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Wagner T, Pfeifle H, Hildebrand G, Zhang Y. Production of a Cheese-Like Aroma via Fermentation of Plant Proteins and Coconut Oil with the Basidiomycetes Cyclocybe aegerita and Trametes versicolor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6544-6553. [PMID: 38484109 DOI: 10.1021/acs.jafc.4c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Cheese is one of the most common dairy products and is characterized by its complex aroma. However, in times of climate change and resource scarcity, the possibility to mimic the characteristic cheese-like aroma from plant-based sources is in demand to offer alternatives to cheese. Accordingly, the production of a natural cheese-like aroma via fermentation of four plant-based proteins and coconut oil with basidiomycetes has been addressed. Mixtures of soy and sunflower protein with coconut oil (15 g/L) have shown the formation of a cheese-like aroma after 72 and 56 h after fermentation with Cyclocybe aegerita and Trametes versicolor, respectively. Isovaleric acid, butanoic acid, ethyl butanoate, 1-octen-3-ol, and various ketones were identified as the key odorants. Similarities to typical cheeses were observed by the principal component analysis. Overall, the finding offered an approach to a sustainable production of a natural cheese-like aroma from a plant source, thus contributing to the development of cheese alternatives.
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Affiliation(s)
- Tim Wagner
- Institute of Food Science and Biotechnology, Department of Flavor Chemistry, University of Hohenheim, Fruwirthstraße 12, Stuttgart 70599, Germany
| | - Helena Pfeifle
- Institute of Food Science and Biotechnology, Department of Flavor Chemistry, University of Hohenheim, Fruwirthstraße 12, Stuttgart 70599, Germany
| | - Gabriel Hildebrand
- Institute of Food Science and Biotechnology, Department of Flavor Chemistry, University of Hohenheim, Fruwirthstraße 12, Stuttgart 70599, Germany
| | - Yanyan Zhang
- Institute of Food Science and Biotechnology, Department of Flavor Chemistry, University of Hohenheim, Fruwirthstraße 12, Stuttgart 70599, Germany
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Sommer S, Hoffmann JL, Fraatz MA, Zorn H. Upcycling of black currant pomace for the production of a fermented beverage with Wolfiporia cocos. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:1313-1322. [PMID: 36936114 PMCID: PMC10020415 DOI: 10.1007/s13197-023-05677-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
Pomace as a side stream from black currant juice production is mostly discarded, even though it is rich in nutrients like protein, fiber, sugars, anthocyanins, polyphenols, and other secondary metabolites. Fungi from the division of Basidiomycota have a great enzymatic toolbox to recycle these complex mixtures of nutrients. In particular, the edible medicinal fungus Wolfiporia cocos has been described as a suitable biocatalyst to form pleasant aroma compounds in fermentation processes. Therefore, medium optimization, upscaling, and filtration were performed to produce a beverage based on black currant pomace fermented with W. cocos. A trained panel described the beverage as highly pleasant, reminiscent of honey, flowers and berries with a well-balanced sour and sweet taste. The flavor compounds linalool (citrus), geraniol (flowery), phenylacetic acid (honey), methyl phenylacetate (honey), eugenol (clove), and 2-phenylethanol (rose) were produced during fermentation and the concentrations exceeded their respective odor thresholds. The produced beverage was evaluated with 8.0 ± 1.4 from 10 for the question of whether panelists would buy the product. Fungal fermentation with the edible fungus W. cocos enabled the production of a highly pleasant beverage and additionally may reduce waste by using pomace and table sugar as sole ingredients. Supplementary Information The online version contains supplementary material available at 10.1007/s13197-023-05677-4.
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Affiliation(s)
- Svenja Sommer
- grid.8664.c0000 0001 2165 8627Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Janine Laura Hoffmann
- grid.8664.c0000 0001 2165 8627Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marco Alexander Fraatz
- grid.8664.c0000 0001 2165 8627Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- grid.418010.c0000 0004 0573 9904Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Holger Zorn
- grid.8664.c0000 0001 2165 8627Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- grid.418010.c0000 0004 0573 9904Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
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Aggarwal S, Dorairaj S, Adlakha N. Stoichiometric balance ratio of cellobiose and gentiobiose induces cellulase production in Talaromyces cellulolyticus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:48. [PMID: 36927685 PMCID: PMC10018878 DOI: 10.1186/s13068-023-02296-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND The exact mechanism by which fungal strains sense insoluble cellulose is unknown, but research points to the importance of transglycosylation products generated by fungi during cellulose breakdown. Here, we used multi-omics approach to identify the transglycosylation metabolites and determine their function in cellulase induction in a model strain, Talaromyces cellulolyticus MTCC25456. RESULTS Talaromyces sp. is a novel hypercellulolytic fungal strain. Based on genome scrutiny and biochemical analysis, we predicted the presence of cellulases on the surface of its spores. We performed metabolome analysis to show that these membrane-bound cellulases act on polysaccharides to form a mixture of disaccharides and their transglycosylated derivatives. Inevitably, a high correlation existed between metabolite data and the KEGG enrichment analysis of differentially expressed genes in the carbohydrate metabolic pathway. Analysis of the contribution of the transglycosylation product mixtures to cellulase induction revealed a 57% increase in total cellulase. Further research into the metabolites, using in vitro induction tests and response surface methodology, revealed that Talaromyces sp. produces cell wall-breaking enzymes in response to cellobiose and gentiobiose as a stimulant. Precisely, a 2.5:1 stoichiometric ratio of cellobiose to gentiobiose led to a 2.4-fold increase in cellulase synthesis. The application of the optimized inducers in cre knockout strain significantly increased the enzyme output. CONCLUSION This is the first study on the objective evaluation and enhancement of cellulase production using optimized inducers. Inducer identification and genetic engineering boosted the cellulase production in the cellulolytic fungus Talaromyces sp.
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Affiliation(s)
- Shivam Aggarwal
- Synthetic Biology and Bioprocessing Group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Sathish Dorairaj
- Synthetic Biology and Bioprocessing Group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India
| | - Nidhi Adlakha
- Synthetic Biology and Bioprocessing Group, Regional Centre for Biotechnology, NCR-Biotech Cluster, Faridabad, India.
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Tao A, Zhang H, Duan J, Xiao Y, Liu Y, Li J, Huang J, Zhong T, Yu X. Mechanism and application of fermentation to remove beany flavor from plant-based meat analogs: A mini review. Front Microbiol 2022; 13:1070773. [PMID: 36532431 PMCID: PMC9751450 DOI: 10.3389/fmicb.2022.1070773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/11/2022] [Indexed: 12/05/2022] Open
Abstract
Over the past few decades, there has been a noticeable surge in the market of plant-based meat analogs (PBMA). Such popularity stems from their environmentally friendly production procedures as well as their positive health effects. In order to meet the market demand, it is necessary to look for plant protein processing techniques that can help them match the quality of conventional meat protein from the aspects of sensory, quality and functionality. Bean proteins are ideal options for PBMA with their easy accessibility, high nutrient-density and reasonable price. However, the high polyunsaturated lipids content of beans inevitably leads to the unpleasant beany flavor of soy protein products, which severely affects the promotion of soy protein-based PBMA. In order to solve this issue, various methods including bleaching, enzyme and fermentation etc. are developed. Among these, fermentation is widely investigated due to its high efficiency, less harm to the protein matrix, targeted performance and low budget. In addition, proper utilization of microbiome during the fermentation process not only reduces the unpleasant beany flavors, but also enhances the aroma profile of the final product. In this review, we provide a thorough and succinct overview of the mechanism underlying the formation and elimination of beany flavor with associated fermentation process. The pros and cons of typical fermentation technologies for removing beany flavors are discussed in alongside with their application scenarios. Additionally, the variations among different methods are compared in terms of the strains, fermentation condition, target functionality, matrix for application, sensory perception etc.
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Affiliation(s)
- Anqi Tao
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Hongyu Zhang
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Junnan Duan
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China
| | - Yao Liu
- School of Pharmacy and Food Science, Zhuhai College of Science and Technology, Zhuhai, China
| | - Jianwei Li
- Macau Uni-Win Biotechnology Co., Ltd, Macau, Macau SAR, China
| | - Jieyu Huang
- Macau Uni-Win Biotechnology Co., Ltd, Macau, Macau SAR, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China,*Correspondence: Tian Zhong,
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China,Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China,Xi Yu,
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Chang H, Gacias Amengual N, Botz A, Schwaiger L, Kracher D, Scheiblbrandner S, Csarman F, Ludwig R. Investigating lytic polysaccharide monooxygenase-assisted wood cell wall degradation with microsensors. Nat Commun 2022; 13:6258. [PMID: 36271009 PMCID: PMC9586961 DOI: 10.1038/s41467-022-33963-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/10/2022] [Indexed: 12/25/2022] Open
Abstract
Lytic polysaccharide monooxygenase (LPMO) supports biomass hydrolysis by increasing saccharification efficiency and rate. Recent studies demonstrate that H2O2 rather than O2 is the cosubstrate of the LPMO-catalyzed depolymerization of polysaccharides. Some studies have questioned the physiological relevance of the H2O2-based mechanism for plant cell wall degradation. This study reports the localized and time-resolved determination of LPMO activity on poplar wood cell walls by measuring the H2O2 concentration in their vicinity with a piezo-controlled H2O2 microsensor. The investigated Neurospora crassa LPMO binds to the inner cell wall layer and consumes enzymatically generated H2O2. The results point towards a high catalytic efficiency of LPMO at a low H2O2 concentration that auxiliary oxidoreductases in fungal secretomes can easily generate. Measurements with a glucose microbiosensor additionally demonstrate that LPMO promotes cellobiohydrolase activity on wood cell walls and plays a synergistic role in the fungal extracellular catabolism and in industrial biomass degradation.
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Affiliation(s)
- Hucheng Chang
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Neus Gacias Amengual
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexander Botz
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Lorenz Schwaiger
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Kracher
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria ,grid.410413.30000 0001 2294 748XPresent Address: Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Stefan Scheiblbrandner
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Florian Csarman
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- grid.5173.00000 0001 2298 5320Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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Shabaev AV, Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi. Int J Mol Sci 2022; 23:ijms231810322. [PMID: 36142233 PMCID: PMC9499651 DOI: 10.3390/ijms231810322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
White-rot basidiomycete fungi are a unique group of organisms that evolved an unprecedented arsenal of extracellular enzymes for an efficient degradation of all components of wood such as cellulose, hemicelluloses and lignin. The exoproteomes of white-rot fungi represent a natural enzymatic toolbox for white biotechnology. Currently, only exoproteomes of a narrow taxonomic group of white-rot fungi—fungi belonging to the Polyporales order—are extensively studied. In this article, two white-rot fungi, Peniophora lycii LE-BIN 2142 from the Russulales order and Trametes hirsuta LE-BIN 072 from the Polyporales order, were compared and contrasted in terms of their enzymatic machinery used for degradation of different types of wood substrates—alder, birch and pine sawdust. Our findings suggested that the studied fungi use extremely different enzymatic systems for the degradation of carbohydrates and lignin. While T. hirsuta LE-BIN 072 behaved as a typical white-rot fungus, P. lycii LE-BIN 2142 demonstrated substantial peculiarities. Instead of using cellulolytic and hemicellulolytic hydrolytic enzymes, P. lycii LE-BIN 2142 primarily relies on oxidative polysaccharide-degrading enzymes such as LPMO and GMC oxidoreductase. Moreover, exoproteomes of P. lycii LE-BIN 2142 completely lacked ligninolytic peroxidases, a well-known marker of white-rot fungi, but instead contained several laccase isozymes and previously uncharacterized FAD-binding domain-containing proteins.
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7
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Gao L, Liu G, Zhao Q, Xiao Z, Sun W, Hao X, Liu X, Zhang Z, Zhang P. Customized optimization of lignocellulolytic enzyme cocktails for efficient conversion of pectin-rich biomass residues. Carbohydr Polym 2022; 297:120025. [DOI: 10.1016/j.carbpol.2022.120025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/18/2022] [Accepted: 08/21/2022] [Indexed: 11/02/2022]
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Trochine A, Bellora N, Nizovoy P, Duran R, Greif G, de García V, Batthyany C, Robello C, Libkind D. Genomic and proteomic analysis of Tausonia pullulans reveals a key role for a GH15 glucoamylase in starch hydrolysis. Appl Microbiol Biotechnol 2022; 106:4655-4667. [PMID: 35713658 DOI: 10.1007/s00253-022-12025-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022]
Abstract
Basidiomycetous yeasts remain an almost unexplored source of enzymes with great potential in several industries. Tausonia pullulans (Tremellomycetes) is a psychrotolerant yeast with several extracellular enzymatic activities reported, although the responsible genes are not known. We performed the genomic sequencing, assembly and annotation of T. pullulans strain CRUB 1754 (Perito Moreno glacier, Argentina), a gene survey of carbohydrate-active enzymes (CAZymes), and analyzed its secretome by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) after growth in glucose (GLU) or starch (STA) as main carbon sources. T. pullulans has 7210 predicted genes, 3.6% being CAZymes. When compared to other Tremellomycetes, it contains a high number of CAZy domains, and in particular higher quantities of glucoamylases (GH15), pectinolytic enzymes (GH28) and lignocellulose decay enzymes (GH7). When the secretome of T. pullulans was analyzed experimentally after growth in starch or glucose, 98 proteins were identified. The 60% of total spectral counts belonged to GHs, oxidoreductases and to other CAZymes. A 65 kDa glucoamylase of family GH15 (TpGA1) showed the highest fold change (tenfold increase in starch). This enzyme contains a conserved active site and showed extensive N-glycosylation. This study increases the knowledge on the extracellular hydrolytic enzymes of basidiomycetous yeasts and, in particular, establishes T. pullulans as a potential source of carbohydrate-active enzymes. KEY POINTS: • Tausonia pullulans genome harbors a high number of genes coding for CAZymes. • Among CAZy domains/families, the glycoside hydrolases are the most abundant. • Secretome analysis in glucose or starch as main C sources identified 98 proteins. • A 65 kDa GH15 glucoamylase showed the highest fold increase upon culture in starch.
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Affiliation(s)
- Andrea Trochine
- Centro de Referencia en Levaduras Y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas Y Geoambientales (IPATEC), CONICET-Universidad Nacional del Comahue, Quintral 1250, (CP8400) San Carlos de Bariloche, Río Negro, Argentina.
| | - Nicolás Bellora
- Instituto de Tecnologías Nucleares Para La Salud (INTECNUS), RP82, (CP8400) San Carlos de Bariloche, Río Negro, Argentina
| | - Paula Nizovoy
- Centro de Referencia en Levaduras Y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas Y Geoambientales (IPATEC), CONICET-Universidad Nacional del Comahue, Quintral 1250, (CP8400) San Carlos de Bariloche, Río Negro, Argentina
| | - Rosario Duran
- Institut Pasteur de Montevideo (IPMont), Mataojo 2020, (CP11400), Montevideo, Uruguay
- Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, (CP 11600), Montevideo, Uruguay
| | - Gonzalo Greif
- Institut Pasteur de Montevideo (IPMont), Mataojo 2020, (CP11400), Montevideo, Uruguay
| | - Virginia de García
- Instituto de Investigación Y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN), Buenos Aires 1400, (CP8300), Neuquén, Argentina
| | - Carlos Batthyany
- Institut Pasteur de Montevideo (IPMont), Mataojo 2020, (CP11400), Montevideo, Uruguay
- Facultad de Medicina (UDELAR), Av. Gral. Flores 2125, (CP1180), Montevideo, Uruguay
| | - Carlos Robello
- Institut Pasteur de Montevideo (IPMont), Mataojo 2020, (CP11400), Montevideo, Uruguay
- Facultad de Medicina (UDELAR), Av. Gral. Flores 2125, (CP1180), Montevideo, Uruguay
| | - Diego Libkind
- Centro de Referencia en Levaduras Y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas Y Geoambientales (IPATEC), CONICET-Universidad Nacional del Comahue, Quintral 1250, (CP8400) San Carlos de Bariloche, Río Negro, Argentina
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Bhalla A, Arce J, Ubanwa B, Singh G, Sani RK, Balan V. Thermophilic Geobacillus WSUCF1 Secretome for Saccharification of Ammonia Fiber Expansion and Extractive Ammonia Pretreated Corn Stover. Front Microbiol 2022; 13:844287. [PMID: 35694290 PMCID: PMC9176393 DOI: 10.3389/fmicb.2022.844287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
A thermophilic Geobacillus bacterial strain, WSUCF1 contains different carbohydrate-active enzymes (CAZymes) capable of hydrolyzing hemicellulose in lignocellulosic biomass. We used proteomic, genomic, and bioinformatic tools, and genomic data to analyze the relative abundance of cellulolytic, hemicellulolytic, and lignin modifying enzymes present in the secretomes. Results showed that CAZyme profiles of secretomes varied based on the substrate type and complexity, composition, and pretreatment conditions. The enzyme activity of secretomes also changed depending on the substrate used. The secretomes were used in combination with commercial and purified enzymes to carry out saccharification of ammonia fiber expansion (AFEX)-pretreated corn stover and extractive ammonia (EA)-pretreated corn stover. When WSUCF1 bacterial secretome produced at different conditions was combined with a small percentage of commercial enzymes, we observed efficient saccharification of EA-CS, and the results were comparable to using a commercial enzyme cocktail (87% glucan and 70% xylan conversion). It also opens the possibility of producing CAZymes in a biorefinery using inexpensive substrates, such as AFEX-pretreated corn stover and Avicel, and eliminates expensive enzyme processing steps that are used in enzyme manufacturing. Implementing in-house enzyme production is expected to significantly reduce the cost of enzymes and biofuel processing cost.
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Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
| | - Jessie Arce
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Bryan Ubanwa
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, India
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkatesh Balan
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
- *Correspondence: Venkatesh Balan,
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Modelling and Environmental Profile Associated with the Valorization of Wheat Straw as Carbon Source in the Biotechnological Production of Manganese Peroxidase. SUSTAINABILITY 2022. [DOI: 10.3390/su14084842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Interest in the development of biorefineries and biotechnological processes based on renewable resources has multiplied in recent years. This driving force is the result of the availability of lignocellulosic biomass and the range of applications that arise from its use and valorization. The approach of second-generation sugars from lignocellulosic biomass opens up the possibility of producing biotechnological products such as enzymes as a feasible alternative in the framework of biorefineries. It is in this context that this manuscript is framed, focusing on the modelling of a large-scale fermentative biotechnological process to produce the enzyme manganese peroxidase (MnP) by the fungus Irpex lacteus using wheat straw as a carbon source. The production scheme is based on the sequence of four stages: pretreatment of wheat straw, seed fermenters, enzyme production and downstream processes. For its environmental assessment, the Life Cycle Assessment methodology, which allows the identification and quantification of environmental impacts associated with the process, was utilized. As the main finding, the stages of the process with the highest environmental burdens are those of pretreatment and fermentation, mainly due to energy requirements. With the aim of proposing improvement scenarios, sensitivity analyses were developed around the identified hotspots. An improvement in the efficiency of steam consumption leads to a reduction of environmental damage of up to 30%.
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Sowa MA, Kreuter N, Sella N, Albuquerque W, Manhard J, Siegl A, Ghezellou P, Li B, Spengler B, Weichhard E, Rühl M, Zorn H, Gand M. Replacement of Pregastric Lipases in Cheese Production: Identification and Heterologous Expression of a Lipase from Pleurotus citrinopileatus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2998-3008. [PMID: 35213163 DOI: 10.1021/acs.jafc.1c07160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Traditionally produced piquant cheeses such as Feta or Provolone rely on pregastric lipolytic enzymes of animal origin to intensify flavor formation during ripening. Herein, we report a novel fungal lipase, derived from the phylum Basidiomycota to replace animal-derived products. A screening of 31 strains for the desired hydrolytic activities was performed, which revealed a promising fungal species. The secretome of an edible golden oyster mushroom, Pleurotus citrinopileatus, provided suitable enzymatic activity, and the coding sequence of the corresponding enzyme was identified by combining transcriptome and liquid chromatography high-resolution electrospray tandem mass spectroscopy (LC-HR-ESI-MS/MS) data. Recombinant expression in Escherichia coli BL21 (DE3) using chaperones GroES-GroEL and DnaK-DnaJ-GrpE was established. The recombinant lipolytic enzyme was purified and biochemically characterized in terms of thermal and pH stability, optimal reaction conditions, and kinetic data toward p-nitrophenyl esters. An application in the microscale production of Feta-type brine cheese revealed promising sensory properties, which were confirmed by headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS) analyses in comparison with the reference enzyme opti-zym z10uc from goat origin. Supplementation with 2.3 U of the heterologously expressed fungal lipase produced the most comparable free fatty acid profile after 30 days of ripening. The flavor and texture formed during the application of the new lipase from P. citrinopileatus proved to be competitive to the use of pregastric lipases and could therefore replace the products of animal origin.
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Affiliation(s)
- Miriam A Sowa
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Nadja Kreuter
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Nadine Sella
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Wendell Albuquerque
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Julia Manhard
- optiferm GmbH, Oberzollhauser Steige 4, Oy-Mittelberg 87466, Germany
| | - Alexander Siegl
- optiferm GmbH, Oberzollhauser Steige 4, Oy-Mittelberg 87466, Germany
| | - Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Binglin Li
- College of Food Science and Engineering, Northwest University, Tai Bai Bei Lu 229, Xi'an, Shaanxi 710000, China
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Edgar Weichhard
- optiferm GmbH, Oberzollhauser Steige 4, Oy-Mittelberg 87466, Germany
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Giessen 35392, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, Giessen 35392, Germany
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
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12
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Nedele AK, Bär A, Mayer N, Schiebelbein R, Zhang Y. Characterization of cheesy odor formed during fermentation of soy drink with Agrocybe aegerita. Food Chem 2022; 381:132170. [PMID: 35121327 DOI: 10.1016/j.foodchem.2022.132170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/04/2022]
Abstract
The market for plant protein-based substitutes for cheeses is growing, but the sensory properties are distinctively different from the original products. Hence, natural and vegan cheesy flavors are needed to aromatize the products. A cheesy, sweaty and parmesan-like aroma was produced by fermentation of soy drink with Agrocybe aegerita. Aroma dilution analysis revealed short-chain fatty acids (SCFAs) as main influencing cheesy odorants analyzed by gas chromatography-mass spectrometry-olfactometry. In comparison to the five cheese varieties, the SCFA profile of the fermented soy drink revealed similarities with Parmesan and Emmental cheese. Meanwhile, principal component analysis showed an approximation of the aroma profile after fermentation with A. aegerita to those of cheeses. 3-Methylbutanoic acid was synthesized from the protein fraction, while the oil fraction contributed to the formation of unbranched SCFAs like butanoic acid. Accordingly, the production of these compounds can be increased by addition of the fractions.
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Affiliation(s)
- Ann-Kathrin Nedele
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Alessa Bär
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Nicole Mayer
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Raphaela Schiebelbein
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Yanyan Zhang
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
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13
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Monclaro AV, Gorgulho Silva CDO, Gomes HAR, Moreira LRDS, Filho EXF. The enzyme interactome concept in filamentous fungi linked to biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126200. [PMID: 34710591 DOI: 10.1016/j.biortech.2021.126200] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Biomass represents an abundant and inexpensive source of sugars and aromatic compounds that can be used as raw materials for conversion into value-added bioproducts. Filamentous fungi are sources of plant cell wall degrading enzymes in nature. Understanding the interactions between enzymes is crucial for optimizing biomass degradation processes. Herein, the concept of the interactome is presented as a holistic approach that depicts the interactions among enzymes, substrates, metabolites, and inhibitors. The interactome encompasses several stages of biomass degradation, starting with the sensing of the substrate and the subsequent synthesis of hydrolytic and oxidative enzymes (fungus-substrate interaction). Enzyme-enzyme interactions are exemplified in the complex processes of lignocellulosic biomass degradation. The enzyme-substrate-metabolite-inhibitor interaction also provides a better understanding of biomass conversion, allowing bioproduct production from recalcitrant agro-industrial residues, thus bringing greater value to residual biomass. Finally, technological applications are presented for optimizing the interactome at various levels.
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Affiliation(s)
- Antonielle Vieira Monclaro
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; Center for Advanced Process Technology and Urban Resource Efficiency (CAPTURE), Frieda Saeysstraat, 9052 Ghent, Belgium
| | - Caio de Oliveira Gorgulho Silva
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432 Ås, Norway; Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Helder Andrey Rocha Gomes
- Health Science School, University Center of the Federal District (UDF), DF, Brasília 70390045, Brazil
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14
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Bahram M, Netherway T. Fungi as mediators linking organisms and ecosystems. FEMS Microbiol Rev 2021; 46:6468741. [PMID: 34919672 PMCID: PMC8892540 DOI: 10.1093/femsre/fuab058] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
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Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
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15
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Sommer S, Fraatz MA, Büttner J, Salem AA, Rühl M, Zorn H. Wild Strawberry-like Flavor Produced by the Fungus Wolfiporia cocos─Identification of Character Impact Compounds by Aroma Dilution Analysis after Dynamic Headspace Extraction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14222-14230. [PMID: 34786939 DOI: 10.1021/acs.jafc.1c05770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Brown-rot fungi are particularly suitable for the sustainable and cost-efficient biotechnological production of natural flavors. In this study, Wolfiporia cocos was employed for the fermentation of European black currant pomace supplemented with aspartate in surface cultures to produce a flavor reminiscent of wild strawberries. Aroma dilution analysis (ADA) by means of dynamic headspace extraction was developed as a suitable technique for solid samples. The character impact compounds were quantified by stable isotope dilution analysis and standard addition and validated by recombination experiments. (R)-Linalool (1879 μg kg-1, ADA 211), methyl anthranilate (2206 μg kg-1, 210), 2-aminobenzaldehyde (771 μg kg-1, 25), and geraniol (138 μg kg-1, 25) were identified as key aroma compounds. Recombination experiments demonstrated that the combination of the four analyzed compounds was responsible for the odor impression reminiscent of wild strawberries.
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Affiliation(s)
- Svenja Sommer
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Marco A Fraatz
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Julia Büttner
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Ahmed A Salem
- Agricultural Microbiology Department, Faculty of Agriculture, Benha University, Moshtohor, 13736 Benha, Qalyubia, Egypt
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
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16
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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17
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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18
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Cai Y, Ma X, Zhang Q, Yu F, Zhao Q, Huang W, Song J, Liu W. Physiological Characteristics and Comparative Secretome Analysis of Morchella importuna Grown on Glucose, Rice Straw, Sawdust, Wheat Grain, and MIX Substrates. Front Microbiol 2021; 12:636344. [PMID: 34113321 PMCID: PMC8185036 DOI: 10.3389/fmicb.2021.636344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/12/2021] [Indexed: 01/23/2023] Open
Abstract
Morels (Morchella sp.) are economically important edible macro-fungi, which can grow on various synthetic or semi-synthetic media. However, the complex nutritional metabolism and requirements of these fungi remain ill-defined. This study, based on the plant biomass commonly used in the artificial cultivation of morels, assessed and compared the growth characteristics and extracellular enzymes of Morchella importuna cultivated on glucose, rice straw, sawdust, wheat grain, and a mixture of equal proportions of the three latter plant substrates (MIX). M. importuna could grow on all five tested media but displayed significant variations in mycelial growth rate, biomass, and sclerotium yield on the different media. The most suitable medium for M. importuna was wheat and wheat-containing medium, followed by glucose, while rice straw and sawdust were the least suitable. A total of 268 secretory proteins were identified by liquid chromatography coupled with tandem mass spectrometry detection. Functional classification and label-free comparative analysis of these proteins revealed that carbohydrate-active enzyme (CAZYme) proteins were the predominant component of the secretome of M. importuna, followed by protease, peptidase, and other proteins. The abundances of CAZYme proteins differed among the tested media, ranging from 64% on glucose to 88% on rice straw. The CAZYme classes of glycoside hydrolases and carbohydrate-binding module were enriched in the five secretomes. Furthermore, the enzyme activities of CMCase, lignase, amylase, xylase, pNPCase, and pNPGase were detected during the continuous culture of M. importuna in MIX medium, and the relative expression of the corresponding genes were detected by quantitative real-time PCR. The combined data of growth potential, secretome, extracellular enzyme activity, and gene expression on different substrates inferred that M. importuna was weak in lignocellulose degradation but a good starch decomposer. Specifically, in terms of the degradation of cellulose, the ability to degrade cellulose into oligosaccharides was weaker compared with further degradation into monosaccharides, and this might be the speed-limiting step of cellulose utilization in M. importuna. In addition, M. importuna had a strong ability to decompose various hemicellulose glycosidic bonds, especially α- and β-galactosidase. Only a very few lignin-degradation-related proteins were detected, and these were in low abundance, consistent with the presence of weak lignin degradation ability. Furthermore, the presence of lipase and chitinase implied that M. importuna was capable of decomposition of its own mycelia in vitro. The study provides key data that facilitates a further understanding of the complex nutritional metabolism of M. importuna.
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Affiliation(s)
- YingLi Cai
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - XiaoLong Ma
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - QianQian Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, China
| | - FuQiang Yu
- Germplasm Bank of Wild Species in Southwestern China, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Qi Zhao
- Germplasm Bank of Wild Species in Southwestern China, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Wei Huang
- Institute of Applied Mycology, Southwest Forestry University, Kunming, China
| | - JiaXin Song
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, China
| | - Wei Liu
- Institute of Vegetable, Wuhan Academy of Agricultural Sciences, Wuhan, China.,Germplasm Bank of Wild Species in Southwestern China, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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19
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Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves LV, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol 2021; 97:6095729. [PMID: 33440006 PMCID: PMC7878174 DOI: 10.1093/femsec/fiab003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.
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Affiliation(s)
- Pilar Junier
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Celine Vallotton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Olivia C Trautschold
- Materials Science and Technology, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, CH, 1015, Lausanne, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Danae Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aaron Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Julia M Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Karen Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Demosthenes Morales
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | | | - Armand E K Dichosa
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Simone Lupini
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Hang N Nguyen
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Debora F Rodrigues
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | | | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
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20
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The Secretomes of Aspergillus japonicus and Aspergillus terreus Supplement the Rovabio ® Enzyme Cocktail for the Degradation of Soybean Meal for Animal Feed. J Fungi (Basel) 2021; 7:jof7040278. [PMID: 33917144 PMCID: PMC8067802 DOI: 10.3390/jof7040278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/24/2022] Open
Abstract
One of the challenges of the 21st century will be to feed more than 10 billion people by 2050. In animal feed, one of the promising approaches is to use agriculture by-products such as soybean meal as it represents a rich source of proteins. However, soybean meal proteins are embedded in a complex plant cell wall matrix, mostly composed of pectic polysaccharides, which are recalcitrant to digestion for animals and can cause digestive disorders in poultry breeding. In this study, we explored fungal diversity to find enzymes acting on soybean meal components. An exploration of almost 50 fungal strains enabled the identification of two strains (Aspergillus terreus and Aspergillus japonicus), which improved the solubilization of soybean meal in terms of polysaccharides and proteins. The two Aspergilli strains identified in the frame of this study offer a promising solution to process industrial food coproducts into suitable animal feed solutions.
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21
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Evaluation of Secretome Tenogenic Potential from Adipose Stem Cells (ACS) in Hypoxic Condition with Fresh Frozen Tendon Scaffold Using Scleraxis (Scx), Insulin-Like Growth Factor 1 (IGF-1) and Collagen Type 1. JOURNAL OF BIOMIMETICS BIOMATERIALS AND BIOMEDICAL ENGINEERING 2021. [DOI: 10.4028/www.scientific.net/jbbbe.49.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Various studies have been conducted to see the scaffold that supports the regeneration of tendon. This study aims to analyze thein vitrosecretome tenogenic potential produced by ASCs culture with fresh frozen tendon scaffold in hypoxic conditions. ELISA tests for Scx and IGF-1 levels in secretome were obtained from ASC culture with fresh frozen tendon scaffold under normoxic (21%) and hypoxia (2%) conditions. The immunohistochemical examination of COL-1 was also carried out on the 2ndand 6thdays of cell culture. The secretion of Scx and IGF-1 was increased in secretome from ASC cultures using a fresh frozen tendon scaffold compared with those which did not (p <0.05). In the normoxia condition, Scx and IGF-1 in secretome with fresh frozen tendons had better results than hypoxic conditions (p <0.05). The highest Scx levels were obtained in culture on the 6thday (p <0.05), while the highest IGF-1 levels were obtained in the culture on the 2ndday (p <0.05). There was an increase in the secretion of Scx and IGF-1 from ASC cultures with fresh frozen tendon scaffold under the hypoxic condition of 2%.
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22
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Valette N, Renou J, Boutilliat A, Fernández-González AJ, Gautier V, Silar P, Guyeux C, Charr JC, Cuenot S, Rose C, Gelhaye E, Morel-Rouhier M. OSIP1 is a self-assembling DUF3129 protein required to protect fungal cells from toxins and stressors. Environ Microbiol 2021; 23:1594-1607. [PMID: 33393164 DOI: 10.1111/1462-2920.15381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022]
Abstract
Secreted proteins are key players in fungal physiology and cell protection against external stressing agents and antifungals. Oak stress-induced protein 1 (OSIP1) is a fungal-specific protein with unknown function. By using Podospora anserina and Phanerochaete chrysosporium as models, we combined both in vivo functional approaches and biophysical characterization of OSIP1 recombinant protein. The P. anserina OSIP1Δ mutant showed an increased sensitivity to the antifungal caspofungin compared to the wild type. This correlated with the production of a weakened extracellular exopolysaccharide/protein matrix (ECM). Since the recombinant OSIP1 from P. chrysosporium self-assembled as fibers and was capable of gelation, it is likely that OSIP1 is linked to ECM formation that acts as a physical barrier preventing drug toxicity. Moreover, compared to the wild type, the OSIP1Δ mutant was more sensitive to oak extractives including chaotropic phenols and benzenes. It exhibited a strongly modified secretome pattern and an increased production of proteins associated to the cell-wall integrity signalling pathway, when grown on oak sawdust. This demonstrates that OSIP1 has also an important role in fungal resistance to extractive-induced stress.
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Affiliation(s)
- Nicolas Valette
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Julien Renou
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Alexis Boutilliat
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | | | - Valérie Gautier
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), Paris, 75205, France
| | - Philippe Silar
- Université Paris Diderot, Sorbonne Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain (LIED), Paris, 75205, France
| | - Christophe Guyeux
- Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, 16 route de Gray, Besançon, 25030, France
| | - Jean-Claude Charr
- Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, 16 route de Gray, Besançon, 25030, France
| | - Stéphane Cuenot
- Institut des Matériaux Jean Rouxel, Université de Nantes, 2 rue de la Houssinière, Nantes Cedex 3, 44322, France
| | - Christophe Rose
- Université de Lorraine, AgroParisTech, INRAE, UMR Silva, Nancy, 54000, France
| | - Eric Gelhaye
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
| | - Mélanie Morel-Rouhier
- Université de Lorraine, INRAE, Interactions Arbres/Micro-organismes (IAM), UMR 1136, Nancy, 54000, France
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Scope and limitations of biocatalytic carbonyl reduction with white-rot fungi. Bioorg Chem 2021; 108:104651. [PMID: 33508677 DOI: 10.1016/j.bioorg.2021.104651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/07/2021] [Indexed: 11/24/2022]
Abstract
The reductive activity of various basidiomycetous fungi towards carbonyl compounds was screened on an analytical level. Some strains displayed high reductive activities toward aromatic carbonyls and aliphatic ketones. Utilizing growing whole-cell cultures of Dichomitus albidofuscus, the reactions were up-scaled to a preparative level in an aqueous system. The reactions showed excellent selectivities and gave the respective alcohols in high yields. Carboxylic acids were also reduced to aldehydes and alcohols under the same conditions. In particular, benzoic, vanillic, ferulic, and p-coumaric acid were reduced to benzyl alcohol, vanillin, dihydroconiferyl alcohol and 1-hydroxy-3-(4-hydroxyphenyl)propan, respectively.
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Optimization of flow cytometry parameters for high-throughput screening of spores of the filamentous fungus Trichoderma reesei. J Biotechnol 2020; 321:78-86. [DOI: 10.1016/j.jbiotec.2020.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 11/22/2022]
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Haddad Momeni M, Leth ML, Sternberg C, Schoof E, Nielsen MW, Holck J, Workman CT, Hoof JB, Abou Hachem M. Loss of AA13 LPMOs impairs degradation of resistant starch and reduces the growth of Aspergillus nidulans. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:135. [PMID: 32774456 PMCID: PMC7405360 DOI: 10.1186/s13068-020-01775-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are often studied in simple models involving activity measurements of a single LPMO or a blend thereof with hydrolytic enzymes towards an insoluble substrate. However, the contribution of LPMOs to polysaccharide breakdown in complex cocktails of hydrolytic and oxidative enzymes, similar to fungal secretomes, remains elusive. Typically, two starch-specific AA13 LPMOs are encoded by mainly Ascomycota genomes. Here, we investigate the impact of LPMO loss on the growth and degradation of starches of varying resistance to amylolytic hydrolases by Aspergillus nidulans. RESULTS Deletion of the genes encoding AnAA13A that possesses a CBM20 starch-binding module, AnAA13B (lacking a CBM20) or both AA13 genes resulted in reduced growth on solid media with resistant, but not soluble processed potato starch. Larger size and amount of residual starch granules were observed for the AA13-deficient strains as compared to the reference and the impairment of starch degradation was more severe for the strain lacking AnAA13A based on a microscopic analysis. After 5 days of growth on raw potato starch in liquid media, the mount of residual starch was about fivefold higher for the AA13 gene deletion strains compared to the reference, which underscores the importance of LPMOs for degradation of especially resistant starches. Proteomic analyses revealed substantial changes in the secretomes of the double AA13 gene deletion, followed by the AnAA13A-deficient strain, whereas only a single protein was significantly different in the proteome of the AnAA13B-deficient strain as compared to the reference. CONCLUSIONS This study shows that the loss of AA13, especially the starch-binding AnAA13A, impairs degradation of resistant potato starch, but has limited impact on less-resistant wheat starch and no impact on processed solubilized starch. The effects of LPMO loss are more pronounced at the later stages of fungal growth, likely due to the accumulation of the less-accessible regions of the substrate. The striking impairment in granular starch degradation due to the loss of a single LPMO from the secretome offers insight into the crucial role played by AA13 in the breakdown of resistant starch and presents a methodological framework to analyse the contribution of distinct LPMOs towards semi-crystalline polysaccharides under in vivo conditions.
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Affiliation(s)
- Majid Haddad Momeni
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Maria Louise Leth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Claus Sternberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Erwin Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Maike Wennekers Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Christopher T. Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Jakob Blæsbjerg Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
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Nedele AK, Gross S, Rigling M, Zhang Y. Reduction of green off-flavor compounds: Comparison of key odorants during fermentation of soy drink with Lycoperdon pyriforme. Food Chem 2020; 334:127591. [PMID: 32721838 DOI: 10.1016/j.foodchem.2020.127591] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 02/02/2023]
Abstract
The consumption of soy drink in Western countries is limited due to its green off-flavor. Hence, fermentation of soy drink with Lycoperdon pyriforme to tailor the aroma has been investigated. After 28 h the green off-flavor was not perceived by 60% of the sensory panel (n = 23). Molecular sensory changes of soy drink during fermentation were decoded by means of direct immersion-stir bar sorptive extraction coupled with gas chromatography-mass spectrometry-olfactometry and aroma dilution analysis. The semi-quantification of key odorants revealed a significant decrease of the representative green odorants (i.e., hexanal, (E)-2-nonenal, (E,E)-2,4-decadienal) of soy drink, among of which hexanal even turned below its odor threshold. The quantitative reduction of these odorants correlated with the organoleptic difference. Besides that, nutritionally relevant parameters of soy drink including protein, fat, and polyphenol content kept consistent during the short fermentation process.
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Affiliation(s)
- Ann-Kathrin Nedele
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Sophie Gross
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Marina Rigling
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
| | - Yanyan Zhang
- Department of Flavor Chemistry, Institute of Food Science and Biotechnology, University of Hohenheim, Fruwirthstr. 12, 70599 Stuttgart, Germany.
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Ibrahimi H, Gadzovska‐Simic S, Tusevski O, Haziri A. Generation of flavor compounds by biotransformation of genetically modified hairy roots of Hypericum perforatum (L.) with basidiomycetes. Food Sci Nutr 2020; 8:2809-2816. [PMID: 32566198 PMCID: PMC7300056 DOI: 10.1002/fsn3.1573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/16/2020] [Accepted: 03/22/2020] [Indexed: 11/11/2022] Open
Abstract
Altogether, 14 basidiomycetes (12BAD, 95PCH, 9WCOC, 5PSA, 96BCI, 331SHIBD, 4MSC, 74HFA, 220MPS, 115PFLA, 111 ICO C, 16LED, 6TSU, and 61LYP) were grown on solid and in liquid media using hairy roots of genetically modified Hypericum perforatum (L.) as the only source of carbon and nitrogen. After the first screening by GC-MS/MS-O, two fungi (115PFLA and 61LYP) which resulted in the most pleasant complex natural flavor by biotransformation were selected for further analysis. Twenty-four new volatile compounds were produced, from which 21 were identified (ethyl hexanoate, ethyl octanoate, benzaldehyde, 2-undecanone, (E,E)-2,4-decadienal, 1-octen-3-one, (E)-2-nonenal, ethyl nonanoate, 2-heptenal, 1-methoxy-4-methylbenzene, 3-octanone, 1-decen-3-one, (E)-2-octenal, 1-octen-3-ol, β-linalool, ±trans-nerolidol, anisole, methyl benzoate, 2-pentylfuran, 1,3-dichloro-2-methoxybenzene, and 1-dodecanol). Thereof, 15 compounds were perceived at the ODP, from which 13 were identified. Compound identification was performed by comparison of Kovats indices (KI) and mass spectra to those of authentic reference compounds on a polar VF-WAXms column using headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS).
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Affiliation(s)
- Hamide Ibrahimi
- Department of ChemistryFaculty of Natural Science and MathematicsUniversity of Prishtina “Hasan Prishtina”PrishtinaKosovo
| | - Sonja Gadzovska‐Simic
- Department of Plant PhysiologyFaculty of Natural Science and MathematicsSs. Cyril and Methodius UniversitySkopjeNorth Macedonia
| | - Oliver Tusevski
- Department of Plant PhysiologyFaculty of Natural Science and MathematicsSs. Cyril and Methodius UniversitySkopjeNorth Macedonia
| | - Arben Haziri
- Department of ChemistryFaculty of Natural Science and MathematicsUniversity of Prishtina “Hasan Prishtina”PrishtinaKosovo
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28
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Enzymes to unravel bioproducts architecture. Biotechnol Adv 2020; 41:107546. [PMID: 32275940 DOI: 10.1016/j.biotechadv.2020.107546] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022]
Abstract
Enzymes are essential and ubiquitous biocatalysts involved in various metabolic pathways and used in many industrial processes. Here, we reframe enzymes not just as biocatalysts transforming bioproducts but also as sensitive probes for exploring the structure and composition of complex bioproducts, like meat tissue, dairy products and plant materials, in both food and non-food bioprocesses. This review details the global strategy and presents the most recent investigations to prepare and use enzymes as relevant probes, with a focus on glycoside-hydrolases involved in plant deconstruction and proteases and lipases involved in food digestion. First, to expand the enzyme repertoire to fit bioproduct complexity, novel enzymes are mined from biodiversity and can be artificially engineered. Enzymes are further characterized by exploring sequence/structure/dynamics/function relationships together with the environmental factors influencing enzyme interactions with their substrates. Then, the most advanced experimental and theoretical approaches developed for exploring bioproducts at various scales (from nanometer to millimeter) using active and inactive enzymes as probes are illustrated. Overall, combining multimodal and multiscale approaches brings a better understanding of native-form or transformed bioproduct architecture and composition, and paves the way to mainstream the use of enzymes as probes.
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Torres-Barajas LR, Alvarez-Zúñiga MT, Mendoza-Hernández G, Aguilar-Osorio G. Analysis of polysaccharide hydrolases secreted by Aspergillus flavipes FP-500 on corn cobs and wheat bran as complex carbon sources. Prep Biochem Biotechnol 2019; 50:390-400. [DOI: 10.1080/10826068.2019.1700518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lizzete Ruth Torres-Barajas
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - María Teresa Alvarez-Zúñiga
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
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Yang Y, Fang A, Yu Y, Bi C, Zhou C. Integrated transcriptomic and secretomic approaches reveal critical pathogenicity factors in Pseudofabraea citricarpa inciting citrus target spot. Microb Biotechnol 2019; 12:1260-1273. [PMID: 31162831 PMCID: PMC6801157 DOI: 10.1111/1751-7915.13440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022] Open
Abstract
Target spot is a newly emerging citrus disease caused by Pseudofabraea citricarpa. Outbreaks of this disease result in massive economic losses to citrus production. Here, an integrated study involving comparative transcriptomic and secretomic analyses was conducted to determine the critical pathogenicity factors of P. citricarpa involved in the induction of citrus target spot. A total of 701 transcripts and their cognate proteins were quantified and integrated. Among these transcripts and proteins, 99 exhibited the same expression patterns. Our quantitative integrated multi-omic data highlight several potentially pivotal pathogenicity factors, including 16 unigenes that were annotated as plant cell-wall-degrading enzymes, 13 unigenes homologous to virulence factors from various fungi, and one unigene described as a small cysteine-rich secreted protein, were screened and analysed. The screening of differentially expressed genes that encode secondary metabolism core enzymes implicated terpene metabolism in the pathogenicity of P. citricarpa. Overall, results indicated that plant cell wall degradation, plant-pathogen protein/polyribonucleotide interaction, and terpene biosynthesis have critical roles in the pathogenicity of P. citricarpa. This work demonstrated that integrated omic approaches enable the identification of pathogenicity/virulence factors and provide insights into the mechanisms underlying the pathogenicity of fungi. These insights would aid the development of effective disease management strategies.
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Affiliation(s)
- Yuheng Yang
- College of Plant ProtectionSouthwest UniversityChongqing400715China
| | - Anfei Fang
- College of Plant ProtectionSouthwest UniversityChongqing400715China
| | - Yang Yu
- College of Plant ProtectionSouthwest UniversityChongqing400715China
| | - Chaowei Bi
- College of Plant ProtectionSouthwest UniversityChongqing400715China
| | - Changyong Zhou
- Citrus Research InstituteSouthwest UniversityChongqing400712China
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A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei. mSystems 2019; 4:4/4/e00161-19. [PMID: 31213522 PMCID: PMC6581689 DOI: 10.1128/msystems.00161-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in response to two different cellulose sources. In vivo experimental validation confirmed the role of this new regulator in several other processes related to carbon source utilization and nutrient transport. Therefore, this work revealed novel forms of regulatory interaction in this model system for plant biomass deconstruction and also represented a new approach that could be easy applied to other organisms. Filamentous fungi are remarkable producers of enzymes dedicated to the degradation of sugar polymers found in the plant cell wall. Here, we integrated transcriptomic data to identify novel transcription factors (TFs) related to the control of gene expression of lignocellulosic hydrolases in Trichoderma reesei and Aspergillus nidulans. Using various sets of differentially expressed genes, we identified some putative cis-regulatory elements that were related to known binding sites for Saccharomyces cerevisiae TFs. Comparative genomics allowed the identification of six transcriptional factors in filamentous fungi that have corresponding S. cerevisiae homologs. Additionally, a knockout strain of T. reesei lacking one of these TFs (S. cerevisiaeAZF1 homolog) displayed strong reductions in the levels of expression of several cellulase-encoding genes in response to both Avicel and sugarcane bagasse, revealing a new player in the complex regulatory network operating in filamentous fungi during plant biomass degradation. Finally, RNA sequencing (RNA-seq) analysis showed the scope of the AZF1 homologue in regulating a number of processes in T. reesei, and chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) provided evidence for the direct interaction of this TF in the promoter regions of cel7a, cel45a, and swo. Therefore, we identified here a novel TF which plays a positive effect in the expression of cellulase-encoding genes in T. reesei. IMPORTANCE In this work, we used a systems biology approach to map new regulatory interactions in Trichoderma reesei controlling the expression of genes encoding cellulase and hemicellulase. By integrating transcriptomics related to complex biomass degradation, we were able to identify a novel transcriptional regulator which is able to activate the expression of these genes in response to two different cellulose sources. In vivo experimental validation confirmed the role of this new regulator in several other processes related to carbon source utilization and nutrient transport. Therefore, this work revealed novel forms of regulatory interaction in this model system for plant biomass deconstruction and also represented a new approach that could be easy applied to other organisms.
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Bauer I, Lechner L, Pidroni A, Petrone AM, Merschak P, Lindner H, Kremser L, Graessle S, Golderer G, Allipour S, Brosch G. Type I and II PRMTs regulate catabolic as well as detoxifying processes in Aspergillus nidulans. Fungal Genet Biol 2019; 129:86-100. [PMID: 31145992 DOI: 10.1016/j.fgb.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 05/03/2019] [Accepted: 05/24/2019] [Indexed: 11/28/2022]
Abstract
In filamentous fungi, arginine methylation has been implicated in morphogenesis, mycotoxin biosynthesis, pathogenicity, and stress response although the exact role of this posttranslational modification in these processes remains obscure. Here, we present the first genome-wide transcriptome analysis in filamentous fungi that compared expression levels of genes regulated by type I and type II protein arginine methyltransferases (PRMTs). In Aspergillus nidulans, three conserved type I and II PRMTs are present that catalyze asymmetric or symmetric dimethylation of arginines. We generated a double type I mutant (ΔrmtA/rmtB) and a combined type I and type II mutant (ΔrmtB/rmtC) to perform genome-wide comparison of their effects on gene expression, but also to monitor putative overlapping activities and reciprocal regulations of type I and type II PRMTs in Aspergillus. Our study demonstrates, that rmtA and rmtC as type I and type II representatives act together as repressors of proteins that are secreted into the extracellular region as the majority of up-regulated genes are mainly involved in catabolic pathways that constitute the secretome of Aspergillus. In addition to a strong up-regulation of secretory genes we found a significant enrichment of down-regulated genes involved in processes related to oxidation-reduction, transmembrane transport and secondary metabolite biosynthesis. Strikingly, nearly 50% of down-regulated genes in both double mutants correspond to redox reaction/oxidoreductase processes, a remarkable finding in light of our recently observed oxidative stress phenotypes of ΔrmtA and ΔrmtC. Finally, analysis of nuclear and cytoplasmic extracts for mono-methylated proteins revealed the presence of both, common and specific substrates of RmtA and RmtC. Thus, our data indicate that type I and II PRMTs in Aspergillus seem to co-regulate the same biological processes but also specifically affect other pathways in a non-redundant fashion.
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Affiliation(s)
- Ingo Bauer
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lukas Lechner
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Angelo Pidroni
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Anna-Maria Petrone
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Petra Merschak
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Stefan Graessle
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Georg Golderer
- Division of Biological Chemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Shadab Allipour
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria.
| | - Gerald Brosch
- Division of Molecular Biology, Medical University of Innsbruck, 6020 Innsbruck, Austria.
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Swamy KBS, Zhou N. Experimental evolution: its principles and applications in developing stress-tolerant yeasts. Appl Microbiol Biotechnol 2019; 103:2067-2077. [PMID: 30659332 DOI: 10.1007/s00253-019-09616-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 10/27/2022]
Abstract
Stress tolerance and resistance in industrial yeast strains are important attributes for cost-effective bioprocessing. The source of stress-tolerant yeasts ranges from extremophilic environments to laboratory engineered strains. However, industrial stress-tolerant yeasts are very rare in nature as the natural environment forces them to evolve traits that optimize survival and reproduction and not the ability to withstand harsh habitat-irrelevant industrial conditions. Experimental evolution is a frequent method used to uncover the mechanisms of evolution and microbial adaption towards environmental stresses. It optimizes biological systems by means of adaptation to environmental stresses and thus has immense power of development of robust stress-tolerant yeasts. This mini-review briefly outlines the basics and implications of evolution experiments and their applications to industrial biotechnology. This work is meant to serve as an introduction to those new to the field of experimental evolution, and as a guide to biologists working in the field of yeast stress response. Future perspectives of experimental evolution for potential biotechnological applications have also been elucidated.
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Affiliation(s)
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, P Bag 16, Palapye, Botswana
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Filiatrault-Chastel C, Navarro D, Haon M, Grisel S, Herpoël-Gimbert I, Chevret D, Fanuel M, Henrissat B, Heiss-Blanquet S, Margeot A, Berrin JG. AA16, a new lytic polysaccharide monooxygenase family identified in fungal secretomes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:55. [PMID: 30923563 PMCID: PMC6420742 DOI: 10.1186/s13068-019-1394-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulosic biomass is considered as a promising alternative to fossil resources for the production of fuels, materials and chemicals. Efficient enzymatic systems are needed to degrade the plant cell wall and overcome its recalcitrance. A widely used producer of cellulolytic cocktails is the ascomycete Trichoderma reesei, but this organism secretes a limited set of enzymes. To improve the saccharification yields, one strategy is to upgrade the T. reesei enzyme cocktail with enzymes produced by other biomass-degrading filamentous fungi isolated from biodiversity. RESULTS In this study, the enzymatic cocktails secreted by five strains from the genus Aspergillus (Aspergillus japonicus strains BRFM 405, 1487, 1489, 1490 and Aspergillus niger strain BRFM 430) were tested for their ability to boost a T. reesei reference cocktail for the saccharification of pretreated biomass. Proteomic analysis of fungal secretomes that significantly improved biomass degradation showed that the presence of proteins belonging to a putative LPMO family previously identified by genome analysis and awaiting experimental demonstration of activity. Members of this novel LPMO family, named AA16, are encountered in fungi and oomycetes with life styles oriented toward interactions with plant biomass. One AA16 protein from Aspergillus aculeatus (AaAA16) was produced to high level in Pichia pastoris. LPMO-type enzyme activity was demonstrated on cellulose with oxidative cleavage at the C1 position of the glucose unit. AaAA16 LPMO was found to significantly improve the activity of T. reesei CBHI on cellulosic substrates. CONCLUSIONS Although Aspergillus spp. has been investigated for decades for their CAZymes diversity, we identified members of a new fungal LPMO family using secretomics and functional assays. Properties of the founding member of the AA16 family characterized herein could be of interest for use in biorefineries.
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Affiliation(s)
- Camille Filiatrault-Chastel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - David Navarro
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Mireille Haon
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Sacha Grisel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Isabelle Herpoël-Gimbert
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Didier Chevret
- Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Institut Micalis, UMR1319, INRA, Agro-ParisTech, Jouy-En-Josas, France
| | - Mathieu Fanuel
- UR1268, INRA, Biopolymères Interactions Assemblages, Nantes, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257, CNRS, Aix Marseille Université, Marseille, France
- USC1408, INRA, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
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Efferth T. Beyond malaria: The inhibition of viruses by artemisinin-type compounds. Biotechnol Adv 2018; 36:1730-1737. [DOI: 10.1016/j.biotechadv.2018.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/29/2017] [Accepted: 01/01/2018] [Indexed: 12/12/2022]
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Quantitative multiplexed profiling of Penicillium funiculosum secretome grown on polymeric cellulase inducers and glucose. J Proteomics 2018; 179:150-160. [PMID: 29597011 DOI: 10.1016/j.jprot.2018.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/16/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
Filamentous fungi respond to the need to secure utilisable carbon from their growth milieu by secreting unique extracellular proteins depending upon the types of polymeric substrates. We have here profiled the variations in the secretome pattern of a non-model hypercellulolytic fungus - Penicillium funiculosum, grown in minimal media containing four different polymeric cellulase inducers, i.e., Avicel, wheat bran, ammonium-pretreated wheat straw and Avicel & wheat bran, and glucose over its early and late log phases of growth. Of the 137 secreted proteins validated at 1% FDR, we identified the quantified proteins in three clusters as early, persistently or lately expressed. The type of carbon substrate present in the culture media significantly affected the levels of cellulolytic enzymes expression by the fungus. The top abundant proteins quantified in the secretome for Avicel and wheat bran were cellobiohydrolaseI [GH7-CBM1], cellobiohydrolaseII [GH6-CBM1], β-glucosidase [GH3], arabinofuranosidase [GH51] and β-xylosidase [GH3], with bicupin being highest in case of wheat straw. Our results further suggested that the fungus secreted the extracellular proteins in waves, such that the initial responders act to hydrolyse the composite substrates in the culture environment before the second wave of proteins which tend to be more tailored to the specific substrate in the cultivating media. BIOLOGICAL SIGNIFICANCE In this article, we have comprehensively examined the dynamics of the secretome of a non-model hypercellulolytic fungus produced in response to model and composite cellulase inducers. Our study has provided additional insights into how the fungus enzyme machinery responds to the presence of different polymeric cellulase inducers over the two different growth phases (early growth and late growth phase). The comprehensive typing and quantification of the different proteins present in the secretomes of the cellulolytic fungal strains in response to diverse nutrient sources hold many prospects in understanding the fungus unique enzyme machinery and dynamics for the downstream biotechnological applications.
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Yoav S, Salame TM, Feldman D, Levinson D, Ioelovich M, Morag E, Yarden O, Bayer EA, Hadar Y. Effects of cre1 modification in the white-rot fungus Pleurotus ostreatus PC9: altering substrate preference during biological pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:212. [PMID: 30065786 PMCID: PMC6062969 DOI: 10.1186/s13068-018-1209-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 07/18/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND During the process of bioethanol production, cellulose is hydrolyzed into its monomeric soluble units. For efficient hydrolysis, a chemical and/or mechanical pretreatment step is required. Such pretreatment is designed to increase enzymatic digestibility of the cellulose chains inter alia by de-crystallization of the cellulose chains and by removing barriers, such as lignin from the plant cell wall. Biological pretreatment, in which lignin is decomposed or modified by white-rot fungi, has also been considered. One disadvantage in biological pretreatment, however, is the consumption of the cellulose by the fungus. Thus, fungal species that attack lignin with only minimal cellulose loss are advantageous. The secretomes of white-rot fungi contain carbohydrate-active enzymes (CAZymes) including lignin-modifying enzymes. Thus, modification of secretome composition can alter the ratio of lignin/cellulose degradation. RESULTS Pleurotus ostreatus PC9 was genetically modified to either overexpress or eliminate (by gene replacement) the transcriptional regulator CRE1, known to act as a repressor in the process of carbon catabolite repression. The cre1-overexpressing transformant demonstrated lower secreted cellulolytic activity and slightly increased selectivity (based on the chemical composition of pretreated wheat straw), whereas the knockout transformant demonstrated increased cellulolytic activity and significantly reduced residual cellulose, thereby displaying lower selectivity. Pretreatment of wheat straw using the wild-type PC9 resulted in 2.8-fold higher yields of soluble sugar compared to untreated wheat straw. The overexpression transformant showed similar yields (2.6-fold), but the knockout transformant exhibited lower yields (1.2-fold) of soluble sugar. Based on proteomic secretome analysis, production of numerous CAZymes was affected by modification of the expression level of cre1. CONCLUSIONS The gene cre1 functions as a regulator for expression of fungal CAZymes active against plant cell wall lignocelluloses, hence altering the substrate preference of the fungi tested. While the cre1 knockout resulted in a less efficient biological pretreatment, i.e., less saccharification of the treated biomass, the converse manipulation of cre1 (overexpression) failed to improve efficiency. Despite the inverse nature of the two genetic alterations, the expected "mirror image" (i.e., opposite regulatory response) was not observed, indicating that the secretion level of CAZymes, was not exclusively dependent on CRE1 activity.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Tomer M. Salame
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Daria Feldman
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Dana Levinson
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | | | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Edward A. Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100 Israel
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Poudel S, Giannone RJ, Basen M, Nookaew I, Poole FL, Kelly RM, Adams MWW, Hettich RL. The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:80. [PMID: 29588665 PMCID: PMC5865380 DOI: 10.1186/s13068-018-1076-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/09/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates. RESULTS Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. CONCLUSIONS This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.
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Affiliation(s)
- Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA
| | - Richard J. Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Mirko Basen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
- Present Address: Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt Am Main, Germany
| | - Intawat Nookaew
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA
| | - Farris L. Poole
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert M. Kelly
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Michael W. W. Adams
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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Liñeiro E, Macias-Sánchez AJ, Espinazo M, Cantoral JM, Moraga J, Collado IG, Fernández-Acero FJ. Phenotypic Effects and Inhibition of Botrydial Biosynthesis Induced by Different Plant-Based Elicitors in Botrytis cinerea. Curr Microbiol 2017; 75:431-440. [PMID: 29147762 PMCID: PMC5842495 DOI: 10.1007/s00284-017-1399-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/13/2017] [Indexed: 11/27/2022]
Abstract
Botrytis cinerea is considered a model organism for the study of plant-pathogen interaction showing great genetic diversity and a high degree of morphological variability depending on environmental conditions. The use of new compounds and plant-based elicitors may trigger the expression of different B. cinerea genes, providing new sources of virulence factors. This work is focused on elucidating the phenotypic effect in B. cinerea of different carbon sources such as glucose, cellulose and tomato cell walls (TCW). Production of botrydial and dihydrobotrydial toxins was evaluated using thin-layer chromatography (TLC), proton nuclear magnetic resonance spectroscopy (1H-NMR) and mass spectrometry (UPLC-HRESIMS). Expression of the toxin biosynthesis gene BcBOT2 was followed using RT-qPCR. Results show an inhibition of the toxin biosynthesis pathway when TCW are present as a sole carbon source, suggesting that the toxin is only produced when rich molecules, like glucose, are available for fungal metabolism. That suggests a connection between gene expression of virulence factors and environmental conditions, where the silent genes can be induced by different culture conditions.
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Affiliation(s)
- Eva Liñeiro
- Microbiology Laboratory, Andalusian Center for Grape and Grapevine Research, Faculty of Marine and Environmental Sciences, University of Cadiz, Polígono Rio San Pedro s/n, 11510, Puerto Real, Cádiz, Spain
| | - Antonio J Macias-Sánchez
- Organic Chemistry Department, Faculty of Science, University of Cadiz, Puerto Real, Cádiz, Spain
| | - Marisa Espinazo
- Microbiology Laboratory, Andalusian Center for Grape and Grapevine Research, Faculty of Marine and Environmental Sciences, University of Cadiz, Polígono Rio San Pedro s/n, 11510, Puerto Real, Cádiz, Spain
| | - Jesús M Cantoral
- Microbiology Laboratory, Andalusian Center for Grape and Grapevine Research, Faculty of Marine and Environmental Sciences, University of Cadiz, Polígono Rio San Pedro s/n, 11510, Puerto Real, Cádiz, Spain
| | - Javier Moraga
- Microbiology Laboratory, Andalusian Center for Grape and Grapevine Research, Faculty of Marine and Environmental Sciences, University of Cadiz, Polígono Rio San Pedro s/n, 11510, Puerto Real, Cádiz, Spain
- Organic Chemistry Department, Faculty of Science, University of Cadiz, Puerto Real, Cádiz, Spain
| | - Isidro G Collado
- Organic Chemistry Department, Faculty of Science, University of Cadiz, Puerto Real, Cádiz, Spain
| | - Francisco J Fernández-Acero
- Microbiology Laboratory, Andalusian Center for Grape and Grapevine Research, Faculty of Marine and Environmental Sciences, University of Cadiz, Polígono Rio San Pedro s/n, 11510, Puerto Real, Cádiz, Spain.
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Lin J, Zhang X, Song B, Xue W, Su X, Chen X, Dong Z. Improving cellulase production in submerged fermentation by the expression of a Vitreoscilla hemoglobin in Trichoderma reesei. AMB Express 2017; 7:203. [PMID: 29143239 PMCID: PMC5688050 DOI: 10.1186/s13568-017-0507-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 11/07/2017] [Indexed: 12/26/2022] Open
Abstract
Trichoderma reesei is well known as an industrial workhorse fungus in cellulase production. The low dissolved oxygen supply in the highly viscous medium of T. reesei remains a major bottleneck that hampers growth and cellulase production in submerged fermentation. Vitreoscilla hemoglobin (VHb) has been demonstrated to improve metabolism and protein production in different heterologous hosts under hypoxic conditions, but the use of VHb in T. reesei remains uninvestigated. This study examines the effect of VHb in improving T. reesei performance in submerged fermentation. The VHb gene (vgb)-expressing cassette was successfully transformed into the TU-6 strain, integrated into the genome of T. reesei, and functionally expressed with biological activity, which was confirmed by carbon monoxide difference analysis. Compared to the parent strain, the expression of VHb increased the glucose consumption rate of the transformant. Moreover, in cellulase-inducing medium total protein secretion of the VHb expressing strain was 2.2-fold of the parental strain and the filter paper cellulase activity was increased by 58% under oxygen-limiting conditions. In summary, our results demonstrate that VHb has beneficial effects on improving total protein secretion and cellulase activity of T. reesei in submerged fermentation.
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Investigation of the indigenous fungal community populating barley grains: Secretomes and xylanolytic potential. J Proteomics 2017; 169:153-164. [DOI: 10.1016/j.jprot.2017.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/03/2017] [Accepted: 03/13/2017] [Indexed: 11/23/2022]
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Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696). GENOME ANNOUNCEMENTS 2017; 5:5/32/e00731-17. [PMID: 28798174 PMCID: PMC5552983 DOI: 10.1128/genomea.00731-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Phanerochaete chrysosporium (ATCC 20696) has a catabolic ability to degrade lignin. Here, we report whole-genome sequencing used to identify genes related to lignin modification. We determined the 39-Mb draft genome sequence of this fungus, comprising 13,560 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes.
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Immobilization of indigenous holocellulase on iron oxide (Fe 2 O 3 ) nanoparticles enhanced hydrolysis of alkali pretreated paddy straw. Int J Biol Macromol 2017; 96:538-549. [DOI: 10.1016/j.ijbiomac.2016.11.109] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/26/2016] [Accepted: 11/28/2016] [Indexed: 11/19/2022]
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Kamel L, Tang N, Malbreil M, San Clemente H, Le Marquer M, Roux C, Frei dit Frey N. The Comparison of Expressed Candidate Secreted Proteins from Two Arbuscular Mycorrhizal Fungi Unravels Common and Specific Molecular Tools to Invade Different Host Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:124. [PMID: 28223991 PMCID: PMC5293756 DOI: 10.3389/fpls.2017.00124] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/20/2017] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF), belonging to the fungal phylum Glomeromycota, form mutualistic symbioses with roots of almost 80% of land plants. The release of genomic data from the ubiquitous AMF Rhizophagus irregularis revealed that this species possesses a large set of putative secreted proteins (RiSPs) that could be of major importance for establishing the symbiosis. In the present study, we aimed to identify SPs involved in the establishment of AM symbiosis based on comparative gene expression analyses. We first curated the secretome of the R. irregularis DAOM 197198 strain based on two available genomic assemblies. Then we analyzed the expression patterns of the putative RiSPs obtained from the fungus in symbiotic association with three phylogenetically distant host plants-a monocot, a dicot and a liverwort-in comparison with non-symbiotic stages. We found that 33 out of 84 RiSPs induced in planta were commonly up-regulated in these three hosts. Most of these common RiSPs are small proteins of unknown function that may represent putative host non-specific effector proteins. We further investigated the expressed secretome of Gigaspora rosea, an AM fungal species phylogenetically distant from R. irregularis. G. rosea also presents original symbiotic features, a narrower host spectrum and a restrictive geographic distribution compared to R. irregularis. Interestingly, when analyzing up-regulated G. rosea SPs (GrSPs) in different hosts, a higher ratio of host-specific GrSPs was found compared to RiSPs. Such difference of expression patterns may mirror the restrained host spectrum of G. rosea compared to R. irregularis. Finally, we identified a set of conserved SPs, commonly up-regulated by both fungi in all hosts tested, that could correspond to common keys of AMF to colonize host plants. Our data thus highlight the specificities of two distant AM fungi and help in understanding their conserved and specific strategies to invade different hosts.
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Affiliation(s)
- Laurent Kamel
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
- Agronutrition, Laboratoire de BiotechnologiesLabege, France
| | - Nianwu Tang
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Mathilde Malbreil
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Morgane Le Marquer
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Nicolas Frei dit Frey
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
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Ivanova C, Ramoni J, Aouam T, Frischmann A, Seiboth B, Baker SE, Le Crom S, Lemoine S, Margeot A, Bidard F. Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:209. [PMID: 28912831 PMCID: PMC5588705 DOI: 10.1186/s13068-017-0897-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/29/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete Trichoderma reesei, the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype. RESULTS Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor vib1, and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of vib1 under the control of its native promoter as well as overexpression of vib1 under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of vib1 in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of vib1 in QM9414 and Rut-C30 had no effect on cellulase production, most likely because vib1 is already expressed at an optimal level under normal conditions. CONCLUSION We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor vib1 as a key regulator of cellulases in T. reesei whose expression is absent in QM9978. We propose that in T. reesei, as in Neurospora crassa, vib1 is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.
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Affiliation(s)
- Christa Ivanova
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
- Present Address: Genetics of Biofilms Unit, Department of Microbiology, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jonas Ramoni
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Thiziri Aouam
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Alexa Frischmann
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Molecular Biotechnology, Research Division Biochemical Technology, Institute of Chemical Engineering, TU-Wien, 1060 Vienna, Austria
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Stéphane Le Crom
- Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, 75005 Paris, France
| | - Sophie Lemoine
- École normale supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l’École normale supérieure (IBENS), Plateforme Génomique, 75005 Paris, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France
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Immobilization of LccC Laccase from Aspergillus nidulans on Hard Surfaces via Fungal Hydrophobins. Appl Environ Microbiol 2016; 82:6395-6402. [PMID: 27565614 DOI: 10.1128/aem.01413-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 11/20/2022] Open
Abstract
Fungal hydrophobins are small amphiphilic proteins that can be used for coatings on hydrophilic and hydrophobic surfaces. Through the formation of monolayers, they change the hydrophobicity of a given surface. Especially, the class I hydrophobins are interesting for biotechnology, because their layers are stable at high temperatures and can only be removed with strong solvents. These proteins self-assemble into monolayers under physiological conditions and undergo conformational changes that stabilize the layer structure. Several studies have demonstrated how the fusion of hydrophobins with short peptides allows the specific modification of the properties of a given surface or have increased the protein production levels through controlled localization of hydrophobin molecules inside the cell. Here, we fused the Aspergillus nidulans laccase LccC to the class I hydrophobins DewA and DewB and used the fusion proteins to functionalize surfaces with immobilized enzymes. In contrast to previous studies with enzymes fused to class II hydrophobins, the DewA-LccC fusion protein is secreted into the culture medium. The crude culture supernatant was directly used for coatings of glass and polystyrene without additional purification steps. The highest laccase surface activity was achieved after protein immobilization on modified hydrophilic polystyrene at pH 7. This study presents an easy-to-use alternative to classical enzyme immobilization techniques and can be applied not only for laccases but also for other biotechnologically relevant enzymes. IMPORTANCE Although fusion with small peptides to modify hydrophobin properties has already been performed in several studies, fusion with an enzyme presents a more challenging task. Both protein partners need to remain in active form so that the hydrophobins can interact with one another and form layers, and so the enzyme (e.g., laccase) will remain active at the same time. Also, because of the amphiphilic nature of hydrophobins, their production and purification remain challenging so far and often include steps that would irreversibly disrupt most enzymes. In our study, we present the first functional fusion proteins of class I hydrophobins from A. nidulans with a laccase. The resulting fusion enzyme is directly secreted into the culture medium by the fungus and can be used for the functionalization of hard surfaces.
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Degradation and polymerization of monolignols by Abortiporus biennis, and induction of its degradation with a reducing agent. J Microbiol 2016; 54:675-85. [DOI: 10.1007/s12275-016-6158-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/22/2016] [Accepted: 08/25/2016] [Indexed: 01/22/2023]
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Beinhauer J, Lenobel R, Loginov D, Chamrád I, Řehulka P, Sedlářová M, Marchetti-Deschmann M, Allmaier G, Šebela M. Identification ofBremia lactucaeandOidium neolycopersiciproteins extracted for intact spore MALDI mass spectrometric biotyping. Electrophoresis 2016; 37:2940-2952. [DOI: 10.1002/elps.201600144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/19/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023]
Affiliation(s)
- Jana Beinhauer
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - René Lenobel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Dmitry Loginov
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Ivo Chamrád
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
| | - Pavel Řehulka
- Institute of Molecular Pathology, Faculty of Military Health Sciences; University of Defence; Hradec Králové Czech Republic
| | - Michaela Sedlářová
- Department of Botany, Faculty of Science; Palacký University; Olomouc Czech Republic
| | | | - Günter Allmaier
- Institute of Chemical Technologies and Analytics; Vienna University of Technology (TU Wien); Vienna Austria
| | - Marek Šebela
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science; Palacký University; Olomouc Czech Republic
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de Mattos-Shipley K, Ford K, Alberti F, Banks A, Bailey A, Foster G. The good, the bad and the tasty: The many roles of mushrooms. Stud Mycol 2016; 85:125-157. [PMID: 28082758 PMCID: PMC5220184 DOI: 10.1016/j.simyco.2016.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Fungi are often inconspicuous in nature and this means it is all too easy to overlook their importance. Often referred to as the "Forgotten Kingdom", fungi are key components of life on this planet. The phylum Basidiomycota, considered to contain the most complex and evolutionarily advanced members of this Kingdom, includes some of the most iconic fungal species such as the gilled mushrooms, puffballs and bracket fungi. Basidiomycetes inhabit a wide range of ecological niches, carrying out vital ecosystem roles, particularly in carbon cycling and as symbiotic partners with a range of other organisms. Specifically in the context of human use, the basidiomycetes are a highly valuable food source and are increasingly medicinally important. In this review, seven main categories, or 'roles', for basidiomycetes have been suggested by the authors: as model species, edible species, toxic species, medicinal basidiomycetes, symbionts, decomposers and pathogens, and two species have been chosen as representatives of each category. Although this is in no way an exhaustive discussion of the importance of basidiomycetes, this review aims to give a broad overview of the importance of these organisms, exploring the various ways they can be exploited to the benefit of human society.
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Affiliation(s)
- K.M.J. de Mattos-Shipley
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - K.L. Ford
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - F. Alberti
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - A.M. Banks
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
- School of Biology, Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - A.M. Bailey
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - G.D. Foster
- School of Biological Sciences, Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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50
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Book AJ, Lewin GR, McDonald BR, Takasuka TE, Wendt-Pienkowski E, Doering DT, Suh S, Raffa KF, Fox BG, Currie CR. Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression. PLoS Biol 2016; 14:e1002475. [PMID: 27276034 PMCID: PMC4898821 DOI: 10.1371/journal.pbio.1002475] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/05/2016] [Indexed: 11/23/2022] Open
Abstract
The evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology. Cellulose deconstruction helps shape the global carbon cycle; this study shows that high cellulolytic ability evolved in select lineages of the bacterial genus Streptomyces through key changes in gene content and transcriptional regulation. Only specific microbes can deconstruct the vast stores of carbon within plant biomass. Studying the distribution, diversity, and evolution of these cellulolytic organisms improves our understanding of the ecological functions of microbes in the environment and their contributions to the global carbon cycle. The bacterial genus Streptomyces is abundant in soil, appears to readily form symbiotic associations with eukaryotic hosts, and has long been thought to contribute to plant biomass degradation. Here, we show that the ability to rapidly deconstruct cellulose is surprisingly rare in the genus Streptomyces but is enriched in symbiotic stains associated with diverse insect hosts that feed on plant biomass. By using a combination of genomic, transcriptomic, and genetic analyses, we identify key changes in gene content and expression that confer cellulolytic activity. Our results support the idea that a complex interplay of genomic changes, occurring over ancient time scales, shapes the evolution of the ecologically important ability to deconstruct plant biomass.
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Affiliation(s)
- Adam J. Book
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gina R. Lewin
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bradon R. McDonald
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Taichi E. Takasuka
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Evelyn Wendt-Pienkowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Drew T. Doering
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Steven Suh
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kenneth F. Raffa
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian G. Fox
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cameron R. Currie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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