes the methodologies for the isolation of seaweed-derived endophytic fungi, as well as describes the anticancer compounds isolated from such microorganisms, reported in the literature from 2009 to the present. In addition, it describes how some biotechnological processes can help in the discovery of bioactive compounds, especially with anticancer activity.
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Affiliation(s)
- Thaiz Rodrigues Teixeira
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, RibeirãoPreto, SP 14040903, Brazil.
| | - Gustavo Souza Dos Santos
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, RibeirãoPreto, SP 14040903, Brazil.
| | - Lorene Armstrong
- Department of Pharmaceutical Sciences, State University of Ponta Grossa, Ponta Grossa, PR 84030900, Brazil.
| | - Pio Colepicolo
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05508-000, Brazil.
| | - Hosana Maria Debonsi
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, RibeirãoPreto, SP 14040903, Brazil.
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Zhang L, Song X, Shao X, Wu Y, Zhang X, Wang S, Pan J, Hu S, Li Z. Lead immobilization assisted by fungal decomposition of organophosphate under various pH values. Sci Rep 2019; 9:13353. [PMID: 31527665 PMCID: PMC6746775 DOI: 10.1038/s41598-019-49976-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/04/2019] [Indexed: 11/08/2022] Open
Abstract
Organic phosphates (OP) account for approximately 30-90% of total soil P. However, it is too stable to be utilized by plants as available P source. Aspergillus niger (A. niger) has considerable ability to secret phytase to decompose OP. Meanwhile, mineralization of lead (Pb) is efficient to achieve its remediation. This study hence investigated Pb immobilization by A. niger assisted decomposition of OP under variable acidic environments. A. niger can survive in the acidic environment as low as pH = 1.5. However, alternation of environmental pH within 3.5-6.5 significantly changed fungal phytase secretion. In particular, weakly acidic stimulation (pH of ~5.5) increased phytase activity secreted by A. niger to 0.075 µmol/min/mL, hence elevating P release to a maximal concentration of ~20 mg/L. After Pb addition, ATR-IR and TEM results demonstrated the formation of abundant chloropyromorphite [Pb5(PO4)3Cl] mineral on the surface of mycelium at pH = 5.5. Anglesite, with a higher solubility than pyromorphite, was precipitated massively in other treatments with pH lower or higher than 5.5. This study elucidated the great potential of applying OP for Pb immobilization in contaminated water.
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Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xinwei Song
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiaoqing Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Yiling Wu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xinyu Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shimei Wang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jianjun Pan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shuijin Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
- Jiangsu Key Laboratory for Organic Waste Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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9
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Liu T, Zou LJ, Tian DW, Can QY, Zhu ML, Mo MH, Zhang KQ. Proteomic changes in Arthrobotrys oligospora conidia in response to benzaldehyde-induced fungistatic stress. J Proteomics 2018; 192:358-365. [PMID: 30282050 DOI: 10.1016/j.jprot.2018.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 11/26/2022]
Abstract
Soil fungistasis limits the effect of fungal agents designed to control plant-parasitic nematodes. Benzaldehyde is a fungistatic factor produced by soil microorganisms that can suppress conidial germination, but the molecular mechanism of this suppression is unknown. In this study, three conidial proteomes of Arthrobotrys oligospora ATCC24927, a nematode-trapping fungus, were obtained, quantified, and compared. Under benzaldehyde fungistatic stress, conidial protein expression profile changed significantly. Screening with a twofold selection criterion revealed 164 up-regulated and 110 down-regulated proteins. 17 proteins related to protein translation were down-regulated and gene transcription analysis suggested that the repression of proteins translation might be one mechanism by which benzaldehyde inhibites conidial germination. Benzaldehyde also resulted in the down-regulation of respiratory chain proteins and mitochondrial processes, as well as the repression of conidial DNA synthesis. In addition, the conidia up-regulated several proteins that enable it to resist benzaldehyde-induced fungistatis, and this was confirmed by a functional assessment of two knockout mutants. This study reveals putative mechanisms by which benzaldehyde causes fungistasis as well as the proteomic response of conidia to benzaldehyde. SIGNIFICANCE: Soil fungistasis limits the effect of fungal agents designed to control plant-parasitic nematodes. Benzaldehyde is one of fungistatic factors produced by soil microorganisms that can suppress conidial germination. In this study, we found that conidial protein expression profile changed significantly under benzaldehyde fungistatic stress. This research revealed new mechanistic data that describe how benzaldehyde is responsible for fungiststis by inhibiting conidial germination. Moreover, we also found that conidia can resist benzaldehyde by up-regulating proteins such as benzaldehyde dehydrogenase and heat shock proteins. This study also showed that proteomics methods play important roles in addressing soil fungistatic mechanisms.
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Affiliation(s)
- Tong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Li-Juan Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Dong-Wei Tian
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Qi-Yan Can
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou 450001, PR China
| | - Ming-Liang Zhu
- Yunnan of China National Tobacco Corporation, Kunming 650202, PR China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Engineering Research Center of Biocontrol of Plant Disease & Pest, Yunnan University, Kunming 650091, PR China.
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China; Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China.
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10
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Shankar J, Tiwari S, Shishodia SK, Gangwar M, Hoda S, Thakur R, Vijayaraghavan P. Molecular Insights Into Development and Virulence Determinants of Aspergilli: A Proteomic Perspective. Front Cell Infect Microbiol 2018; 8:180. [PMID: 29896454 PMCID: PMC5986918 DOI: 10.3389/fcimb.2018.00180] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/09/2018] [Indexed: 12/25/2022] Open
Abstract
Aspergillus species are the major cause of health concern worldwide in immunocompromised individuals. Opportunistic Aspergilli cause invasive to allergic aspergillosis, whereas non-infectious Aspergilli have contributed to understand the biology of eukaryotic organisms and serve as a model organism. Morphotypes of Aspergilli such as conidia or mycelia/hyphae helped them to survive in favorable or unfavorable environmental conditions. These morphotypes contribute to virulence, pathogenicity and invasion into hosts by excreting proteins, enzymes or toxins. Morphological transition of Aspergillus species has been a critical step to infect host or to colonize on food products. Thus, we reviewed proteins from Aspergilli to understand the biological processes, biochemical, and cellular pathways that are involved in transition and morphogenesis. We majorly analyzed proteomic studies on A. fumigatus, A. flavus, A. terreus, and A. niger to gain insight into mechanisms involved in the transition from conidia to mycelia along with the role of secondary metabolites. Proteome analysis of morphotypes of Aspergilli provided information on key biological pathways required to exit conidial dormancy, consortia of virulent factors and mycotoxins during the transition. The application of proteomic approaches has uncovered the biological processes during development as well as intermediates of secondary metabolite biosynthesis pathway. We listed key proteins/ enzymes or toxins at different morphological types of Aspergillus that could be applicable in discovery of novel therapeutic targets or metabolite based diagnostic markers.
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Affiliation(s)
- Jata Shankar
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Shraddha Tiwari
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Sonia K Shishodia
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Manali Gangwar
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
| | - Shanu Hoda
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Raman Thakur
- Genomic Laboratory, Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, India
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Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. Sci Rep 2018; 8:6617. [PMID: 29700415 PMCID: PMC5919931 DOI: 10.1038/s41598-018-25016-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
Aspergillus fumigatus and multiple other Aspergillus species cause a wide range of lung infections, collectively termed aspergillosis. Aspergilli are ubiquitous in environment with healthy immune systems routinely eliminating inhaled conidia, however, Aspergilli can become an opportunistic pathogen in immune-compromised patients. The aspergillosis mortality rate and emergence of drug-resistance reveals an urgent need to identify novel targets. Secreted and cell membrane proteins play a critical role in fungal-host interactions and pathogenesis. Using a computational pipeline integrating data from high-throughput experiments and bioinformatic predictions, we have identified secreted and cell membrane proteins in ten Aspergillus species known to cause aspergillosis. Small secreted and effector-like proteins similar to agents of fungal-plant pathogenesis were also identified within each secretome. A comparison with humans revealed that at least 70% of Aspergillus secretomes have no sequence similarity with the human proteome. An analysis of antigenic qualities of Aspergillus proteins revealed that the secretome is significantly more antigenic than cell membrane proteins or the complete proteome. Finally, overlaying an expression dataset, four A. fumigatus proteins upregulated during infection and with available structures, were found to be structurally similar to known drug target proteins in other organisms, and were able to dock in silico with the respective drug.
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12
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Schubert M, Spiegel H, Schillberg S, Nölke G. Aspergillus-specific antibodies - Targets and applications. Biotechnol Adv 2018; 36:1167-1184. [PMID: 29608951 DOI: 10.1016/j.biotechadv.2018.03.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/16/2022]
Abstract
Aspergillus is a fungal genus comprising several hundred species, many of which can damage the health of plants, animals and humans by direct infection and/or due to the production of toxic secondary metabolites known as mycotoxins. Aspergillus-specific antibodies have been generated against polypeptides, polysaccharides and secondary metabolites found in the cell wall or secretions, and these can be used to detect and monitor infections or to quantify mycotoxin contamination in food and feed. However, most Aspergillus-specific antibodies are generated against heterogeneous antigen preparations and the specific target remains unknown. Target identification is important because this can help to characterize fungal morphology, confirm host penetration by opportunistic pathogens, detect specific disease-related biomarkers, identify new candidate targets for antifungal drug design, and qualify antibodies for diagnostic and therapeutic applications. In this review, we discuss how antibodies are raised against heterogeneous Aspergillus antigen preparations and how they can be characterized, focusing on strategies to identify their specific antigens and epitopes. We also discuss the therapeutic, diagnostic and biotechnological applications of Aspergillus-specific antibodies.
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Affiliation(s)
- Max Schubert
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Holger Spiegel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; Justus-Liebig University Giessen, Institute for Phytopathology and Applied Zoology, Phytopathology Department, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
| | - Greta Nölke
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany
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13
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Quantitative proteomics revealed partial fungistatic mechanism of ammonia against conidial germination of nematode-trapping fungus Arthrobotrys oligospora ATCC24927. Int J Biochem Cell Biol 2018; 98:104-112. [PMID: 29544894 DOI: 10.1016/j.biocel.2018.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/20/2022]
Abstract
Ammonia is one of the fungistatic factors in soil that can suppress conidial germination, but the molecular mechanism underlying the suppression is unknown. In this study, the proteomes of fungistatic conidia, fresh conidia and germinated conidia of Arthrobotrys oligospora ATCC24927 were determined and quantified. The protein expression profile of fungistatic conidia was significantly different from those in the other two conditions. 281 proteins were down expressed in fungistatic conidia and characterized by GO annotation. Gene transcription analysis and inhibition of puromycin (a protein translation inhibitor) on conidial germination suggested that down expression of 33 protein translation related proteins might well result in repression of protein synthesis and inhibition of conidial germination. In addition, 16 down-expressed proteins were mapped to the Ras/mitogen-activated protein (Ras/MAP) regulatory networks which regulate conidial DNA synthesis. The conidial DNA synthesis was found to be definitely inhibited under by ammonia, and function studies of two Ras/MAP proteins by using knock-out strains provided partial evidence that Ras/MAP pathway regulate the conidial germination. These results suggested that down-expression of Ras/MAP related proteins might result in inhibition of DNA synthesis and finally result in inhibition conidial germination. This study revealed partial fungistatic mechanism of ammonia against conidial germination.
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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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15
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Poirier F, Boursier C, Mesnage R, Oestreicher N, Nicolas V, Vélot C. Proteomic analysis of the soil filamentous fungus Aspergillus nidulans exposed to a Roundup formulation at a dose causing no macroscopic effect: a functional study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25933-25946. [PMID: 28940012 DOI: 10.1007/s11356-017-0217-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Roundup® is a glyphosate-based herbicide (GBH) used worldwide both in agriculture and private gardens. Thus, it constitutes a substantial source of environmental contaminations, especially for water and soil, and may impact a number of non-target organisms essential for ecosystem balance. The soil filamentous fungus Aspergillus nidulans has been shown to be highly affected by a commercial formulation of Roundup® (R450), containing 450 g/L of glyphosate (GLY), at doses far below recommended agricultural application rate. In the present study, we used two-dimensional gel electrophoresis combined to mass spectrometry to analyze proteomic pattern changes in A. nidulans exposed to R450 at a dose corresponding to the no-observed-adverse-effect level (NOAEL) for macroscopic parameters (31.5 mg/L GLY among adjuvants). Comparative analysis revealed a total of 82 differentially expressed proteins between control and R450-treated samples, and 85% of them (70) were unambiguously identified. Their molecular functions were mainly assigned to cell detoxification and stress response (16%), protein synthesis (14%), amino acid metabolism (13%), glycolysis/gluconeogenesis/glycerol metabolism/pentose phosphate pathway (13%) and Krebs TCA cycle/acetyl-CoA synthesis/ATP metabolism (10%). These results bring new insights into the understanding of the toxicity induced by higher doses of this herbicide in the soil model organism A. nidulans. To our knowledge, this study represents the first evidence of protein expression modulation and, thus, possible metabolic disturbance, in response to an herbicide treatment at a dose that does not cause any visible effect. These data are likely to challenge the concept of "substantial equivalence" when applied to herbicide-tolerant plants.
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Affiliation(s)
- Florence Poirier
- Université Paris 13, UFR SMBH, Plateforme PPUP13, 1 rue de Chablis, 93017, Bobigny cedex, France
| | - Céline Boursier
- UMS-IPSIT, US31 Inserm-UMS3679 CNRS, Plateformes Trans-Prot et d'Imagerie Cellulaire, Université Paris-Sud, Faculté de Pharmacie, Tour E1, 5 Rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France
| | - Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, SE1 9RT, London, UK
- CRIIGEN, 81 rue Monceau, 75008, Paris, France
| | - Nathalie Oestreicher
- Laboratoire VEAC, Université Paris-Sud, Faculté des Sciences, Bât. 360, Rue du Doyen André Guinier, 91405, Orsay, France
- Pôle Risques MRSH-CNRS, Université de Caen, Esplanade de la Paix, 14032, Caen, France
| | - Valérie Nicolas
- UMS-IPSIT, US31 Inserm-UMS3679 CNRS, Plateformes Trans-Prot et d'Imagerie Cellulaire, Université Paris-Sud, Faculté de Pharmacie, Tour E1, 5 Rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France
| | - Christian Vélot
- CRIIGEN, 81 rue Monceau, 75008, Paris, France.
- Laboratoire VEAC, Université Paris-Sud, Faculté des Sciences, Bât. 360, Rue du Doyen André Guinier, 91405, Orsay, France.
- Pôle Risques MRSH-CNRS, Université de Caen, Esplanade de la Paix, 14032, Caen, France.
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Thakur R, Shankar J. Proteome Profile of Aspergillus terreus Conidia at Germinating Stage: Identification of Probable Virulent Factors and Enzymes from Mycotoxin Pathways. Mycopathologia 2017. [PMID: 28647921 DOI: 10.1007/s11046-017-0161-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Aspergillus terreus is an emerging opportunistic fungal pathogen that causes invasive aspergillosis in immunocompromised individuals. The main risk group of individuals for this organism is leukopenic patients, individuals having cancers, bone marrow transplant persons and those who have immunological disorders. The lack of early diagnostic marker for A. terreus and intrinsic resistance to Amphotericin B, further limits the successful therapy of A. terreus-associated infections. The germination of inhaled conidia is the key step to establish successful invasion in host tissues or organs. Thus, profiling of expressed proteins during germination of conidia not only shed light on proteins that are involved in invasion or virulence but may also provide early diagnostic markers. We used nanoLC-Q-TOF to study the proteome of germinating conidia (at 16 h time points) of A. terreus. We observed expression of 373 proteins in germinating conidia of A. terreus. A total of 74 proteins were uncharacterized in the database. The expressed proteins were associated with various processes like cell wall modulation, virulence factors and secondary metabolite biosynthesis. The most abundant proteins were associated with protein biosynthesis, carbohydrate metabolism and unknown functions. Among virulent proteins, mitogen-activated protein kinase (hog1) and mitogen-activated protein kinase (mpkC) are key virulent proteins observed in our study. We observed 7 enzymes from terretonin and 10 enzymes from geodin mycotoxin biosynthesis pathway. Interestingly, we observed expression of terrelysin protein, associated with blood cell lysis. Quantitative RT-PCR analysis showed 26-fold increase in transcripts encoding for dihydrogeodin oxidase and 885-fold for terrelysin gene in germinating conidia in comparison to conidia. Further, we propose that terrelysin protein and secondary metabolite such as geodin could be explored as diagnostic marker for A. terreus-associated infections.
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Affiliation(s)
- Raman Thakur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat Solan, Himachal Pradesh, 173234, India
| | - Jata Shankar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat Solan, Himachal Pradesh, 173234, India.
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Santussi WM, Bordon KCF, Rodrigues Alves APN, Cologna CT, Said S, Arantes EC. Antifungal Activity against Filamentous Fungi of Ts1, a Multifunctional Toxin from Tityus serrulatus Scorpion Venom. Front Microbiol 2017. [PMID: 28634472 PMCID: PMC5459920 DOI: 10.3389/fmicb.2017.00984] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Antimicrobial peptides (AMPs) are ubiquitous and multipotent components of the innate immune defense arsenal used by both prokaryotic and eukaryotic organisms. The search for new AMPs has increased in recent years, due to the growing development of microbial resistance to therapeutical drugs. In this work, we evaluate the effects of Tityus serrulatus venom (Tsv), its fractions and its major toxin Ts1, a beta-neurotoxin, on fungi growth. The fractions were obtained by ion-exchange chromatography of Tsv. The growth inhibition of 11 pathogenic and non-pathogenic filamentous fungi (Aspergillus fumigatus, A. nidulans, A. niger, A. terreus, Neurospora crassa, Penicillium corylophilum, P. ochrochloron, P. verrucosum, P. viridicatum, P. waksmanii, and Talaromyces flavus) was evaluated by quantitative microplate reader assay. Tsv (100 and 500 μg/well, which correspond to 1 and 5 mg/mL, respectively, of total soluble protein) was active in inhibiting growth of A. nidulans, A. terreus, P. corylophilum, and P. verrucosum, especially in the higher concentration used and at the first 30 h. After this period, fungi might have used Tsv components as alternative sources of nutrients, and therefore, increased their growth tax. Only fractions IX, X, XI, XIIA, XIIB (3 and 7.5 μg/well, which correspond to 30 and 75 μg/mL, respectively, of total soluble protein) and Ts1 (1.5, 3, and 6 μg/well, which correspond to 2.18, 4.36, and 8.72 μM, respectively) showed antifungal activity. Ts1 showed to be a non-morphogenic toxin with dose-dependent activity against A. nidulans, inhibiting 100% of fungal growth from 3 μg/well (4.36 μM). The inhibitory effect of Ts1 against A. nidulans growth was accompanied by fungistatic effects and was not amended by 1 mM CaCl2 or tetrodotoxin (46.98 and 93.96 μM). The structural differences between Ts1 and drosomycin, a potent cysteine-rich antifungal peptide, are discussed here. Our results highlight the antifungal potential of the first cysteine-containing scorpion toxin. Since Ts1 is a multifunctional toxin, we suggest that it could be used as a template in the design of engineered scorpion AMPs and in the search for new mechanisms of action of antifungal drugs.
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Affiliation(s)
- Welligton M Santussi
- Laboratory of Animal Toxins, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São PauloRibeirão Preto, Brazil
| | - Karla C F Bordon
- Laboratory of Animal Toxins, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São PauloRibeirão Preto, Brazil
| | - Ana P N Rodrigues Alves
- Laboratory of Animal Toxins, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São PauloRibeirão Preto, Brazil
| | - Camila T Cologna
- Laboratory of Animal Toxins, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São PauloRibeirão Preto, Brazil
| | - Suraia Said
- Laboratory of Industrial Enzymology, Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São PauloRibeirão Preto, Brazil
| | - Eliane C Arantes
- Laboratory of Animal Toxins, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São PauloRibeirão Preto, Brazil
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18
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Proteomics as a Tool to Identify New Targets Against Aspergillus and Scedosporium in the Context of Cystic Fibrosis. Mycopathologia 2017; 183:273-289. [PMID: 28484941 DOI: 10.1007/s11046-017-0139-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/25/2017] [Indexed: 12/26/2022]
Abstract
Cystic fibrosis (CF) is a genetic disorder that increases the risk of suffering microbial, including fungal, infections. In this paper, proteomics-based information was collated relating to secreted and cell wall proteins with potential medical applications from the most common filamentous fungi in CF, i.e., Aspergillus and Scedosporium/Lomentospora species. Among the Aspergillus fumigatus secreted allergens, β-1,3-endoglucanase, the alkaline protease 1 (Alp1/oryzin), Asp f 2, Asp f 13/15, chitinase, chitosanase, dipeptidyl-peptidase V (DppV), the metalloprotease Asp f 5, mitogillin/Asp f 1, and thioredoxin reductase receive a special mention. In addition, the antigens β-glucosidase 1, catalase, glucan endo-1,3-β-glucosidase EglC, β-1,3-glucanosyltransferases Gel1 and Gel2, and glutaminase A were also identified in secretomes of other Aspergillus species associated with CF: Aspergillus flavus, Aspergillus niger, Aspergillus nidulans, and Aspergillus terreus. Regarding cell wall proteins, cytochrome P450 and eEF-3 were proposed as diagnostic targets, and alkaline protease 2 (Alp2), Asp f 3 (putative peroxiredoxin pmp20), probable glycosidases Asp f 9/Crf1 and Crf2, GPI-anchored protein Ecm33, β-1,3-glucanosyltransferase Gel4, conidial hydrophobin Hyp1/RodA, and secreted aspartyl protease Pep2 as protective vaccines in A. fumigatus. On the other hand, for Scedosporium/Lomentospora species, the heat shock protein Hsp70 stands out as a relevant secreted and cell wall antigen. Additionally, the secreted aspartyl proteinase and an ortholog of Asp f 13, as well as the cell wall endo-1,3-β-D-glucosidase and 1,3-β-glucanosyl transferase, were also found to be significant proteins. In conclusion, proteins mentioned in this review may be promising candidates for developing innovative diagnostic and therapeutic tools for fungal infections in CF patients.
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Pellon A, Ramirez-Garcia A, Buldain I, Antoran A, Rementeria A, Hernando FL. Molecular and cellular responses of the pathogenic fungus Lomentospora prolificans to the antifungal drug voriconazole. PLoS One 2017; 12:e0174885. [PMID: 28362854 PMCID: PMC5376303 DOI: 10.1371/journal.pone.0174885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/16/2017] [Indexed: 11/18/2022] Open
Abstract
The filamentous fungus Lomentospora (Scedosporium) prolificans is an emerging opportunistic pathogen associated with fatal infections in patients with disturbed immune function. Unfortunately, conventional therapies are hardly of any use against this fungus due to its intrinsic resistance. Therefore, we performed an integrated study of the L. prolificans responses to the first option to treat these mycoses, namely voriconazole, with the aim of unveiling mechanisms involved in the resistance to this compound. To do that, we used a wide range of techniques, including fluorescence and electron microscopy to study morphological alterations, ion chromatography to measure changes in cell-wall carbohydrate composition, and proteomics-based techniques to identify the proteins differentially expressed under the presence of the drug. Significantly, we showed drastic changes occurring in cell shape after voriconazole exposure, L. prolificans hyphae being shorter and wider than under control conditions. Interestingly, we proved that the architecture and carbohydrate composition of the cell wall had been modified in the presence of the drug. Specifically, L. prolificans constructed a more complex organelle with a higher presence of glucans and mannans. In addition to this, we identified several differentially expressed proteins, including Srp1 and heat shock protein 70 (Hsp70), as the most overexpressed under voriconazole-induced stress conditions. The mechanisms described in this study, which may be directly related to L. prolificans antifungal resistance or tolerance, could be used as targets to improve existing therapies or to develop new ones in order to successfully eliminate these mycoses.
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Affiliation(s)
- Aize Pellon
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Andoni Ramirez-Garcia
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
- * E-mail:
| | - Idoia Buldain
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Aitziber Antoran
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Aitor Rementeria
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fernando L. Hernando
- Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
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20
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Cui S, Wang T, Hu H, Liu L, Song A, Chen H. Investigating the expression of F10 and G11 xylanases in Aspergillus niger A09 with qPCR. Can J Microbiol 2016; 62:744-52. [DOI: 10.1139/cjm-2015-0394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There exist significant differences between the 2 main types of xylanases, family F10 and G11. A clear understanding of the expression pattern of microbial F10 and G11 under different culture conditions would facilitate better production and industrial application of xylanase. In this study, the fungal xylanase producer Aspergillus niger A09 was systematically investigated in terms of induced expression of xylanase F10 and G11. Results showed that carbon and nitrogen sources could influence xylanase F10 and G11 transcript abundance, with G11 more susceptible to changes in culture media composition. The most favorable carbon and nitrogen sources for high G11 and low F10 production by A. niger A09 were xylan (2%) and (NH4)2C2O4 (0.3%), respectively. Following cultivation at 33 °C for 60 h, the highest xylanase activity (1132 IU per gram of wet mycelia) was observed. On the basis of differential gene expression of F10 and G11, as well as their different properties, we deduced that the F10 protein initially targeted xylan and hydrolyzed it into fragments including xylose, after which xylose acted as the inducer of F10 and G11 gene expression. These speculations also accounted for our failure to identify conditions favoring the high production of F10 but a low production of G11.
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Affiliation(s)
- Shixiu Cui
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
| | - Tianwen Wang
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Hong Hu
- Institute of Biology Co., Ltd., Henan Academy of Sciences, Zhengzhou 450008, People’s Republic of China
| | - Liangwei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
| | - Andong Song
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, People’s Republic of China
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21
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Volke-Sepulveda T, Salgado-Bautista D, Bergmann C, Wells L, Gutierrez-Sanchez G, Favela-Torres E. Secretomic Insight into Glucose Metabolism of Aspergillus brasiliensis in Solid-State Fermentation. J Proteome Res 2016; 15:3856-3871. [PMID: 27548361 DOI: 10.1021/acs.jproteome.6b00663] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The genus Aspergillus is ubiquitous in nature and includes various species extensively exploited industrially due to their ability to produce and secrete a variety of enzymes and metabolites. Most processes are performed in submerged fermentation (SmF); however, solid-state fermentation (SSF) offers several advantages, including lower catabolite repression and substrate inhibition and higher productivity and stability of the enzymes produced. This study aimed to explain the improved metabolic behavior of A. brasiliensis ATCC9642 in SSF at high glucose concentrations through a proteomic approach. Online respirometric analysis provided reproducible samples for secretomic studies when the maximum CO2 production rate occurred, ensuring consistent physiological states. Extracellular extracts from SSF cultures were treated by SDS-PAGE, digested with trypsin, and analyzed by LC-MS/MS. Of 531 sequences identified, 207 proteins were analyzed. Twenty-five were identified as the most abundant unregulated proteins; 87 were found to be up-regulated and 95 were down-regulated with increasing glucose concentration. Of the regulated proteins, 120 were enzymes, most involved in the metabolism of carbohydrates (51), amino acids (23), and nucleotides (9). This study shows the high protein secretory activity of A. brasiliensis under SSF conditions. High glucose concentration favors catabolic activities, while some stress-related proteins and those involved in proteolysis are down-regulated.
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Affiliation(s)
- Tania Volke-Sepulveda
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina, Distrito Federal, C.P. 09340, México
| | - Daniel Salgado-Bautista
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina, Distrito Federal, C.P. 09340, México
| | - Carl Bergmann
- Complex Carbohydrate Research Center , 315 Riverbend Road, Athens, Georgia 30605, United States
| | - Lance Wells
- Complex Carbohydrate Research Center , 315 Riverbend Road, Athens, Georgia 30605, United States
| | | | - Ernesto Favela-Torres
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina, Distrito Federal, C.P. 09340, México
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22
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Silber J, Kramer A, Labes A, Tasdemir D. From Discovery to Production: Biotechnology of Marine Fungi for the Production of New Antibiotics. Mar Drugs 2016; 14:md14070137. [PMID: 27455283 PMCID: PMC4962027 DOI: 10.3390/md14070137] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/06/2016] [Accepted: 07/12/2016] [Indexed: 02/02/2023] Open
Abstract
Filamentous fungi are well known for their capability of producing antibiotic natural products. Recent studies have demonstrated the potential of antimicrobials with vast chemodiversity from marine fungi. Development of such natural products into lead compounds requires sustainable supply. Marine biotechnology can significantly contribute to the production of new antibiotics at various levels of the process chain including discovery, production, downstream processing, and lead development. However, the number of biotechnological processes described for large-scale production from marine fungi is far from the sum of the newly-discovered natural antibiotics. Methods and technologies applied in marine fungal biotechnology largely derive from analogous terrestrial processes and rarely reflect the specific demands of the marine fungi. The current developments in metabolic engineering and marine microbiology are not yet transferred into processes, but offer numerous options for improvement of production processes and establishment of new process chains. This review summarises the current state in biotechnological production of marine fungal antibiotics and points out the enormous potential of biotechnology in all stages of the discovery-to-development pipeline. At the same time, the literature survey reveals that more biotechnology transfer and method developments are needed for a sustainable and innovative production of marine fungal antibiotics.
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Affiliation(s)
- Johanna Silber
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
| | - Annemarie Kramer
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
| | - Antje Labes
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
| | - Deniz Tasdemir
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Marine Natural Products Chemistry Research Unit, GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Am Kiel-Kanal 44, Kiel 24106, Germany.
- Faculty of Mathematics and Natural Sciences, University of Kiel, Christian-Albrechts-Platz 4, Kiel 24118, Germany.
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23
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Piras C, Roncada P, Rodrigues PM, Bonizzi L, Soggiu A. Proteomics in food: Quality, safety, microbes, and allergens. Proteomics 2016; 16:799-815. [PMID: 26603968 DOI: 10.1002/pmic.201500369] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/21/2015] [Accepted: 11/17/2015] [Indexed: 02/04/2023]
Abstract
Food safety and quality and their associated risks pose a major concern worldwide regarding not only the relative economical losses but also the potential danger to consumer's health. Customer's confidence in the integrity of the food supply could be hampered by inappropriate food safety measures. A lack of measures and reliable assays to evaluate and maintain a good control of food characteristics may affect the food industry economy and shatter consumer confidence. It is imperative to create and to establish fast and reliable analytical methods that allow a good and rapid analysis of food products during the whole food chain. Proteomics can represent a powerful tool to address this issue, due to its proven excellent quantitative and qualitative drawbacks in protein analysis. This review illustrates the applications of proteomics in the past few years in food science focusing on food of animal origin with some brief hints on other types. Aim of this review is to highlight the importance of this science as a valuable tool to assess food quality and safety. Emphasis is also posed in food processing, allergies, and possible contaminants like bacteria, fungi, and other pathogens.
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Affiliation(s)
- Cristian Piras
- Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli studi di Milano, Milano, Italy
| | - Paola Roncada
- Istituto Sperimentale Italiano L. Spallanzani, Milano, Italy
| | - Pedro M Rodrigues
- CCMAR, Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Luigi Bonizzi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli studi di Milano, Milano, Italy
| | - Alessio Soggiu
- Dipartimento di Scienze Veterinarie e Sanità Pubblica (DIVET), Università degli studi di Milano, Milano, Italy
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24
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Emri T, Szarvas V, Orosz E, Antal K, Park H, Han KH, Yu JH, Pócsi I. Core oxidative stress response in Aspergillus nidulans. BMC Genomics 2015; 16:478. [PMID: 26115917 PMCID: PMC4482186 DOI: 10.1186/s12864-015-1705-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 06/15/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The b-Zip transcription factor AtfA plays a key role in regulating stress responses in the filamentous fungus Aspergillus nidulans. To identify the core regulons of AtfA, we examined genome-wide expression changes caused by various stresses in the presence/absence of AtfA using A. nidulans microarrays. We also intended to address the intriguing question regarding the existence of core environmental stress response in this important model eukaryote. RESULTS Examination of the genome wide expression changes caused by five different oxidative stress conditions in wild type and the atfA null mutant has identified a significant number of stereotypically regulated genes (Core Oxidative Stress Response genes). The deletion of atfA increased the oxidative stress sensitivity of A. nidulans and affected mRNA accumulation of several genes under both unstressed and stressed conditions. The numbers of genes under the AtfA control appear to be specific to a stress-type. We also found that both oxidative and salt stresses induced expression of some secondary metabolite gene clusters and the deletion of atfA enhanced the stress responsiveness of additional clusters. Moreover, certain clusters were down-regulated by the stresses tested. CONCLUSION Our data suggest that the observed co-regulations were most likely consequences of the overlapping physiological effects of the stressors and not of the existence of a general environmental stress response. The function of AtfA in governing various stress responses is much smaller than anticipated and/or other regulators may play a redundant or overlapping role with AtfA. Both stress inducible and stress repressive regulations of secondary metabolism seem to be frequent features in A. nidulans.
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Affiliation(s)
- Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| | - Vera Szarvas
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| | - Erzsébet Orosz
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
| | - Károly Antal
- Department of Zoology, Faculty of Sciences, Eszterházy Károly College, Eszterházy út 1, H-3300, Eger, Hungary.
| | - HeeSoo Park
- Department of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI, 53706, USA.
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, 565-701, Wanju, Republic of Korea.
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI, 53706, USA.
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, P.O. Box 63, H-4032, Debrecen, Hungary.
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Yamada R, Yoshie T, Sakai S, Wakai S, Asai-Nakashima N, Okazaki F, Ogino C, Hisada H, Tsutsumi H, Hata Y, Kondo A. Effective saccharification of kraft pulp by using a cellulase cocktail prepared from genetically engineered Aspergillus oryzae. Biosci Biotechnol Biochem 2015; 79:1034-7. [DOI: 10.1080/09168451.2015.1006568] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Abstract
Kraft pulp is a promising feedstock for bioproduction. The efficiency of kraft pulp saccharification was improved by using a cellulase cocktail prepared from genetically engineered Aspergillus oryzae. Application of the cellulase cocktail was demonstrated by simultaneous saccharification and fermentation, using kraft pulp and non-cellulolytic yeast. Such application would make possible to do an efficient production of other chemicals from kraft pulp.
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Affiliation(s)
- Ryosuke Yamada
- Organization of Advanced Science and Technology, Kobe University, Kobe, Japan
| | - Toshihide Yoshie
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Shoji Sakai
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Satoshi Wakai
- Organization of Advanced Science and Technology, Kobe University, Kobe, Japan
| | | | - Fumiyoshi Okazaki
- Organization of Advanced Science and Technology, Kobe University, Kobe, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | | | | | - Yoji Hata
- Research Institute, Gekkeikan Sake Co. Ltd., Kyoto, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
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26
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Kamath KS, Kumar SS, Kaur J, Venkatakrishnan V, Paulsen IT, Nevalainen H, Molloy MP. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl 2015; 9:134-46. [DOI: 10.1002/prca.201400122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/27/2014] [Accepted: 11/18/2014] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sheemal Shanista Kumar
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Jashanpreet Kaur
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | | | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Mark P. Molloy
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
- Australian Proteome Analysis Facility; Macquarie University; Sydney Australia
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Heinekamp T, Schmidt H, Lapp K, Pähtz V, Shopova I, Köster-Eiserfunke N, Krüger T, Kniemeyer O, Brakhage AA. Interference of Aspergillus fumigatus with the immune response. Semin Immunopathol 2014; 37:141-52. [PMID: 25404120 PMCID: PMC4326658 DOI: 10.1007/s00281-014-0465-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/04/2014] [Indexed: 01/13/2023]
Abstract
Aspergillus fumigatus is a saprotrophic filamentous fungus and also the most prevalent airborne fungal pathogen of humans. Depending on the host’s immune status, the variety of diseases caused by A. fumigatus ranges from allergies in immunocompetent hosts to life-threatening invasive infections in patients with impaired immunity. In contrast to the majority of other Aspergillus species, which are in most cases nonpathogenic, A. fumigatus features an armory of virulence determinants to establish an infection. For example, A. fumigatus is able to evade the human complement system by binding or degrading complement regulators. Furthermore, the fungus interferes with lung epithelial cells, alveolar macrophages, and neutrophil granulocytes to prevent killing by these immune cells. This chapter summarizes the different strategies of A. fumigatus to manipulate the immune response. We also discuss the potential impact of recent advances in immunoproteomics to improve diagnosis and therapy of an A. fumigatus infection.
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Affiliation(s)
- Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Jena, Germany,
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28
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Pellon A, Ramirez-Garcia A, Antoran A, Fernandez-Molina JV, Abad-Diaz-de-Cerio A, Montañez D, Sevilla MJ, Rementeria A, Hernando FL. Scedosporium prolificans immunomes against human salivary immunoglobulin A. Fungal Biol 2014; 118:94-105. [DOI: 10.1016/j.funbio.2013.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 11/25/2022]
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29
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Martins I, Hartmann DO, Alves PC, Planchon S, Renaut J, Leitão MC, Rebelo LP, Silva Pereira C. Proteomic alterations induced by ionic liquids in Aspergillus nidulans and Neurospora crassa. J Proteomics 2013; 94:262-78. [DOI: 10.1016/j.jprot.2013.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 09/13/2013] [Accepted: 09/27/2013] [Indexed: 02/03/2023]
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Kroll K, Pähtz V, Kniemeyer O. Elucidating the fungal stress response by proteomics. J Proteomics 2013; 97:151-63. [PMID: 23756228 DOI: 10.1016/j.jprot.2013.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
Abstract
Fungal species need to cope with stress, both in the natural environment and during interaction of human- or plant pathogenic fungi with their host. Many regulatory circuits governing the fungal stress response have already been discovered. However, there are still large gaps in the knowledge concerning the changes of the proteome during adaptation to environmental stress conditions. With the application of proteomic methods, particularly 2D-gel and gel-free, LC/MS-based methods, first insights into the composition and dynamic changes of the fungal stress proteome could be obtained. Here, we review the recent proteome data generated for filamentous fungi and yeasts. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Kristin Kroll
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany
| | - Vera Pähtz
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), 07747 Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany; Friedrich Schiller University, Institute of Microbiology, Philosophenweg 12, 07743 Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care Jena, University Hospital (CSCC), 07747 Jena, Germany.
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32
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Transcriptional changes in the transition from vegetative cells to asexual development in the model fungus Aspergillus nidulans. EUKARYOTIC CELL 2012; 12:311-21. [PMID: 23264642 DOI: 10.1128/ec.00274-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Morphogenesis encompasses programmed changes in gene expression that lead to the development of specialized cell types. In the model fungus Aspergillus nidulans, asexual development involves the formation of characteristic cell types, collectively known as the conidiophore. With the aim of determining the transcriptional changes that occur upon induction of asexual development, we have applied massive mRNA sequencing to compare the expression pattern of 19-h-old submerged vegetative cells (hyphae) with that of similar hyphae after exposure to the air for 5 h. We found that the expression of 2,222 (20.3%) of the predicted 10,943 A. nidulans transcripts was significantly modified after air exposure, 2,035 being downregulated and 187 upregulated. The activation during this transition of genes that belong specifically to the asexual developmental pathway was confirmed. Another remarkable quantitative change occurred in the expression of genes involved in carbon or nitrogen primary metabolism. Genes participating in polar growth or sexual development were transcriptionally repressed, as were those belonging to the HogA/SakA stress response mitogen-activated protein (MAP) kinase pathway. We also identified significant expression changes in several genes purportedly involved in redox balance, transmembrane transport, secondary metabolite production, or transcriptional regulation, mainly binuclear-zinc cluster transcription factors. Genes coding for these four activities were usually grouped in metabolic clusters, which may bring regulatory implications for the induction of asexual development. These results provide a blueprint for further stage-specific gene expression studies during conidiophore development.
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Wiedner SD, Burnum KE, Pederson LM, Anderson LN, Fortuin S, Chauvigné-Hines LM, Shukla AK, Ansong C, Panisko EA, Smith RD, Wright AT. Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum. J Biol Chem 2012; 287:33447-59. [PMID: 22865858 PMCID: PMC3460446 DOI: 10.1074/jbc.m112.394106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/27/2012] [Indexed: 11/06/2022] Open
Abstract
Environmental adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised host lung. We hypothesized that exposure of the fungal pathogen to human serum would lead to significant alterations to the organism's physiology, including metabolic activity and stress response. Shifts in functional pathway and corresponding enzyme reactivity of A. fumigatus upon exposure to the human host may represent much needed prognostic indicators of fungal infection. To address this, we employed a multiplexed activity-based protein profiling (ABPP) approach coupled to quantitative mass spectrometry-based proteomics to measure broad enzyme reactivity of the fungus cultured with and without human serum. ABPP showed a shift from aerobic respiration to ethanol fermentation and utilization over time in the presence of human serum, which was not observed in serum-free culture. Our approach provides direct insight into this pathogen's ability to survive, adapt, and proliferate. Additionally, our multiplexed ABPP approach captured a broad swath of enzyme reactivity and functional pathways and provides a method for rapid assessment of the A. fumigatus response to external stimuli.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ellen A. Panisko
- the Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, Washington 99352
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34
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Knuf C, Nielsen J. Aspergilli: Systems biology and industrial applications. Biotechnol J 2012; 7:1147-55. [DOI: 10.1002/biot.201200169] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/25/2012] [Accepted: 07/10/2012] [Indexed: 12/12/2022]
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35
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Etxebeste O, Herrero-García E, Cortese MS, Garzia A, Oiartzabal-Arano E, de los Ríos V, Ugalde U, Espeso EA. GmcA is a putative glucose-methanol-choline oxidoreductase required for the induction of asexual development in Aspergillus nidulans. PLoS One 2012; 7:e40292. [PMID: 22792266 PMCID: PMC3390393 DOI: 10.1371/journal.pone.0040292] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/05/2012] [Indexed: 11/18/2022] Open
Abstract
Aspergillus nidulans asexual differentiation is induced by Upstream Developmental Activators (UDAs) that include the bZIP-type Transcription Factor (TF) FlbB. A 2D-PAGE/MS-MS-coupled screen for proteins differentially expressed in the presence and absence of FlbB identified 18 candidates. Most candidates belong to GO term classes involved in osmotic and/or oxidative stress response. Among these, we focused on GmcA, a putative glucose-methanol-choline oxidoreductase which is upregulated in a ΔflbB background. GmcA is not required for growth since no differences were detected in the radial extension upon deletion of gmcA. However, its activity is required to induce conidiation under specific culture conditions. A ΔgmcA strain conidiates profusely under acid conditions but displays a characteristic fluffy aconidial phenotype in alkaline medium. The absence of asexual development in a ΔgmcA strain can be suppressed, on one hand, using high concentrations of non-fermentable carbon sources like glycerol, and on the other hand, when the cMyb-type UDA TF flbD is overexpressed. Overall, the results obtained in this work support a role for GmcA at early stages of conidiophore initiation.
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Affiliation(s)
- Oier Etxebeste
- Department of Applied Chemistry, Faculty of Chemistry, University of The Basque Country, Manuel de Lardizabal, San Sebastian, Spain.
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36
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Kim JM, Park JA, Kim DH. Comparative proteomic analysis of chestnut blight fungus,Cryphonectria parasitica, under tannic-acid-inducing and hypovirus-regulating conditions. Can J Microbiol 2012; 58:863-71. [DOI: 10.1139/w2012-065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chestnut blight fungus, Cryphonectria parasitica , and its hypovirus present a useful model system for investigating the mechanisms of hypoviral infection. To identify gene products associated with fungal pathogenicity and hypoviral regulation, we attempted a proteomic analysis of the virus-free EP155/2 strain and its isogenic virus-infected UEP1 strain in response to tannic acid (TA), which is abundant in the bark of chestnut trees. In this study, pretreatment of mycelia grown on TA-supplemented media was developed for proteomic analysis. Approximately 704 proteins from the mycelia of the EP155/2 strain were reproducibly present in 3 independent extractions. Among these, 111 and 79 spots were found to be responsive to hypovirus infection and TA supplementation, respectively. The TA-grown UEP1 strain yielded 28 spots showing an expression pattern different from that of untreated UEP1. Thirty protein spots showing considerable differences in spot density were selected for further analysis. Hybrid tandem LC-MS/MS spectrometry of the 30 selected protein spots revealed that 29 were identified while 1 was unidentified. Among the identified 29 proteins, 15 were metabolic enzymes; 5 were stress-related, of which 4 were heat-shock proteins and 1 was glutathione S-transferase; 5 were signaling and cellular process-related proteins; 2 were structural proteins; and 2 matched proteins of hypothetical genes.
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Affiliation(s)
- Jung-Mi Kim
- Department of Bio-Environmental Chemistry, Wonkwang University, Iksan, Chonbuk 570-749, Korea
| | - Jin-Ah Park
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, Chonbuk 561-756, Korea
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, Chonbuk 561-756, Korea
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37
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Suh MJ, Fedorova ND, Cagas SE, Hastings S, Fleischmann RD, Peterson SN, Perlin DS, Nierman WC, Pieper R, Momany M. Development stage-specific proteomic profiling uncovers small, lineage specific proteins most abundant in the Aspergillus Fumigatus conidial proteome. Proteome Sci 2012; 10:30. [PMID: 22545825 PMCID: PMC3424117 DOI: 10.1186/1477-5956-10-30] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 04/30/2012] [Indexed: 11/14/2022] Open
Abstract
Background The pathogenic mold Aspergillus fumigatus is the most frequent infectious cause of death in severely immunocompromised individuals such as leukemia and bone marrow transplant patients. Germination of inhaled conidia (asexual spores) in the host is critical for the initiation of infection, but little is known about the underlying mechanisms of this process. Results To gain insights into early germination events and facilitate the identification of potential stage-specific biomarkers and vaccine candidates, we have used quantitative shotgun proteomics to elucidate patterns of protein abundance changes during early fungal development. Four different stages were examined: dormant conidia, isotropically expanding conidia, hyphae in which germ tube emergence has just begun, and pre-septation hyphae. To enrich for glycan-linked cell wall proteins we used an alkaline cell extraction method. Shotgun proteomic resulted in the identification of 375 unique gene products with high confidence, with no evidence for enrichment of cell wall-immobilized and secreted proteins. The most interesting discovery was the identification of 52 proteins enriched in dormant conidia including 28 proteins that have never been detected in the A. fumigatus conidial proteome such as signaling protein Pil1, chaperones BipA and calnexin, and transcription factor HapB. Additionally we found many small, Aspergillus specific proteins of unknown function including 17 hypothetical proteins. Thus, the most abundant protein, Grg1 (AFUA_5G14210), was also one of the smallest proteins detected in this study (M.W. 7,367). Among previously characterized proteins were melanin pigment and pseurotin A biosynthesis enzymes, histones H3 and H4.1, and other proteins involved in conidiation and response to oxidative or hypoxic stress. In contrast, expanding conidia, hyphae with early germ tubes, and pre-septation hyphae samples were enriched for proteins responsible for housekeeping functions, particularly translation, respiratory metabolism, amino acid and carbohydrate biosynthesis, and the tricarboxylic acid cycle. Conclusions The observed temporal expression patterns suggest that the A. fumigatus conidia are dominated by small, lineage-specific proteins. Some of them may play key roles in host-pathogen interactions, signal transduction during conidial germination, or survival in hostile environments.
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Affiliation(s)
- Moo-Jin Suh
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Natalie D Fedorova
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Steven E Cagas
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - Susan Hastings
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | | | - Scott N Peterson
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - David S Perlin
- University of Medicine and Dentistry of New Jersey, Newark, NJ, USA
| | - William C Nierman
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Rembert Pieper
- The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
| | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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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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