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Jasińska A, Walaszczyk A, Paraszkiewicz K. Omics-Based Approaches in Research on Textile Dye Microbial Decolorization. Molecules 2024; 29:2771. [PMID: 38930836 DOI: 10.3390/molecules29122771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The development of the textile industry has negative effects on the natural environment. Cotton cultivation, dyeing fabrics, washing, and finishing require a lot of water and energy and use many chemicals. One of the most dangerous pollutants generated by the textile industry is dyes. Most of them are characterized by a complex chemical structure and an unfavorable impact on the environment. Especially azo dyes, whose decomposition by bacteria may lead to the formation of carcinogenic aromatic amines and raise a lot of concern. Using the metabolic potential of microorganisms that biodegrade dyes seems to be a promising solution for their elimination from contaminated environments. The development of omics sciences such as genomics, transcriptomics, proteomics, and metabolomics has allowed for a comprehensive approach to the processes occurring in cells. Especially multi-omics, which combines data from different biomolecular levels, providing an integrative understanding of the whole biodegradation process. Thanks to this, it is possible to elucidate the molecular basis of the mechanisms of dye biodegradation and to develop effective methods of bioremediation of dye-contaminated environments.
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Affiliation(s)
- Anna Jasińska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Aleksandra Walaszczyk
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
| | - Katarzyna Paraszkiewicz
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
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Huo C, Guo Y, Zhao Y. Enhancing quality of ruminant feed through fungal treatment: Usage of bamboo shoot residues. PLoS One 2024; 19:e0302185. [PMID: 38805421 PMCID: PMC11132483 DOI: 10.1371/journal.pone.0302185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
In this investigation, we explore the harnessing of bamboo shoot residues (BSR) as a viable source for ruminant feed through fungal treatment, with the overarching objective of elevating feed quality and optimizing bamboo shoot utilization. The white-rot fungi (Wr.fungi), Aspergillus niger (A.niger), and its co-cultures (A.niger&Wr.fungi) were employed to ferment BSR. And the impact of different fermentation methods and culture time on the chemical composition (Crude protein Ash, neutral detergent fibre and acid detergent fibers), enzyme activity (Cellulase, Laccase, Filter paperase and Lignin peroxidase activities), and rumen digestibility in vitro were assessed. The findings reveal a nota ble 30.39% increase in crude protein in fermented BSR, accompanied by respective decreases of 13.02% and 17.31% in acid detergent fiber and neutral detergent fibre content. Enzyme activities experienced augmentation post-fermentation with A.niger&Wr.fungi. Specifically, the peak Cellulase, Laccase, and Lignin peroxidase activities for BSR with Wr.fungi treatment reached 748.4 U/g, 156.92 U/g, and 291.61 U/g, respectively, on the sixth day of fermentation. Concurrently, NH3-N concentration exhibited an upward trend with prolonged fermentation time. Total volatile fatty acids registered a decline, and the Acetate/Propionate ratio reached its nadir after 6 days of fermentation under the A.niger&Wr.fungi treatment. These outcomes furnish a theoretical foundation for the development of ruminant feeds treated via fungal co-culture.
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Affiliation(s)
- Chunyan Huo
- Center for Efficient Utilization of Tufted Bamboo Resources, and Center for Quality Inspection and Testing Center of Economic Forest Products, National Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming, China
| | - Yuhong Guo
- Center for Efficient Utilization of Tufted Bamboo Resources, and Center for Quality Inspection and Testing Center of Economic Forest Products, National Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming, China
| | - Yihe Zhao
- Center for Efficient Utilization of Tufted Bamboo Resources, and Center for Quality Inspection and Testing Center of Economic Forest Products, National Forestry and Grassland Administration, Yunnan Academy of Forestry and Grassland, Kunming, China
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3
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Scott CJR, McGregor NGS, Leadbeater DR, Oates NC, Hoßbach J, Abood A, Setchfield A, Dowle A, Overkleeft HS, Davies GJ, Bruce NC. Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates. Microbiol Spectr 2024:e0394323. [PMID: 38757984 DOI: 10.1128/spectrum.03943-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.
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Affiliation(s)
- Conor J R Scott
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Janina Hoßbach
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Amira Abood
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Alexander Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, United Kingdom
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Liu B, Dai Y, Cheng X, He X, Bei Q, Wang Y, Zhou Y, Zhu B, Zhang K, Tian X, Duan M, Xie X, Wang L. Straw mulch improves soil carbon and nitrogen cycle by mediating microbial community structure and function in the maize field. Front Microbiol 2023; 14:1217966. [PMID: 37533822 PMCID: PMC10391546 DOI: 10.3389/fmicb.2023.1217966] [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: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
This study was conducted to investigate the capability of the microbial community characteristics and soil variables to promote carbon and nitrogen cycles in maize fields under straw mulch. We covered the surface soil of the maize field with different amounts of wheat straw (0 kg/ha, 2,250 kg/ha, and 4,500 kg/ha) and used 16S rRNA and ITS sequencing, Biology ECO-plate, traditional enzymology, TOC analyzer, and HPLC to measure bacterial and fungal community composition and functions, characteristics of microbial carbon source metabolism, carbon and nitrogen fraction, enzyme activity, and organic acid content in the maize rhizosphere and non-rhizosphere. The results indicated that short-term straw mulch insignificantly affected the alpha diversity of bacterial and fungal communities whereas significantly influenced their beta diversity. The results of functional prediction revealed that straw mulch considerably boosted the relative abundances of bacteria belonging to chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, and nitrogen fixation and inhibited fermentation and nitrate reduction in maize rhizosphere soil. These processes primarily drove the C and N cycles in soil. Straw mulch also improved fungal saprotrophs by raising the proportion of Chaetomiaceae and Chaetosphaeriaceae. The Biology ECO-plate results illustrated that straw mulch weakened the metabolism capacity of microbial labile carbon resources. As a result, the labile C and N fractions were raised under straw mulch. Our results also showed that straw mulch primarily regulated the microbial community structure in rhizosphere soil by significantly decreasing Firmicutes and Ascomycota relative abundance while increasing Basidiomycota. The fungal community structure is more than bacterial for affecting soil microbial biomass carbon, readily oxidizable organic carbon, dissolved organic carbon, available nitrogen, ammonium, and nitrate directly and indirectly through malic acid content and cellulase, protease, and amylase activity. Overall, our findings imply that straw mulch might influence the bacterial and fungal community structures, thereby boosting the production of labile C and N components and accelerating the C and N cycle in maize fields.
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Affiliation(s)
- Bangyan Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yisha Dai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xin Cheng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xian He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Qicheng Bei
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Yifan Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Yuling Zhou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Bo Zhu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Kangping Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoqin Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Meichun Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Xiaoyu Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
| | - Longchang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, China
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Qi J, Li F, Jia L, Zhang X, Deng S, Luo B, Zhou Y, Fan M, Xia Y. Fungal Selectivity and Biodegradation Effects by White and Brown Rot Fungi for Wood Biomass Pretreatment. Polymers (Basel) 2023; 15:polym15081957. [PMID: 37112109 PMCID: PMC10144154 DOI: 10.3390/polym15081957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
The biodegradation path and mechanism of wood varies depending on diverse fungi and tree species, as fungi possess selectivity in degradation of versatile wood components. This paper aims to clarify the actual and precise selectivity of white and brown rot fungi and the biodegradation effects on different tree species. Softwood (Pinus yunnanensis and Cunninghamia lanceolata) and hardwood (Populus yunnanensis and Hevea brasiliensis) were subjected to a biopretreating process by white rot fungus Trametes versicolor, and brown rot fungi Gloeophyllum trabeum and Rhodonia placenta with various conversion periods. The results showed that the white rot fungus Trametes versicolor had a selective biodegradation in softwood, which preferentially convert wood hemicellulose and lignin, but cellulose was retained selectively. Conversely, Trametes versicolor achieved simultaneous conversion of cellulose, hemicellulose and lignin in hardwood. Both brown rot fungi species preferentially converted carbohydrates, but R. placenta had a selectivity for the conversion of cellulose. In addition, morphological observation showed that the microstructures within wood changed significantly, and the enlarged pores and the improved accessibility could be beneficial for the penetration and accessibility of treating substrates. The research outcomes could serve as fundamental knowhows and offer potentials for effective bioenergy production and bioengineering of bioresources, and provide a reference for further application of fungal biotechnology.
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Affiliation(s)
- Jiyun Qi
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
| | - Fangfang Li
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
| | - Lu Jia
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
| | - Xiaoyuan Zhang
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
| | - Shuduan Deng
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
| | - Bei Luo
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
| | - Yonghui Zhou
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Mizi Fan
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Yan Xia
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, Southwest Forestry University, Kunming 650224, China
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge UB8 3PH, UK
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Screening the Carbon Source Type in Solid-State Fermentation with Phanerochaete chrysosporium to Improve the Forage Value of Corn Straw and Rice Straw. Animals (Basel) 2023; 13:ani13050888. [PMID: 36899745 PMCID: PMC10000110 DOI: 10.3390/ani13050888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Poor quality straw can be made more digestible and palatable through delignification using white rot fungi as a biological treatment in SSF. The decomposition of organic matter by white rot fungi is improved when a carbon source is added. Reducing the fermentation cycle can also help retain more nutrients in straw feed. To increase rumen digestibility and nutrient utilization, corn straw and rice straw were subjected to SSF with white rot fungi (Phanerochaete chrysosporium) for 21 days. The type of carbon source (glucose, sucrose, molasses, or soluble starch) was optimized, and the nutrient composition and in vitro fermentation parameters of the fermented straw were assessed. In the fermented corn straw and rice straw supplemented with different carbon sources, the results showed a decrease in lignin content, dry matter, cellulose, and hemicellulose loss, and an increase in crude protein content after 21 days. Total volatile fatty acid and ammonium nitrogen concentrations increased significantly (p < 0.01) during in vitro fermentation. Overall, the most enhanced nutritional values for corn straw and rice straw were observed after 14 days of SSF in the groups using molasses or glucose as a carbon source.
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Zhu X, Zhou Z, Guo G, Li J, Yan H, Li F. Proteomics and metabolomics analysis of the lignin degradation mechanism of lignin-degrading fungus Aspergillus fumigatus G-13. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1062-1076. [PMID: 36723181 DOI: 10.1039/d2ay01446g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Aspergillus fumigatus has the potential to degrade lignocellulosic biomass, but the degradation mechanism is not clear. The purpose of this study is to analyze the differential proteins and metabolites produced by Aspergillus fumigatus G-13 in the degradation of different lignin model compounds. Ferulic acid, sinapic acid, and p-coumaric acid were used as carbon sources. By controlling the culture conditions, and adding a cellulose co-substrate and an auxiliary carbon source, the enzymatic production law of three lignin model compounds degraded by Aspergillus fumigatus G-13 was investigated. Proteomics and metabolomics analysis were conducted for the two groups with the largest difference in enzyme activity expression. The results showed that a total of 1447 peptides were identified by proteomics analysis. Among them, 134 proteins were significantly changed, 73 proteins were up-regulated, and 61 proteins were down-regulated. The key proteins that degrade lignin model compounds are catechol dioxygenase, glutathione reductase, dextranase, isoamyl alcohol oxidase, glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase. Enrichment analysis of differential metabolite functions revealed that Aspergillus fumigatus G-13 is associated with several pathways related to the degradation of lignin. Among them, starch and sucrose metabolism, pentose phosphate pathway, glutathione metabolism, and the ortho-cleavage pathway of dihydroxylated aromatic rings are closely related to lignin degradation. The information presented in this paper will be helpful for future research on the degradation or depolymerization of natural lignocellulosic substrates.
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Affiliation(s)
- Xudong Zhu
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Zijing Zhou
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Gaijuan Guo
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Jinda Li
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Hong Yan
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
| | - Fen Li
- Heilongjiang Provincial Key Laboratory of CO2 Resource Utilization and Energy Catalytic Materials, China
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, No. 4, Linyuan Road, Harbin 150040, P. R. China
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Zerva A, Siaperas R, Taxeidis G, Kyriakidi M, Vouyiouka S, Zervakis GI, Topakas E. Investigation of Abortiporus biennis lignocellulolytic toolbox, and the role of laccases in polystyrene degradation. CHEMOSPHERE 2023; 312:137338. [PMID: 36423718 DOI: 10.1016/j.chemosphere.2022.137338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
White-rot basidiomycetes are the only microorganisms able to produce both hydrolytic (cellulases and hemicellulases) and oxidative (ligninolytic) enzymes for degrading all lignocellulose constituents. Their enzymatic machinery makes them ideal for the discovery of novel enzymes with desirable properties. In the present work, Abortiporus biennis, a white-rot fungus, was studied in regard to its lignocellulolytic potential. Secretomics and biochemical analyses were employed to study the strain's enzymatic arsenal, after growth in corn stover cultures and xylose-based defined media. The results revealed the presence of all the necessary enzymatic activities for complete breakdown of biomass, while the prominent role of oxidative enzymes in the lignocellulolytic strategy of the strain became evident. Two novel laccases, AbiLac1 and AbiLac2, were isolated from the culture supernatant with ion-exchange chromatography. Characterization of purified laccases revealed their ability to oxidize a wide variety of phenolic and non-phenolic substrates. AbiLac1 was found to oxidize polystyrene powder, showing high depolymerization potential, based on radical chain scission mechanism as evidenced by molecular weight decrease. The results of the present study demonstrate the biotechnological potential of the unexplored enzymatic machinery of white-rot basidiomycetes, including the design of improved lignocellulolytic cocktails, as well as the degradation and/or valorization of plastic waste materials.
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Affiliation(s)
- Anastasia Zerva
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Romanos Siaperas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - George Taxeidis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Maria Kyriakidi
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Stamatina Vouyiouka
- Laboratory of Polymer Technology, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece
| | - Georgios I Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855, Athens, Greece
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens, 15772, Greece.
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Wu Z, Peng K, Zhang Y, Wang M, Yong C, Chen L, Qu P, Huang H, Sun E, Pan M. Lignocellulose dissociation with biological pretreatment towards the biochemical platform: A review. Mater Today Bio 2022; 16:100445. [PMID: 36212906 PMCID: PMC9535326 DOI: 10.1016/j.mtbio.2022.100445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022]
Abstract
Lignocellulose utilization has been gaining great attention worldwide due to its abundance, accessibility, renewability and recyclability. Destruction and dissociation of the cross-linked, hierarchical structure within cellulose hemicellulose and lignin is the key procedure during chemical utilization of lignocellulose. Of the pretreatments, biological treatment, which can effectively target the complex structures, is attractive due to its mild reaction conditions and environmentally friendly characteristics. Herein, we report a comprehensive review of the current biological pretreatments for lignocellulose dissociation and their corresponding degradation mechanisms. Firstly, we analyze the layered, hierarchical structure of cell wall, and the cross-linked network between cellulose, hemicellulose and lignin, then highlight that the cracking of β-aryl ether is considered the key to lignin degradation because of its dominant position. Secondly, we explore the effect of biological pretreatments, such as fungi, bacteria, microbial consortium, and enzymes, on substrate structure and degradation efficiency. Additionally, combining biological pretreatment with other methods (chemical methods and catalytic materials) may reduce the time necessary for the whole process, which also help to strengthen the lignocellulose dissociation efficiency. Thirdly, we summarize the related applications of lignocellulose, such as fuel production, chemicals platform, and bio-pulping, which could effectively alleviate the energy pressure through bioconversion into high value-added products. Based on reviewing of current progress of lignocellulose pretreatment, the challenges and future prospects are emphasized. Genetic engineering and other technologies to modify strains or enzymes for improved biotransformation efficiency will be the focus of future research.
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Affiliation(s)
- Zengyou Wu
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Kun Peng
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yin Zhang
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Mei Wang
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Cheng Yong
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ling Chen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ping Qu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hongying Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Enhui Sun
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, China
- College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville, 3209, South Africa
- Corresponding author. Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization/Key Laboratory of Saline-Alkali Soil Improvement and Utilization (Coastal Saline-Alkali Lands), Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Mingzhu Pan
- College of Materials Science and Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Corresponding author.
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10
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Lee ME, Ko YJ, Hwang DH, Cho BH, Jeong WY, Bhardwaj N, Han SO. Surface display of enzyme complex on Corynebacterium glutamicum as a whole cell biocatalyst and its consolidated bioprocessing using fungal-pretreated lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 362:127758. [PMID: 35963485 DOI: 10.1016/j.biortech.2022.127758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
A novel whole cell biocatalyst using fungal-pretreated lignocellulosic biomass was developed by displaying the enzyme complex consisting of N-acetylglucosaminidase (cNAG) and endoglucanse E (cCelE) on Corynebacterium glutamicum, hereafter called mNC. mNC showed a maximum 4.43-fold cNAG and 2.40-fold cCelE activity compared to single enzyme-secreting C. glutamicum. mNC also showed the highest efficiency of sugar production in various types of cellulose and fungal-pretreated biomass. The growth of mNC was 5.06-fold higher than that of the control. Then, the ability of mNC to produce a valuable chemical was confirmed. mNC overexpressing isopropanol biosynthesis genes showed a maximum titer of 218.9 ± 11.73 mg/L isopropanol and maintained high efficiency for isopropanol production in the recycling test, which was 90.07 ± 4.12 % during 4 cycles. This strategy can be applied to the direct saccharification of fungal-pretreated lignocellulosic biomass efficiently leading to the production of valuable products in various industrial fields.
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Affiliation(s)
- Myeong-Eun Lee
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea
| | - Dong-Hyeok Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Byeong-Hyeon Cho
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Wu-Young Jeong
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Nisha Bhardwaj
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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11
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Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
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12
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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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13
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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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14
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Kimani V, Ullrich R, Büttner E, Herzog R, Kellner H, Jehmlich N, Hofrichter M, Liers C. First Dye-Decolorizing Peroxidase from an Ascomycetous Fungus Secreted by Xylaria grammica. Biomolecules 2021; 11:biom11091391. [PMID: 34572604 PMCID: PMC8469222 DOI: 10.3390/biom11091391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Fungal DyP-type peroxidases have so far been described exclusively for basidiomycetes. Moreover, peroxidases from ascomycetes that oxidize Mn2+ ions are yet not known. Methods: We describe here the physicochemical, biocatalytic, and molecular characterization of a DyP-type peroxidase (DyP, EC 1.11.1.19) from an ascomycetous fungus. Results: The enzyme oxidizes classic peroxidase substrates such as 2,6-DMP but also veratryl alcohol and notably Mn2+ to Mn3+ ions, suggesting a physiological function of this DyP in lignin modification. The KM value (49 µM) indicates that Mn2+ ions bind with high affinity to the XgrDyP protein but their subsequent oxidation into reactive Mn3+ proceeds with moderate efficiency compared to MnPs and VPs. Mn2+ oxidation was most effective at an acidic pH (between 4.0 and 5.0) and a hypothetical surface exposed an Mn2+ binding site comprising three acidic amino acids (two aspartates and one glutamate) could be localized within the hypothetical XgrDyP structure. The oxidation of Mn2+ ions is seemingly supported by four aromatic amino acids that mediate an electron transfer from the surface to the heme center. Conclusions: Our findings shed new light on the possible involvement of DyP-type peroxidases in lignocellulose degradation, especially by fungi that lack prototypical ligninolytic class II peroxidases.
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Affiliation(s)
- Virginia Kimani
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
- Kenya Industrial Research and Development Institute, Nairobi P.O. Box 30650-00100, Kenya
| | - René Ullrich
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Enrico Büttner
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Robert Herzog
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Harald Kellner
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research–UFZ, Department of Molecular System Biology, 04318 Leipzig, Germany;
| | - Martin Hofrichter
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
| | - Christiane Liers
- Unit of Environmental Biotechnology, International Institute Zittau, Dresden University of Technology, Markt 23, 02763 Zittau, Germany; (V.K.); (R.U.); (E.B.); (R.H.); (H.K.); (M.H.)
- Correspondence: ; Tel.: +49-3583-6124154
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15
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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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16
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Li F, Zhang J, Ma F, Chen Q, Xiao Q, Zhang X, Xie S, Yu H. Lytic polysaccharide monooxygenases promote oxidative cleavage of lignin and lignin-carbohydrate complexes during fungal degradation of lignocellulose. Environ Microbiol 2021; 23:4547-4560. [PMID: 34169632 DOI: 10.1111/1462-2920.15648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/06/2023]
Abstract
Overcoming lignocellulosic biomass recalcitrance, especially the cleavage of cross-linkages in lignin-carbohydrate complexes (LCCs) and lignin, is essential for both the carbon cycle and industrial biorefinery. Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes that play a key role in fungal polysaccharide oxidative degradation. Nevertheless, comprehensive analysis showed that LPMOs from a white-rot fungus, Pleurotus ostreatus, correlated well with the Fenton reaction and were involved in the degradation of recalcitrant nonpolysaccharide fractions in this research. Thus, LPMOs participated in the extracellular Fenton reaction by enhancing iron reduction in quinone redox cycling. A Fenton reaction system consisting of LPMOs, hydroquinone, and ferric iron can efficiently produce hydroxy radicals and then cleave LCCs or lignin linkages. This finding indicates that LPMOs are underestimated auxiliary enzymes in eliminating biomass recalcitrance.
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Affiliation(s)
- Fei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jialong Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fuying Ma
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qing Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiuyun Xiao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaoyu Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shangxian Xie
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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17
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Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Res 2021; 27:5856740. [PMID: 32531032 PMCID: PMC7406137 DOI: 10.1093/dnares/dsaa011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
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Affiliation(s)
- Shingo Miyauchi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Hayat Hage
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Elodie Drula
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Jean-Guy Berrin
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - David Navarro
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Anne Favel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Delphine Chaduli
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Sacha Grisel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Mireille Haon
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - François Piumi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | | | - Anne Lomascolo
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Steven Ahrendt
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt M LaButti
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Didier Chevret
- INRAE, UMR1319, Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Chris Daum
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jérôme Mariette
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Allen C Gathman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Matthieu Hainaut
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | | | - Ursula Kües
- Department of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University Göttingen, Göttingen, Germany.,Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Walt Lilly
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Anna Lipzen
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Mélanie Morel-Rouhier
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Emmanuelle Morin
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Jasmyn Pangilinan
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Han A B Wösten
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | | | - Robert Riley
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Eric Record
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marie-Noëlle Rosso
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
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18
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Characterization of a Dye-Decolorizing Peroxidase from Irpex lacteus Expressed in Escherichia coli: An Enzyme with Wide Substrate Specificity Able to Transform Lignosulfonates. J Fungi (Basel) 2021; 7:jof7050325. [PMID: 33922393 PMCID: PMC8145141 DOI: 10.3390/jof7050325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
A dye-decolorizing peroxidase (DyP) from Irpex lacteus was cloned and heterologously expressed as inclusion bodies in Escherichia coli. The protein was purified in one chromatographic step after its in vitro activation. It was active on ABTS, 2,6-dimethoxyphenol (DMP), and anthraquinoid and azo dyes as reported for other fungal DyPs, but it was also able to oxidize Mn2+ (as manganese peroxidases and versatile peroxidases) and veratryl alcohol (VA) (as lignin peroxidases and versatile peroxidases). This corroborated that I. lacteus DyPs are the only enzymes able to oxidize high redox potential dyes, VA and Mn+2. Phylogenetic analysis grouped this enzyme with other type D-DyPs from basidiomycetes. In addition to its interest for dye decolorization, the results of the transformation of softwood and hardwood lignosulfonates suggest a putative biological role of this enzyme in the degradation of phenolic lignin.
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19
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Nayan N, Sonnenberg AS, Hendriks WH, Cone JW. Prospects and feasibility of fungal pretreatment of agricultural biomass for ruminant feeding. Anim Feed Sci Technol 2020. [DOI: 10.1016/j.anifeedsci.2020.114577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Zhao X, Wang F, Fang Y, Zhou D, Wang S, Wu D, Wang L, Zhong R. High-potency white-rot fungal strains and duration of fermentation to optimize corn straw as ruminant feed. BIORESOURCE TECHNOLOGY 2020; 312:123512. [PMID: 32473472 DOI: 10.1016/j.biortech.2020.123512] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 05/06/2023]
Abstract
Five white-rot fungi Pleurotus ostreatus, Lentinus edodes, Hericium erinaceus, Pleurotus eryngii and Flammulina filiformis were studied (solid-state incubation and in vitro gas production) to determine lignin degradation and optimal duration of fermentation of corn straw. All fungi significantly decreased lignin, with optimal reductions after 28 d. Although cellulose also decreased, L. edodes and P. eryngii minimized these losses. In intro dry matter digestibility, total volatile fatty acid concentration and total gas production of fermented corn straw decreased (P < 0.001) as fermentation was prolonged, with improved rumen fermentability for all fungal treatments except F. filiformis. Total gas production in L. edodes did not decrease but peaked on day 28, whereas F. filiformis reduced methane emission. In conclusion, fermentation of corn straw with P. eryngii or L. edodes for 28 d degraded lignin and improved nutritional value as ruminant feed.
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Affiliation(s)
- Xueli Zhao
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agoecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; College of Animal Science, Southwest University, Chongqing 402460, China
| | - Fei Wang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agoecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Yi Fang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agoecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Daowei Zhou
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agoecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Shuiping Wang
- College of Animal Science, Southwest University, Chongqing 402460, China
| | - Duanqin Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, Hunan, China
| | - Lixia Wang
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agoecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Rongzhen Zhong
- Jilin Provincial Key Laboratory of Grassland Farming, Northeast Institute of Geography and Agoecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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Liu J, Yang J, Wang R, Liu L, Zhang Y, Bao H, Jang JM, Wang E, Yuan H. Comparative characterization of extracellular enzymes secreted by Phanerochaete chrysosporium during solid-state and submerged fermentation. Int J Biol Macromol 2020; 152:288-294. [DOI: 10.1016/j.ijbiomac.2020.02.256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/22/2020] [Accepted: 02/23/2020] [Indexed: 01/22/2023]
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22
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Jain KK, Kumar A, Shankar A, Pandey D, Chaudhary B, Sharma KK. De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways. Genomics 2020; 112:184-198. [DOI: 10.1016/j.ygeno.2019.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/07/2019] [Accepted: 01/20/2019] [Indexed: 12/23/2022]
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23
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Álvarez-Lindo N, Baleriola J, de Los Ríos V, Suárez T, de la Rosa EJ. RAG-2 deficiency results in fewer phosphorylated histone H2AX foci, but increased retinal ganglion cell death and altered axonal growth. Sci Rep 2019; 9:18486. [PMID: 31811168 PMCID: PMC6898044 DOI: 10.1038/s41598-019-54873-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
DNA double-strand breaks (DSBs), selectively visualized as γ-H2AX+ foci, occur during the development of the central nervous system, including the retina, although their origin and biological significance are poorly understood. Mutant mice with DSB repair mechanism defects exhibit increased numbers of γ-H2AX+ foci, increased cell death during neural development, and alterations in axonogenesis in the embryonic retina. The aim of this study was to identify putative sources of DSBs. One of the identified DSBs sources is LINE-1 retrotransposition. While we did not detect changes in LINE-1 DNA content during the early period of cell death associated with retinal neurogenesis, retinal development was altered in mice lacking RAG-2, a component of the RAG-1,2-complex responsible for initiating somatic recombination in lymphocytes. Although γ-H2AX+ foci were less abundant in the rag2−/− mouse retina, retinal ganglion cell death was increased and axonal growth and navigation were impaired in the RAG-2 deficient mice, a phenotype shared with mutant mice with defective DNA repair mechanisms. These findings demonstrate that RAG-2 is necessary for proper retinal development, and suggest that both DSB generation and repair are genuine processes intrinsic to neural development.
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Affiliation(s)
- Noemí Álvarez-Lindo
- 3D Lab: Development, Differentiation & Degeneration, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB/CSIC), Madrid, Spain
| | - Jimena Baleriola
- 3D Lab: Development, Differentiation & Degeneration, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB/CSIC), Madrid, Spain.,Laboratory of local translation in neurons and glia, Achucarro Basque Center for Neuroscience; Department of Cell Biology and Histology, University of the Basque Country, Leioa; and Ikerbasque Foundation, Bilbao, Bizkaia, Spain
| | - Vivian de Los Ríos
- Proteomics and Genomics, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB/CSIC), Madrid, Spain
| | - Teresa Suárez
- 3D Lab: Development, Differentiation & Degeneration, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB/CSIC), Madrid, Spain
| | - Enrique J de la Rosa
- 3D Lab: Development, Differentiation & Degeneration, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB/CSIC), Madrid, Spain.
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Koh S, Imamura S, Fujino N, Mizuno M, Sato N, Makishima S, Biely P, Amano Y. Characterization of Acetylxylan Esterase from White-Rot Fungus Irpex lacteus. J Appl Glycosci (1999) 2019; 66:131-137. [PMID: 34429691 PMCID: PMC8367635 DOI: 10.5458/jag.jag.jag-2019_0007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/05/2019] [Indexed: 10/26/2022] Open
Abstract
The carbohydrate esterase family 1 (CE1) in CAZy contains acetylxylan esterases (AXEs) and feruloyl esterases (FAEs). Here we cloned a gene coding for an AXE belonging to CE1 from Irpex lacteus (IlAXE1). IlAXE1 was heterologously expressed in Pichia pastoris, and the recombinant enzyme was purified and characterized. IlAXE1 hydrolyzed p-nitrophenyl acetate, α-naphthyl acetate and 4-methylumbelliferyl acetate, however, it did not show any activity on ethyl ferulate and methyl p-coumarate. We also examined the activity on partially acetylated and feruloylated xylan extracted from corncob by hydrothermal reaction. Similarly, ferulic and p-coumaric acids were not liberated, and acetic acid was only detected in the reaction mixture. The results indicated that IlAXE1 is an acetylxylan esterase actually reacted to acetyl xylan. However, since IlAXE1 was unable to completely release acetic acid esterifying xylopyranosyl residues, it is assumed that acetyl groups exhibiting resistance to deacetylation by IlAXE1 are present in corn cob xylan.
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Affiliation(s)
- Sangho Koh
- 1 Department of Bioscience and Textile Technology, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Seika Imamura
- 2 Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University
| | | | - Masahiro Mizuno
- 1 Department of Bioscience and Textile Technology, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,2 Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University.,4 Department of Chemistry and Material Engineering, Faculty of Engineering, Shinshu University
| | | | - Satoshi Makishima
- 4 Department of Chemistry and Material Engineering, Faculty of Engineering, Shinshu University.,5 B Food Science Co., Ltd
| | - Peter Biely
- 6 Institute of Chemistry, Slovak Academy of Sciences
| | - Yoshihiko Amano
- 1 Department of Bioscience and Textile Technology, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,2 Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University.,4 Department of Chemistry and Material Engineering, Faculty of Engineering, Shinshu University
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Manipulating the Expression of Small Secreted Protein 1 (Ssp1) Alters Patterns of Development and Metabolism in the White-Rot Fungus Pleurotus ostreatus. Appl Environ Microbiol 2019; 85:AEM.00761-19. [PMID: 31101610 DOI: 10.1128/aem.00761-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/09/2019] [Indexed: 01/30/2023] Open
Abstract
The function of small secreted proteins (SSPs) in saprotrophic fungi is, for the most part, unknown. The white-rot mushroom Pleurotus ostreatus produces considerable amounts of SSPs at the onset of secondary metabolism, during colony development, and in response to chemical compounds such as 5-hydroxymethylfurfural and aryl alcohols. Genetic manipulation of Ssp1, by knockdown (KDssp1) or overexpression (OEssp1), indicated that they are, in fact, involved in the regulation of the ligninolytic system. To elucidate their potential involvement in fungal development, quantitative secretome analysis was performed during the trophophase and the idiophase and at a transition point between the two growth phases. The mutations conferred a time shift in the secretion and expression patterns: OEssp1 preceded the entrance to idiophase and secondary metabolism, while KDssp1 was delayed. This was also correlated with expression patterns of selected genes. The KDssp1 colony aged at a slower pace, accompanied by a slower decline in biomass over time. In contrast, the OEssp1 strain exhibited severe lysis and aging of the colony at the same time point. These phenomena were accompanied by variations in yellow pigment production, characteristic of entrance of the wild type into idiophase. The pigment was produced earlier and in a larger amount in the OEssp1 strain and was absent from the KDssp1 strain. Furthermore, the dikaryon harboring OEssp1 exhibited a delay in the initiation of fruiting body formation as well as earlier aging. We propose that Ssp1 might function as a part of the fungal communication network and regulate the pattern of fungal development and metabolism in P. ostreatus IMPORTANCE Small secreted proteins (SSPs) are common in fungal saprotrophs, but their roles remain elusive. As such, they comprise part of a gene pool which may be involved in governing fungal lifestyles not limited to symbiosis and pathogenicity, in which they are commonly referred to as "effectors." We propose that Ssp1 in the white-rot fungus Pleurotus ostreatus regulates the transition from primary to secondary metabolism, development, aging, and fruiting body initiation. Our observations uncover a novel regulatory role of effector-like SSPs in a saprotroph, suggesting that they may act in fungal communication as well as in response to environmental cues. The presence of Ssp1 homologues in other fungal species supports a common potential role in environmental sensing and fungal development.
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Valadares F, Gonçalves TA, Damasio A, Milagres AM, Squina FM, Segato F, Ferraz A. The secretome of two representative lignocellulose-decay basidiomycetes growing on sugarcane bagasse solid-state cultures. Enzyme Microb Technol 2019; 130:109370. [PMID: 31421724 DOI: 10.1016/j.enzmictec.2019.109370] [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: 05/01/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/14/2022]
Abstract
Secretome evaluations of lignocellulose-decay basidiomycetes can reveal new enzymes in selected fungal species that degrade specific substrates. Proteins discovered in such studies can support biorefinery development. Brown-rot (Gloeophyllum trabeum) and white-rot (Pleurotus ostreatus) fungi growing in sugarcane bagasse solid-state cultures produced 119 and 63 different extracellular proteins, respectively. Several of the identified enzymes are suitable for in vitro biomass conversion, including a range of cellulases (endoglucanases, cellobiohydrolases and β-glucosidases), hemicellulases (endoxylanases, α-arabinofuranosidases, α-glucuronidases and acetylxylan esterases) and carbohydrate-active auxiliary proteins, such as AA9 lytic polysaccharide monooxygenase, AA1 laccase and AA2 versatile peroxidase. Extracellular oxalate decarboxylase was also detected in both fungal species, exclusively in media containing sugarcane bagasse. Interestingly, intracellular AA6 quinone oxidoreductases were also exclusively produced under sugarcane bagasse induction in both fungi. These enzymes promote quinone redox cycling, which is used to produce Fenton's reagents by lignocellulose-decay fungi. Hitherto undiscovered hypothetical proteins that are predicted in lignocellulose-decay fungi genomes appeared in high relative abundance in the cultures containing sugarcane bagasse, which suggests undisclosed, new biochemical mechanisms that are used by lignocellulose-decay fungi to degrade sugarcane biomass. In general, lignocellulose-decay fungi produce a number of canonical hydrolases, as well as some newly observed enzymes, that are suitable for in vitro biomass digestion in a biorefinery context.
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Affiliation(s)
- Fernanda Valadares
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil
| | - Thiago A Gonçalves
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, 18023-000 Sorocaba, SP, Brazil; Institute of Biology, University of Campinas (UNICAMP), 13080-655, Campinas, SP, Brazil
| | - André Damasio
- Institute of Biology, University of Campinas (UNICAMP), 13080-655, Campinas, SP, Brazil
| | - Adriane Mf Milagres
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, 18023-000 Sorocaba, SP, Brazil
| | - Fernando Segato
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil
| | - André Ferraz
- Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, 12602-810, Lorena, SP, Brazil.
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Li L, Liu B, Yang J, Zhang Q, He C, Jia R. Catalytic properties of a short manganese peroxidase from Irpex lacteus F17 and the role of Glu166 in the Mn 2+-independent activity. Int J Biol Macromol 2019; 136:859-869. [PMID: 31226373 DOI: 10.1016/j.ijbiomac.2019.06.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/30/2023]
Abstract
Il-MnP1 (GenBank: AGO86670.2) has been confirmed by sequence analysis as a short manganese peroxidase (MnP) from Irpex lacteus F17 (CCTCC AF 2014020). To investigate the catalytic properties, the oxidation of typical aromatic substrates and the pathways of guaiacol oxidation by Il-MnP1, both in the presence and absence of Mn2+ at either pH 4.0 or pH 7.4, were analyzed. Results showed that Il-MnP1 exhibited higher oxidative activity in the presence of Mn2+ than in the absence of Mn2+ toward the majority of the selected substrates at pH 4.0. Additionally, the similar product compositions suggested that the oxidation of guaiacol mainly belongs to a series of polymeric reactions of radicals initiated by Il-MnP1, whether they were in the presence and absence of Mn2+ at either pH 4.0 or 7.4. Furthermore, two variants (E166G, E166Q) were found using site-directed mutagenesis, to improve the Mn2+-independent oxidative activity significantly. The catalytic efficiency (Kcat/Km) of E166G and E166Q in 2, 6-dimethoxyphenol oxidation was higher than Il-MnP1 by 170 and 34 times, respectively. The study revealed certain differences in catalytic properties between Mn2+ dependent and independent oxidation by Il-MnP1. More importantly, a residue (E166) was related to the Mn2+-independent activity of a short MnP.
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Affiliation(s)
- Liuqing Li
- School of Life Science, Anhui University, Hefei, Anhui Province, China; Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei,Anhui Province, China
| | - Binjie Liu
- School of Life Science, Anhui University, Hefei, Anhui Province, China; Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei,Anhui Province, China
| | - Jun Yang
- School of Life Science, Anhui University, Hefei, Anhui Province, China; Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei,Anhui Province, China
| | - Qiong Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei, Anhui Province, China
| | - Chao He
- School of Life Science, Anhui University, Hefei, Anhui Province, China; Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei,Anhui Province, China
| | - Rong Jia
- School of Life Science, Anhui University, Hefei, Anhui Province, China; Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei,Anhui Province, China.
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Xie C, Gong W, Zhu Z, Zhou Y, Yan L, Hu Z, Ai L, Peng Y. Mapping the Secretome and Its N-Linked Glycosylation of Pleurotus eryngii and Pleurotus ostreatus Grown on Hemp Stalks. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5486-5495. [PMID: 31012315 DOI: 10.1021/acs.jafc.9b00061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Our previous research showed that Pleurotus eryngii and Pleurotus ostreatus were effective fungi for pretreatment of industrial hemp stalks to improve enzymatic saccharification. The secretomes of these two fungi were analyzed to search for the effective enzyme cocktails degrading hemp lignin during the pretreatment process. In total, 169 and 155 proteins were identified in Pleurotus eryngii and Pleurotus ostreatus, respectively, and 50% of the proteins involved in lignocellulose degradation were CAZymes. Because most of the extracellular proteins secreted by fungi are glycosylated proteins, the N-linked glycosylation of enzymes could be mapped. In total, 27 and 24 N-glycosylated peptides were detected in Pleurotus eryngii and Pleurotus ostreatus secretomes, respectively. N-Glycosylated peptides of laccase, GH92, exoglucanase, phenol oxidase, α-galactosidase, carboxylic ester hydrolase, and pectin lyase were identified. Deglycosylation could decrease enzymatic saccharification of hemp stalks. The activities of laccase, α-galactosidase, and phenol oxidase and the thermal stability of laccase were reduced after deglycosylation.
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Affiliation(s)
- Chunliang Xie
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Wenbing Gong
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Zuohua Zhu
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Yingjun Zhou
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Li Yan
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Zhenxiu Hu
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
| | - Lianzhong Ai
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
- Shanghai Engineering Research Center of Food Microbiology, School of Medical Instrument and Food Engineering , University of Shanghai for Science and Technology , Shanghai 200093 , China
| | - Yuande Peng
- Institute of Bast Fiber Crops , Chinese Academy of Agricultural Sciences , Changsha 410205 , China
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Reina R, Kellner H, Hess J, Jehmlich N, García-Romera I, Aranda E, Hofrichter M, Liers C. Genome and secretome of Chondrostereum purpureum correspond to saprotrophic and phytopathogenic life styles. PLoS One 2019; 14:e0212769. [PMID: 30822315 PMCID: PMC6396904 DOI: 10.1371/journal.pone.0212769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 02/09/2019] [Indexed: 11/28/2022] Open
Abstract
The basidiomycete Chondrostereum purpureum (Silverleaf fungus) is a saprotroph and plant pathogen commercially used for combatting forest "weed" trees in vegetation management. However, little is known about its lignocellulose-degrading capabilities and the enzymatic machinery that is responsible for the degradative potential, and it is not yet clear to which group of wood-rot fungi it actually belongs. Here, we sequenced and analyzed the draft genome of C. purpureum (41.2 Mbp) and performed a quantitative proteomic approach during growth in submerged and solid-state cultures based on soybean meal suspension or containing beech wood supplemented with phenol-rich olive mill residues, respectively. The fungus harbors characteristic lignocellulolytic hydrolases (GH6 and GH7) and oxidoreductases (e.g. laccase, heme peroxidases). High abundance of some of these genes (e.g. 45 laccases, nine GH7) can be explained by gene expansion, e.g. identified for the laccase orthogroup ORTHOMCL11 that exhibits a total of 18 lineage-specific duplications. Other expanded genes families encode for proteins more related to a pathogenic lifestyle (e.g. protease and cytochrome P450s). The fungus responds to the presence of complex growth substrates (lignocellulose, phenolic residues) by the secretion of most of these lignocellulolytic and lignin-modifying enzymes (e.g. alcohol and aryl alcohol oxidases, laccases, GH6, GH7). Based on the genetic and enzymatic constitution, we consider the 'marasmioid' fungus C. purpureum as a 'phytopathogenic' white-rot fungus (WRF) that possesses a complex extracellular enzyme machinery to accomplish efficient lignocellulose degradation during both saprotrophic and phytopathogenic life phases.
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Affiliation(s)
- Rocio Reina
- Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Harald Kellner
- Unit of Environmental Biotechnology, Dresden University of Technology, International Institute Zittau, Zittau, Germany
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Immaculada García-Romera
- Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Elisabet Aranda
- Department of Soil Microbiology and Symbiotic Systems, Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Granada, Spain
| | - Martin Hofrichter
- Unit of Environmental Biotechnology, Dresden University of Technology, International Institute Zittau, Zittau, Germany
| | - Christiane Liers
- Unit of Environmental Biotechnology, Dresden University of Technology, International Institute Zittau, Zittau, Germany
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30
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Microbial manganese peroxidase: a ligninolytic enzyme and its ample opportunities in research. SN APPLIED SCIENCES 2018. [DOI: 10.1007/s42452-018-0046-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Qin X, Luo H, Zhang X, Yao B, Ma F, Su X. Dye-decolorizing peroxidases in Irpex lacteus combining the catalytic properties of heme peroxidases and laccase play important roles in ligninolytic system. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:302. [PMID: 30455731 PMCID: PMC6223037 DOI: 10.1186/s13068-018-1303-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/26/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND The white rot fungus Irpex lacteus exhibits a great potential in biopretreatment of lignocellulose as well as in biodegradation of xenobiotic compounds by extracellular ligninolytic enzymes. Among these enzymes, the possible involvement of dye-decolorizing peroxidase (DyP) in lignin degradation is not clear yet. RESULTS Based on the extracellular enzyme activities and secretome analysis, I. lacteus CD2 produced DyPs as the main ligninolytic enzymes when grown in Kirk's medium supplemented with lignin. Further transcriptome analysis revealed that induced transcription of genes encoding DyPs was accompanied by the increased expression of transcripts for H2O2-generating enzymes such as alcohol oxidase, pyranose 2-oxidase, and glyoxal oxidases. Meanwhile, accumulation of transcripts for glycoside hydrolase and protease was observed, in agreement with abundant proteins. Moreover, the biochemical analysis of IlDyP2 and IlDyP1 confirmed that DyPs were able to catalyze the oxidation of typical peroxidases substrates ABTS, phenolic lignin compounds DMP, and guaiacol as well as non-phenolic lignin compound, veratryl alcohol. More importantly, IlDyP1 enhanced catalytic activity for veratryl alcohol oxidation in the presence of mediator 1-hydroxybenzotriazole, which was similar to the laccase/1-hydroxybenzotriazole system. CONCLUSIONS The results proved for the first time that DyPs depolymerized lignin individually, combining catalytic features of different peroxidases on the functional level. Therefore, DyPs may be considered an important part of ligninolytic system in wood-decaying fungi.
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Affiliation(s)
- Xing Qin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Xiaoyu Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
| | - Fuying Ma
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 China
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Guo H, Wang XD, Lee DJ. Proteomic researches for lignocellulose-degrading enzymes: A mini-review. BIORESOURCE TECHNOLOGY 2018; 265:532-541. [PMID: 29884341 DOI: 10.1016/j.biortech.2018.05.101] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 05/14/2023]
Abstract
Protective action of lignin/hemicellulose networks and crystalline structures of embedded cellulose render lignocellulose material resistant to external enzymatic attack. To eliminate this bottleneck, research has been conducted in which advanced proteomic techniques are applied to identify effective commercial hydrolytic enzymes. This mini-review summarizes researches on lignocellulose-degrading enzymes, the mechanisms of the responses of various lignocellulose-degrading strains and microbial communities to various carbon sources and various biomass substrates, post-translational modifications of lignocellulose-degrading enzymes, new lignocellulose-degrading strains, new lignocellulose-degrading enzymes and a new method of secretome analysis. The challenges in the practical use of enzymatic hydrolysis process to realize lignocellulose biorefineries are discussed, along with the prospects for the same.
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Affiliation(s)
- Hongliang Guo
- College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Xiao-Dong Wang
- Research Center of Engineering Thermophysics, North China Electric Power University, Beijing 102206, China; School of Energy Power and Mechanical Engineering, North China Electric Power University, Beijing 102206, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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Niu D, Zuo S, Jiang D, Tian P, Zheng M, Xu C. Treatment using white rot fungi changed the chemical composition of wheat straw and enhanced digestion by rumen microbiota in vitro. Anim Feed Sci Technol 2018. [DOI: 10.1016/j.anifeedsci.2018.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang Y, Shao Y, Zou X, Yang M, Guo L. Synergistic action between extracellular products from white-rot fungus and cellulase significantly improves enzymatic hydrolysis. Bioengineered 2018; 9:178-185. [PMID: 28384075 PMCID: PMC5972936 DOI: 10.1080/21655979.2017.1308991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With a set of perfect extracellular lignocellulolytic enzymes, white-rot fungus has been recognized as playing an important role in the degradation of lignocellulose materials, which leads to the possibility of creating a composite enzymatic system with high hydrolysis efficiency in vitro. Echinodontium taxodii is a promising white-rot fungus for biologic pretreatment. In this study, we extracted the extracellular products of E. taxodii under solid-state fermentation conditions, mixed the extracellular products with cellulase to build a composite enzymatic system, and systematically evaluated the effect of this system on the hydrolysis of acid-pretreated and raw maize stovers. We found that the extracellular products from E. taxodii could significantly improve the hydrolysis efficiency of cellulase, with a synergistic action between the extracellular products and cellulase. Corn stovers treated with extracellular products were suitable for the enzymatic hydrolysis of cellulase. Furthermore, we found that pure proteins from the extracellular products were not sufficient to generate synergistic action. This finding suggests that non-protein substances may also be involved in the synergistic action between the extracellular products and cellulase.
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Affiliation(s)
- Yushan Wang
- a Department of Biotechnology , Heilongjiang Vocational Institute of Ecological Engineering, Heilongjiang Province , China
| | - Yang Shao
- a Department of Biotechnology , Heilongjiang Vocational Institute of Ecological Engineering, Heilongjiang Province , China
| | - Xinyue Zou
- a Department of Biotechnology , Heilongjiang Vocational Institute of Ecological Engineering, Heilongjiang Province , China
| | - Mandi Yang
- a Department of Biotechnology , Heilongjiang Vocational Institute of Ecological Engineering, Heilongjiang Province , China
| | - Lin Guo
- a Department of Biotechnology , Heilongjiang Vocational Institute of Ecological Engineering, Heilongjiang Province , China
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Qin X, Su X, Luo H, Ma R, Yao B, Ma F. Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:58. [PMID: 29507610 PMCID: PMC5833081 DOI: 10.1186/s13068-018-1060-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/23/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Irpex lacteus is one of the most potent white rot fungi for biological pretreatment of lignocellulose for second biofuel production. To elucidate the underlying molecular mechanism involved in lignocellulose deconstruction, genomic and transcriptomic analyses were carried out for I. lacteus CD2 grown in submerged fermentation using ball-milled corn stover as the carbon source. RESULTS Irpex lacteus CD2 efficiently decomposed 74.9% lignin, 86.3% cellulose, and 83.5% hemicellulose in corn stover within 9 days. Manganese peroxidases were rapidly induced, followed by accumulation of cellulase and hemicellulase. Genomic analysis revealed that I. lacteus CD2 possessed a complete set of lignocellulose-degrading enzyme system composed mainly of class II peroxidases, dye-decolorizing peroxidases, auxiliary enzymes, and 182 glycoside hydrolases. Comparative transcriptomic analysis substantiated the notion of a selection mode of degradation. These analyses also suggested that free radicals, derived either from MnP-organic acid interplay or from Fenton reaction involving Fe2+ and H2O2, could play an important role in lignocellulose degradation. CONCLUSIONS The selective strategy employed by I. lacteus CD2, in combination with low extracellular glycosidases cleaving plant cell wall polysaccharides into fermentable sugars, may account for high pretreatment efficiency of I. lacteus. Our study also hints the importance of free radicals for future designing of novel, robust lignocellulose-degrading enzyme cocktails.
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Affiliation(s)
- Xing Qin
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Fuying Ma
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
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Zerva A, Zervakis GI, Christakopoulos P, Topakas E. Degradation of olive mill wastewater by the induced extracellular ligninolytic enzymes of two wood-rot fungi. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 203:791-798. [PMID: 26947318 DOI: 10.1016/j.jenvman.2016.02.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/17/2016] [Accepted: 02/22/2016] [Indexed: 05/25/2023]
Abstract
Olive mill wastewater (OMWW) is a major problem in olive oil - producing countries, due to its high organic load and concentration in phenols that are toxic for marine life, plants and soil microorganisms. In the present study, two mushroom species were tested in regard to their OMWW's oxidative capacity, Pleurotus citrinopileatus LGAM 28684 and Irpex lacteus LGAM 238. OMWW (25% v/v) degradation was investigated for several culture conditions, namely pH, agitation speed, nitrogen-based supplements and their concentration. The selected values were pH 6, agitation rate 150 rpm, 30 g L-1 corn steep liquor as nitrogen source for P. citrinopileatus and 20 g L-1 diammonium tartrate for I. lacteus. The two strains performed well in cultures supplemented with OMWW, generating very high titers of oxidative enzymes and achieving more than 90% color and phenols reduction within a 24 days cultivation period. In addition, the amount of glucans present in the fungal biomass was assessed. Hence, P. citrinopileatus and I. lacteus appear as potent degraders of OMWW with the ability to use the effluent as a substrate for the production of biotechnologically important enzymes and valuable fungal glucans.
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Affiliation(s)
- Anastasia Zerva
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens 15780, Greece
| | - Georgios I Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Paul Christakopoulos
- Biochemical and Chemical Process Engineering, Division of Sustainable Process Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Evangelos Topakas
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, Athens 15780, Greece.
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Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study. Sci Rep 2017; 7:11356. [PMID: 28900110 PMCID: PMC5595786 DOI: 10.1038/s41598-017-10132-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/06/2017] [Indexed: 11/08/2022] Open
Abstract
Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level for the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.
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Efficient screening of potential cellulases and hemicellulases produced by Bosea sp. FBZP-16 using the combination of enzyme assays and genome analysis. World J Microbiol Biotechnol 2017; 33:29. [PMID: 28058637 DOI: 10.1007/s11274-016-2198-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
Identification of bacteria that produce carbohydrolytic enzymes is extremely important given the increased demand for these enzymes in many industries. Twenty lignocellulose-degrading bacterial isolates from Algerian compost and different soils were screened for their potential to produce different enzymes involved in biomass deconstruction. Based on 16S rRNA gene sequencing, the isolates belonged to Proteobacteria and Actinobacteria. Differences among species were reflected both as the presence/absence of enzymes or at the level of enzyme activity. Among the most active species, Bosea sp. FBZP-16 demonstrated cellulolytic activity on both amorphous cellulose (CMC) and complex lignocellulose (wheat straw) and was selected for whole-genomic sequencing. The genome sequencing revealed the presence of a complex enzymatic machinery required for organic matter decomposition. Analysis of the enzyme-encoding genes indicated that multiple genes for endoglucanase, xylanase, β-glucosidase and β-mannosidase are present in the genome with enzyme activities displayed by the bacterium, while other enzymes, such as certain cellobiohydrolases, were not detected at the genomic level. This indicates that a combination of functional screening of bacterial cultures with the use of genome-derived information is important for the prediction of potential enzyme production. These results provide insight into their possible exploitation for the production of fuels and chemicals derived from plant biomass.
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Qin X, Sun X, Huang H, Bai Y, Wang Y, Luo H, Yao B, Zhang X, Su X. Oxidation of a non-phenolic lignin model compound by two Irpex lacteus manganese peroxidases: evidence for implication of carboxylate and radicals. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:103. [PMID: 28439296 PMCID: PMC5399396 DOI: 10.1186/s13068-017-0787-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/12/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Manganese peroxidase is one of the Class II fungal peroxidases that are able to oxidize the low redox potential phenolic lignin compounds. For high redox potential non-phenolic lignin degradation, mediators such as GSH and unsaturated fatty acids are required in the reaction. However, it is not known whether carboxylic acids are a mediator for non-phenolic lignin degradation. RESULTS The white rot fungus Irpex lacteus is one of the most potent fungi in degradation of lignocellulose and xenobiotics. Two manganese peroxidases (IlMnP1 and IlMnP2) from I. lacteus CD2 were over-expressed in Escherichia coli and successfully refolded from inclusion bodies. Both IlMnP1 and IlMnP2 oxidized the phenolic compounds efficiently. Surprisingly, they could degrade veratryl alcohol, a non-phenolic lignin compound, in a Mn2+-dependent fashion. Malonate or oxalate was found to be also essential in this degradation. The oxidation of non-phenolic lignin was further confirmed by analysis of the reaction products using LC-MS/MS. We proved that Mn2+ and a certain carboxylate are indispensable in oxidation and that the radicals generated under this condition, specifically superoxide radical, are at least partially involved in lignin oxidative degradation. IlMnP1 and IlMnP2 can also efficiently decolorize dyes with different structures. CONCLUSIONS We provide evidence that a carboxylic acid may mediate oxidation of non-phenolic lignin through the action of radicals. MnPs, but not LiP, VP, or DyP, are predominant peroxidases secreted by some white rot fungi such as I. lacteus and the selective lignocellulose degrader Ceriporiopsis subvermispora. Our finding will help understand how these fungi can utilize MnPs and an excreted organic acid, which is usually a normal metabolite, to efficiently degrade the non-phenolic lignin. The unique properties of IlMnP1 and IlMnP2 make them good candidates for exploring molecular mechanisms underlying non-phenolic lignin compounds oxidation by MnPs and for applications in lignocellulose degradation and environmental remediation.
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Affiliation(s)
- Xing Qin
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Xianhua Sun
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
| | - Xiaoyu Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074 People’s Republic of China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081 People’s Republic of China
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Gómez-Gómez L, Parra-Vega V, Rivas-Sendra A, Seguí-Simarro JM, Molina RV, Pallotti C, Rubio-Moraga Á, Diretto G, Prieto A, Ahrazem O. Unraveling Massive Crocins Transport and Accumulation through Proteome and Microscopy Tools during the Development of Saffron Stigma. Int J Mol Sci 2017; 18:E76. [PMID: 28045431 PMCID: PMC5297711 DOI: 10.3390/ijms18010076] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 11/18/2022] Open
Abstract
Crocins, the glucosides of crocetin, are present at high concentrations in saffron stigmas and accumulate in the vacuole. However, the biogenesis of the saffron chromoplast, the changes during the development of the stigma and the transport of crocins to the vacuole, are processes that remain poorly understood. We studied the process of chromoplast differentiation in saffron throughout stigma development by means of transmission electron microscopy. Our results provided an overview of a massive transport of crocins to the vacuole in the later developmental stages, when electron dense drops of a much greater size than plastoglobules (here defined "crocinoplast") were observed in the chromoplast, connected to the vacuole with a subsequent transfer of these large globules inside the vacuole. A proteome analysis of chromoplasts from saffron stigma allowed the identification of several well-known plastid proteins and new candidates involved in crocetin metabolism. Furthermore, expressions throughout five developmental stages of candidate genes responsible for carotenoid and apocarotenoid biogenesis, crocins transport to the vacuole and starch metabolism were analyzed. Correlation matrices and networks were exploited to identify a series of transcripts highly associated to crocetin (such as 1-Deoxy-d-xylulose 5-phosphate synthase (DXS), 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), carotenoid isomerase (CRTISO), Crocetin glucosyltransferase 2 (UGT2), etc.) and crocin (e.g., ζ-carotene desaturase (ZDS) and plastid-lipid-associated proteins (PLAP2)) accumulation; in addition, candidate aldehyde dehydrogenase (ADH) genes were highlighted.
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Affiliation(s)
- Lourdes Gómez-Gómez
- Botanical Institute, Department of Science Technology, Agroforestry and Genetics, Faculty of Pharmacy, University of Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain.
| | - Verónica Parra-Vega
- Cell Biology Group, COMAV Institute, Polytechnic University of Valencia, 46071 Valencia, Spain.
| | - Alba Rivas-Sendra
- Cell Biology Group, COMAV Institute, Polytechnic University of Valencia, 46071 Valencia, Spain.
| | - Jose M Seguí-Simarro
- Cell Biology Group, COMAV Institute, Polytechnic University of Valencia, 46071 Valencia, Spain.
| | - Rosa Victoria Molina
- Department of Vegetal Biology, Polytechnic University of Valencia, 46071 Valencia, Spain.
| | - Claudia Pallotti
- Department of Vegetal Biology, Polytechnic University of Valencia, 46071 Valencia, Spain.
| | - Ángela Rubio-Moraga
- Botanical Institute, Department of Science Technology, Agroforestry and Genetics, Faculty of Pharmacy, University of Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain.
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy.
| | - Alicia Prieto
- The Biological Research Center (CIB) Spanish National Research Council (CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain.
| | - Oussama Ahrazem
- Botanical Institute, Department of Science Technology, Agroforestry and Genetics, Faculty of Pharmacy, University of Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain.
- Faculty of Environmental Sciences and Biochemistry Toledo, University of Castilla-La Mancha, Campus Tecnológico de la Fábrica de Armas, Avda, Carlos III, s/n, 45071 Toledo, Spain.
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Ma J, Zhang K, Huang M, Hector SB, Liu B, Tong C, Liu Q, Zeng J, Gao Y, Xu T, Liu Y, Liu X, Zhu Y. Involvement of Fenton chemistry in rice straw degradation by the lignocellulolytic bacterium Pantoea ananatis Sd-1. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:211. [PMID: 27761153 PMCID: PMC5054592 DOI: 10.1186/s13068-016-0623-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/24/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Lignocellulolytic bacteria have revealed to be a promising source for biofuel production, yet the underlying mechanisms are still worth exploring. Our previous study inferred that the highly efficient lignocellulose degradation by bacterium Pantoea ananatis Sd-1 might involve Fenton chemistry (Fe2+ + H2O2 + H+ → Fe3+ + OH· + H2O), similar to that of white-rot and brown-rot fungi. The aim of this work is to investigate the existence of this Fenton-based oxidation mechanism in the rice straw degradation process of P. ananatis Sd-1. RESULTS After 3 days incubation of unpretreated rice straw with P. ananatis Sd-1, the percentage in weight reduction of rice straw as well as its cellulose, hemicellulose, and lignin components reached 46.7, 43.1, 42.9, and 37.9 %, respectively. The addition of different hydroxyl radical scavengers resulted in a significant decline (P < 0.001) in rice straw degradation. Pyrolysis gas chromatography-mass spectrometry and Fourier transform infrared spectroscopy analysis revealed the consistency of chemical changes of rice straw components that exists between P. ananatis Sd-1 and Fenton reagent treatment. In addition to the increased total iron ion concentration throughout the rice straw decomposition process, the Fe3+-reducing capacity of P. ananatis Sd-1 was induced by rice straw and predominantly contributed by aromatic compounds metabolites. The transcript levels of the glucose-methanol-choline oxidoreductase gene related to hydrogen peroxide production were significantly up-regulated (at least P < 0.01) in rice straw cultures. Higher activities of GMC oxidoreductase and less hydrogen peroxide concentration in rice straw cultures relative to glucose cultures may be responsible for increasing rice straw degradation, which includes Fenton-like reactions. CONCLUSIONS Our results confirmed the Fenton chemistry-assisted degradation model in P. ananatis Sd-1. We are among the first to show that a Fenton-based oxidation mechanism exists in a bacteria degradation system, which provides a new perspective for how natural plant biomass is decomposed by bacteria. This degradative system may offer an alternative approach to the fungi system for lignocellulosic biofuels production.
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Affiliation(s)
- Jiangshan Ma
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Keke Zhang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Mei Huang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Stanton B. Hector
- Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
- DNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Private Bag X1, Matieland, 7602 South Africa
| | - Bin Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Chunyi Tong
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Qian Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Jiarui Zeng
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Yan Gao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Ting Xu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Ying Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Yonghua Zhu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
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Vasina DV, Pavlov AR, Koroleva OV. Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate. BMC Microbiol 2016; 16:106. [PMID: 27296712 PMCID: PMC4906887 DOI: 10.1186/s12866-016-0729-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 06/06/2016] [Indexed: 11/10/2022] Open
Abstract
Background Fungi are organisms with the highest natural capacity to degrade lignocellulose substrates, which is enabled by complex systems of extracellular enzymes, whose expression and secretion depend on the characteristics of substrates and the environment. Results This study reports a secretome analysis for white-rot basidiomycete Trametes hirsuta cultivated on a synthetic media and a lignocellulose substrate. We demonstrate that T. hirsuta st. 072 produces multiple extracellular ligninolytic, cellulolytic, hemicellulolytic, peroxide generating, and proteolytic enzymes, as well as cerato-platanins. In contrast to other white rot species described earlier, which mostly secreted glucanases and mannosidases in response to the presence of the lignocellulose substrate, T. hirsuta expressed a spectrum of extracellular cellulolytic enzymes containing predominantly cellobiases and xylanases. As proteomic analysis could not detect lignin peroxidase (LiP) among the secreted lignin degrading enzymes, we attributed the observed extracellular LiP - like activity to the expressed versatile peroxidase (VP). An accessory enzyme, glyoxal oxidase, was found among the proteins secreted in the media during submerged cultivation of T. hirsuta both in the presence and in the absence of copper. However, aryl-alcohol oxidase (AAO) was not identified, despite the presence of AAO enzymatic activity secreted by the fungus. The spectra of the expressed enzymes dramatically changed depending on the growth conditions. Transfer from submerged cultivation to surface cultivation with the lignocellulose substrate switched off expression of exo-β-1,3-glucanase and α-amylase and turned on secretion of endo-β-1,3-glucanase and a range of glycosidases. In addition, an aspartic peptidase started being expressed instead of family S53 protease. For the first time, we report production of cerato-platanin proteins by Trametes species. The secretion of cerato-platanins was observed only in response to contact with lignocellulose, thus indicating a specific role of these proteins in degradation of the lignocellulose substrates. Conclusions Our results suggest a sequential mechanism of natural substrate degradation by T. hirsuta, in which the fungus produces different sets of enzymes to digest all main components of the substrate during cultivation. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0729-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daria V Vasina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia.
| | - Andrey R Pavlov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
| | - Olga V Koroleva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave, Moscow, 119071, Russia
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Valadares F, Gonçalves TA, Gonçalves DSPO, Segato F, Romanel E, Milagres AMF, Squina FM, Ferraz A. Exploring glycoside hydrolases and accessory proteins from wood decay fungi to enhance sugarcane bagasse saccharification. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:110. [PMID: 27222665 PMCID: PMC4877993 DOI: 10.1186/s13068-016-0525-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/10/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) and accessory proteins are key components for efficient and cost-effective enzymatic hydrolysis of polysaccharides in modern, biochemically based biorefineries. Currently, commercialized GHs and accessory proteins are produced by ascomycetes. However, the role of wood decay basidiomycetes proteins in biomass saccharification has not been extensively pursued. Wood decay fungi degrade polysaccharides in highly lignified tissues in natural environments, and are a promising enzyme source for improving enzymatic cocktails that are designed for in vitro lignocellulose conversion. RESULTS GHs and accessory proteins were produced by representative brown- and white-rot fungi, Laetiporus sulphureus and Pleurotus ostreatus, respectively. Concentrated protein extracts were then used to amend commercial enzymatic cocktails for saccharification of alkaline-sulfite pretreated sugarcane bagasse. The main enzymatic activities found in the wood decay fungal protein extracts were attributed to endoglucanases, xylanases and β-glucosidases. Cellobiohydrolase (CBH) activities in the L. sulphureus and P. ostreatus extracts were low and nonexistent, respectively. The initial glucan conversion rates were boosted when the wood decay fungal proteins were used to replace half of the enzymes from the commercial cocktails. L. sulphureus proteins increased the glucan conversion levels, with values above those observed for the full load of commercial enzymes. Wood decay fungal proteins also enhanced the xylan conversion efficiency due to their high xylanase activities. Proteomic studies revealed 104 and 45 different proteins in the P. ostreatus and L. sulphureus extracts, respectively. The enhancement of the saccharification of alkaline-pretreated substrates by the modified enzymatic cocktails was attributed to the following protein families: GH5- and GH45-endoglucanases, GH3-β-glucosidases, and GH10-xylanases. CONCLUSIONS The extracellular proteins produced by wood decay fungi provide useful tools to improve commercial enzyme cocktails that are currently used for the saccharification of alkaline-pretreated lignocellulosic substrates. The relevant proteins encompass multiple glycoside hydrolase families, including the GH5- and GH45-endoglucanases, GH3-β-glucosidases, and GH10-xylanases.
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Affiliation(s)
- Fernanda Valadares
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Thiago A. Gonçalves
- />Laboratório Nacional de Ciência & Tecnolologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970 Brazil
- />Departamento de Bioquímica, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862 Brazil
| | - Dayelle S. P. O. Gonçalves
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Fernando Segato
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Elisson Romanel
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Adriane M. F. Milagres
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
| | - Fabio M. Squina
- />Laboratório Nacional de Ciência & Tecnolologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970 Brazil
| | - André Ferraz
- />Departamento de Biotecnologia, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP 12602-810 Brazil
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Sun S, Xie S, Chen H, Cheng Y, Shi Y, Qin X, Dai SY, Zhang X, Yuan JS. Genomic and molecular mechanisms for efficient biodegradation of aromatic dye. JOURNAL OF HAZARDOUS MATERIALS 2016; 302:286-295. [PMID: 26476316 DOI: 10.1016/j.jhazmat.2015.09.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 06/05/2023]
Abstract
Understanding the molecular mechanisms for aromatic compound degradation is crucial for the development of effective bioremediation strategies. We report the discovery of a novel phenomenon for improved degradation of Direct Red 5B azo dye by Irpex lacteus CD2 with lignin as a co-substrate. Transcriptomics analysis was performed to elucidate the molecular mechanisms of aromatic degradation in white rot fungus by comparing dye, lignin, and dye/lignin combined treatments. A full spectrum of lignin degradation peroxidases, oxidases, radical producing enzymes, and other relevant components were up-regulated under DR5B and lignin treatments. Lignin induced genes complemented the DR5B induced genes to provide essential enzymes and redox conditions for aromatic compound degradation. The transcriptomics analysis was further verified by manganese peroxidase (MnP) protein over-expression, as revealed by proteomics, dye decolorization assay by purified MnP and increased hydroxyl radical levels, as indicated by an iron reducing activity assay. Overall, the molecular and genomic mechanisms indicated that effective aromatic polymer degradation requires synergistic enzymes and radical-mediated oxidative reactions to form an effective network of chemical processes. This study will help to guide the development of effective bioremediation and biomass degradation strategies.
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Affiliation(s)
- Su Sun
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathology, Texas A&M University, College station, TX, USA
| | - Shangxian Xie
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Hu Chen
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Yanbing Cheng
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Yan Shi
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Xing Qin
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Susie Y Dai
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathology, Texas A&M University, College station, TX, USA
| | - Xiaoyu Zhang
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Joshua S Yuan
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub, and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
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Kuuskeri J, Häkkinen M, Laine P, Smolander OP, Tamene F, Miettinen S, Nousiainen P, Kemell M, Auvinen P, Lundell T. Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:192. [PMID: 27602055 PMCID: PMC5011852 DOI: 10.1186/s13068-016-0608-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/30/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The white-rot Agaricomycetes species Phlebia radiata is an efficient wood-decaying fungus degrading all wood components, including cellulose, hemicellulose, and lignin. We cultivated P. radiata in solid state cultures on spruce wood, and extended the experiment to 6 weeks to gain more knowledge on the time-scale dynamics of protein expression upon growth and wood decay. Total proteome and transcriptome of P. radiata were analyzed by peptide LC-MS/MS and RNA sequencing at specific time points to study the enzymatic machinery on the fungus' natural growth substrate. RESULTS According to proteomics analyses, several CAZy oxidoreductase class-II peroxidases with glyoxal and alcohol oxidases were the most abundant proteins produced on wood together with enzymes important for cellulose utilization, such as GH7 and GH6 cellobiohydrolases. Transcriptome additionally displayed expression of multiple AA9 lytic polysaccharide monooxygenases indicative of oxidative cleavage of wood carbohydrate polymers. Large differences were observed for individual protein quantities at specific time points, with a tendency of enhanced production of specific peroxidases on the first 2 weeks of growth on wood. Among the 10 class-II peroxidases, new MnP1-long, characterized MnP2-long and LiP3 were produced in high protein abundances, while LiP2 and LiP1 were upregulated at highest level as transcripts on wood together with the oxidases and one acetyl xylan esterase, implying their necessity as primary enzymes to function against coniferous wood lignin to gain carbohydrate accessibility and fungal growth. Majority of the CAZy encoding transcripts upregulated on spruce wood represented activities against plant cell wall and were identified in the proteome, comprising main activities of white-rot decay. CONCLUSIONS Our data indicate significant changes in carbohydrate-active enzyme expression during the six-week surveillance of P. radiata growing on wood. Response to wood substrate is seen already during the first weeks. The immediate oxidative enzyme action on lignin and wood cell walls is supported by detected lignin substructure sidechain cleavages, release of phenolic units, and visual changes in xylem cell wall ultrastructure. This study contributes to increasing knowledge on fungal genetics and lignocellulose bioconversion pathways, allowing us to head for systems biology, development of biofuel production, and industrial applications on plant biomass utilizing wood-decay fungi.
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Affiliation(s)
- Jaana Kuuskeri
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
| | - Mari Häkkinen
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
| | - Pia Laine
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Olli-Pekka Smolander
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Fitsum Tamene
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sini Miettinen
- Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Paula Nousiainen
- Laboratory of Organic Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Marianna Kemell
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Taina Lundell
- Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O.Box 56, Viikki Biocenter 1, 00014 Helsinki, Finland
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Thomsen ST, Londoño JEG, Ambye-Jensen M, Heiske S, Kádár Z, Meyer AS. Combination of ensiling and fungal delignification as effective wheat straw pretreatment. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:16. [PMID: 26819628 PMCID: PMC4728756 DOI: 10.1186/s13068-016-0437-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 01/08/2016] [Indexed: 05/14/2023]
Abstract
BACKGROUND Utilization of lignocellulosic feedstocks for bioenergy production in developing countries demands competitive but low-tech conversion routes. White-rot fungi (WRF) inoculation and ensiling are two methods previously investigated for low-tech pretreatment of biomasses such as wheat straw (WS). This study was undertaken to assess whether a combination of forced ensiling with Lactobacillus buchneri and WRF treatment using a low cellulase fungus, Ceriporiopsis subvermispora, could produce a relevant pretreatment effect on WS for bioethanol and biogas production. RESULTS A combination of the ensiling and WRF treatment induced efficient pretreatment of WS by reducing lignin content and increasing enzymatic sugar release, thereby enabling an ethanol yield of 66 % of the theoretical max on the WS glucan, i.e. a yield comparable to yields obtained with high-tech, large-scale pretreatment methods. The pretreatment effect was reached with only a minor total solids loss of 5 % by weight mainly caused by the fungal metabolism. The combination of the biopretreatments did not improve the methane potential of the WS, but improved the initial biogas production rate significantly. CONCLUSION The combination of the L. buchneri ensiling and C. subvermispora WRF treatment provided a significant improvement in the pretreatment effect on WS. This combined biopretreatment produced particularly promising results for ethanol production.
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Affiliation(s)
- Sune T. Thomsen
- />Department of Chemical and Biochemical Engineering, Center for BioProcess Engineering, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jorge E. G. Londoño
- />Department of Chemical and Biochemical Engineering, Center for BioProcess Engineering, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Morten Ambye-Jensen
- />Department of Chemical and Biochemical Engineering, Center for BioProcess Engineering, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- />Department of Engineering, Biological and Chemical Engineering Section, Aarhus University, Aarhus, Denmark
| | - Stefan Heiske
- />Department of Chemical and Biochemical Engineering, Center for BioProcess Engineering, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Zsofia Kádár
- />Department of Chemical and Biochemical Engineering, Center for BioProcess Engineering, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Anne S. Meyer
- />Department of Chemical and Biochemical Engineering, Center for BioProcess Engineering, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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Fernández-Fueyo E, Ruiz-Dueñas FJ, López-Lucendo MF, Pérez-Boada M, Rencoret J, Gutiérrez A, Pisabarro AG, Ramírez L, Martínez AT. A secretomic view of woody and nonwoody lignocellulose degradation by Pleurotus ostreatus. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:49. [PMID: 26933449 PMCID: PMC4772462 DOI: 10.1186/s13068-016-0462-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/11/2016] [Indexed: 05/23/2023]
Abstract
BACKGROUND Pleurotus ostreatus is the second edible mushroom worldwide, and a model fungus for delignification applications, with the advantage of growing on woody and nonwoody feedstocks. Its sequenced genome is available, and this gave us the opportunity to perform proteomic studies to identify the enzymes overproduced in lignocellulose cultures. RESULTS Monokaryotic P. ostreatus (PC9) was grown with poplar wood or wheat straw as the sole C/N source and the extracellular proteins were analyzed, together with those from glucose medium. Using nano-liquid chromatography coupled to tandem mass spectrometry of whole-protein hydrolyzate, over five-hundred proteins were identified. Thirty-four percent were unique of the straw cultures, while only 15 and 6 % were unique of the glucose and poplar cultures, respectively (20 % were produced under the three conditions, and additional 19 % were shared by the two lignocellulose cultures). Semi-quantitative analysis showed oxidoreductases as the main protein type both in the poplar (39 % total abundance) and straw (31 %) secretomes, while carbohydrate-active enzymes (CAZys) were only slightly overproduced (14-16 %). Laccase 10 (LACC10) was the main protein in the two lignocellulose secretomes (10-14 %) and, together with LACC2, LACC9, LACC6, versatile peroxidase 1 (VP1), and manganese peroxidase 3 (MnP3), were strongly overproduced in the lignocellulose cultures. Seven CAZys were also among the top-50 proteins, but only CE16 acetylesterase was overproduced on lignocellulose. When the woody and nonwoody secretomes were compared, GH1 and GH3 β-glycosidases were more abundant on poplar and straw, respectively and, among less abundant proteins, VP2 was overproduced on straw, while VP3 was only found on poplar. The treated lignocellulosic substrates were analyzed by two-dimensional nuclear magnetic resonance (2D NMR), and a decrease of lignin relative to carbohydrate signals was observed, together with the disappearance of some minor lignin substructures, and an increase of sugar reducing ends. CONCLUSIONS Oxidoreductases are strongly induced when P. ostreatus grows on woody and nonwoody lignocellulosic substrates. One laccase occupied the first position in both secretomes, and three more were overproduced together with one VP and one MnP, suggesting an important role in lignocellulose degradation. Preferential removal of lignin vs carbohydrates was shown by 2D NMR, in agreement with the above secretomic results.
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Affiliation(s)
- Elena Fernández-Fueyo
- />Department of Biotechnology, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
| | | | | | - Marta Pérez-Boada
- />Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge Rencoret
- />Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, PO Box 1052, 41080 Seville, Spain
| | - Ana Gutiérrez
- />Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, PO Box 1052, 41080 Seville, Spain
| | - Antonio G. Pisabarro
- />Department of Agrarian Production, Universidad Pública de Navarra, 31006, Pamplona, Spain
| | - Lucía Ramírez
- />Department of Agrarian Production, Universidad Pública de Navarra, 31006, Pamplona, Spain
| | - Angel T. Martínez
- />Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Ogunmolu FE, Kaur I, Gupta M, Bashir Z, Pasari N, Yazdani SS. Proteomics Insights into the Biomass Hydrolysis Potentials of a Hypercellulolytic Fungus Penicillium funiculosum. J Proteome Res 2015; 14:4342-58. [PMID: 26288988 DOI: 10.1021/acs.jproteome.5b00542] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The quest for cheaper and better enzymes needed for the efficient hydrolysis of lignocellulosic biomass has placed filamentous fungi in the limelight for bioprospecting research. In our search for efficient biomass degraders, we identified a strain of Penicillium funiculosum whose secretome demonstrates high saccharification capabilities. Our probe into the secretome of the fungus through qualitative and label-free quantitative mass spectrometry based proteomics studies revealed a high abundance of inducible CAZymes and several nonhydrolytic accessory proteins. The preferential association of these proteins and the attending differential biomass hydrolysis gives an insight into their interactions and clues about possible roles of novel hydrolytic and nonhydrolytic proteins in the synergistic deconstruction of lignocellulosic biomass. Our study thus provides the first comprehensive insight into the repertoire of proteins present in a high-performing secretome of a hypercellulolytic Penicillium funiculosum, their relative abundance in the secretome, and the interaction dynamics of the various protein groups in the secretome. The gleanings from the stoichiometry of these interactions hold a prospect as templates in the design of cost-effective synthetic cocktails for the optimal hydrolysis of biomass.
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Affiliation(s)
- Funso Emmanuel Ogunmolu
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Inderjeet Kaur
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Mayank Gupta
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Zeenat Bashir
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Nandita Pasari
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
| | - Syed Shams Yazdani
- Synthetic Biology and Biofuels Group, ‡Malaria Group, and §DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , Aruna Asaf Ali Marg, 110 067 New Delhi, India
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White biotechnology: State of the art strategies for the development of biocatalysts for biorefining. Biotechnol Adv 2015; 33:1653-70. [PMID: 26303096 DOI: 10.1016/j.biotechadv.2015.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/31/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
White biotechnology is a term that is now often used to describe the implementation of biotechnology in the industrial sphere. Biocatalysts (enzymes and microorganisms) are the key tools of white biotechnology, which is considered to be one of the key technological drivers for the growing bioeconomy. Biocatalysts are already present in sectors such as the chemical and agro-food industries, and are used to manufacture products as diverse as antibiotics, paper pulp, bread or advanced polymers. This review proposes an original and global overview of highly complementary fields of biotechnology at both enzyme and microorganism level. A certain number of state of the art approaches that are now being used to improve the industrial fitness of biocatalysts particularly focused on the biorefinery sector are presented. The first part deals with the technologies that underpin the development of industrial biocatalysts, notably the discovery of new enzymes and enzyme improvement using directed evolution techniques. The second part describes the toolbox available by the cell engineer to shape the metabolism of microorganisms. And finally the last part focuses on the 'omic' technologies that are vital for understanding and guide microbial engineering toward more efficient microbial biocatalysts. Altogether, these techniques and strategies will undoubtedly help to achieve the challenging task of developing consolidated bioprocessing (i.e. CBP) readily available for industrial purpose.
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Comparative proteomic analyses reveal that Gnt2-mediated N-glycosylation affects cell wall glycans and protein content in Fusarium oxysporum. J Proteomics 2015; 128:189-202. [PMID: 26254006 DOI: 10.1016/j.jprot.2015.07.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/09/2015] [Accepted: 07/29/2015] [Indexed: 01/22/2023]
Abstract
Protein N-glycosylation is a ubiquitous post-translational modification that contributes to appropriate protein folding, stability, functionality and localization. N-glycosylation has been identified as an important process for morphogenesis and virulence in several fungal pathogens including Fusarium oxysporum. Here we conducted comparative chemical and proteome-based analyses to better understand the physiological changes associated with protein hypo-N-glycosylation in F. oxysporum N-glycosyltransferase Gnt2-deficient mutant. The results suggest that lack of functional Gnt2 alters the size of galactofuranose chains in cell wall glycans, resulting in polysaccharides with a broad range of polymerization degrees and differential protein glycosylation patterns. Functional Gnt2 is necessary for normal conidium size and morphology and wild-type hyphal fusion rates. Hypo-N-glycosylation in ∆gnt2 mutant results in enhanced oxidative stress resistance and reduced levels of proteins involved in cell wall organization, biogenesis and remodelling. Deletion of gnt2 gene led to accumulation of trafficking vesicles at hyphal tips, reduced secretion of extracellular proteins related to detoxification of antifungal compounds and degradation of plant cell walls, and lowered extracellular polygalacturonase activity. Altogether, the results confirm that Gnt2-mediated N-glycosylation plays a crucial role in morphogenesis and virulence, and demonstrate that Gnt2 is essential for protein function, transport and relative abundance in F. oxysporum.
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