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de Assis MA, da Silva JJB, de Carvalho LM, Parreiras LS, Cairo JPLF, Marone MP, Gonçalves TA, Silva DS, Dantzger M, de Figueiredo FL, Carazzolle MF, Pereira GAG, Damasio A. A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum. J Fungi (Basel) 2024; 10:407. [PMID: 38921393 PMCID: PMC11205114 DOI: 10.3390/jof10060407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Trichoderma erinaceum is a filamentous fungus that was isolated from decaying sugarcane straw at a Brazilian ethanol biorefinery. This fungus shows potential as a source of plant cell wall-degrading enzymes (PCWDEs). In this study, we conducted a comprehensive multiomics investigation of T. erinaceum to gain insights into its enzymatic capabilities and genetic makeup. Firstly, we performed genome sequencing and assembly, which resulted in the identification of 10,942 genes in the T. erinaceum genome. We then conducted transcriptomics and secretome analyses to map the gene expression patterns and identify the enzymes produced by T. erinaceum in the presence of different substrates such as glucose, microcrystalline cellulose, pretreated sugarcane straw, and pretreated energy cane bagasse. Our analyses revealed that T. erinaceum highly expresses genes directly related to lignocellulose degradation when grown on pretreated energy cane and sugarcane substrates. Furthermore, our secretome analysis identified 35 carbohydrate-active enzymes, primarily PCWDEs. To further explore the enzymatic capabilities of T. erinaceum, we selected a β-glucosidase from the secretome data for recombinant production in a fungal strain. The recombinant enzyme demonstrated superior performance in degrading cellobiose and laminaribiose compared to a well-known enzyme derived from Trichoderma reesei. Overall, this comprehensive study provides valuable insights into both the genetic patterns of T. erinaceum and its potential for lignocellulose degradation and enzyme production. The obtained genomic data can serve as an important resource for future genetic engineering efforts aimed at optimizing enzyme production from this fungus.
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Affiliation(s)
- Michelle A. de Assis
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| | - Jovanderson J. B. da Silva
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Lucas M. de Carvalho
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Lucas S. Parreiras
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - João Paulo L. F. Cairo
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
- York Structural Biology Laboratory (YSBL), Department of Chemistry, University of York, York YO10 5DD, UK
| | - Marina P. Marone
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Thiago A. Gonçalves
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| | - Desireé S. Silva
- SENAI Institute for Biomass Innovation, Três Lagoas 79640-250, Brazil;
| | - Miriam Dantzger
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Fernanda L. de Figueiredo
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| | - Marcelo F. Carazzolle
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Gonçalo A. G. Pereira
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
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Gonçalves CGE, Lourenço LDFH, Philippsen HK, Santos AS, Santos LND, Ferreira NR. Crude Enzyme Concentrate of Filamentous Fungus Hydrolyzed Chitosan to Obtain Oligomers of Different Sizes. Polymers (Basel) 2023; 15:polym15092079. [PMID: 37177223 PMCID: PMC10181246 DOI: 10.3390/polym15092079] [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: 02/21/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 05/15/2023] Open
Abstract
Chitosan is a non-cytotoxic polysaccharide that, upon hydrolysis, releases oligomers of different sizes that may have antioxidant, antimicrobial activity and the inhibition of cancer cell growth, among other applications. It is, therefore, a hydrolysis process with great biotechnological relevance. Thus, this study aims to use a crude enzyme concentrate (CEC) produced by a filamentous fungus to obtain oligomers with different molecular weights. The microorganism was cultivated in a liquid medium (modified Czapeck-with carboxymethylcellulose as enzyme inducer). The enzymes present in the CEC were identified by LC-MS/MS, with an emphasis on cellobiohydrolase (E.C 3.2.1.91). The fungus of the Aspergillus genus was identified by amplifying the ITS1-5.8S-ITS2 rDNA region and metaproteomic analysis, where the excreted enzymes were identified with sequence coverage greater than 84% to A. nidulans. Chitosan hydrolysis assays compared the CEC with the commercial enzyme (Celluclast 1.5 L®). The ability to reduce the initial molecular mass of chitosan by 47.80, 75.24, and 93.26% after 2.0, 5.0, and 24 h of reaction, respectively, was observed. FTIR analyses revealed lower absorbance of chitosan oligomers' spectral signals, and their crystallinity was reduced after 3 h of hydrolysis. Based on these results, we can conclude that the crude enzyme concentrate showed a significant technological potential for obtaining chitosan oligomers of different sizes.
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Affiliation(s)
| | | | - Hellen Kempfer Philippsen
- Faculty of Biology, Socioenvironmental and Water Resources Institute, Federal Rural University of the Amazon, Campus Belém, Belem 66077-830, PA, Brazil
| | - Alberdan Silva Santos
- Faculty of Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belem 66075-110, PA, Brazil
| | - Lucely Nogueira Dos Santos
- Graduate Program in Food Science and Technology, Federal University of Pará, Belem 66075-110, PA, Brazil
| | - Nelson Rosa Ferreira
- Graduate Program in Food Science and Technology, Federal University of Pará, Belem 66075-110, PA, Brazil
- Faculty of Food Engineering, Technology Institute, Federal University of Pará, Belem 66075-110, PA, Brazil
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Terrasan CRF, Rubio MV, Gerhardt JA, Cairo JPF, Contesini FJ, Zubieta MP, de Figueiredo FL, Valadares FL, Corrêa TLR, Murakami MT, Franco TT, Davies GJ, Walton PH, Damasio A. Deletion of AA9 Lytic Polysaccharide Monooxygenases Impacts A. nidulans Secretome and Growth on Lignocellulose. Microbiol Spectr 2022; 10:e0212521. [PMID: 35658600 PMCID: PMC9241910 DOI: 10.1128/spectrum.02125-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, and bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. In Aspergillus nidulans, LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are cosecreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that three target LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose-active enzymes with distinct regioselectivity and activity on cellulose with different proportions of crystalline and amorphous regions. AnLPMO9s deletion and overexpression studies corroborate functional data. The abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G was less abundant and constantly secreted, and acts preferentially on crystalline regions of cellulose, uniquely displaying activity on highly crystalline algae cellulose. Single or double deletion of AnLPMO9s resulted in about 25% reduction in fungal growth on sugarcane straw but not on Avicel, demonstrating the contribution of LPMO9s for the saprophytic fungal lifestyle relies on the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of alternative electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification. IMPORTANCE Fungal lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that boost plant biomass degradation in combination with glycoside hydrolases. Secretion of LPMO9s arsenal by Aspergillus nidulans is influenced by the substrate and time of induction. These findings along with the biochemical characterization of novel fungal LPMO9s have implications on our understanding of their concerted action, allowing rational engineering of fungal strains for biotechnological applications such as plant biomass degradation. Additionally, the role of oxidative players in fungal growth on plant biomass was evaluated by deletion and overexpression experiments using a model fungal system.
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Affiliation(s)
- César Rafael Fanchini Terrasan
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Marcelo Ventura Rubio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Jaqueline Aline Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - João Paulo Franco Cairo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fabiano Jares Contesini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Mariane Paludetti Zubieta
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernanda Lopes de Figueiredo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernanda Lima Valadares
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Mario Tyago Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Telma Teixeira Franco
- Interdisciplinary Center of Energy Planning, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Gideon J. Davies
- Department of Chemistry, University of York, York, United Kingdom
| | - Paul H. Walton
- Department of Chemistry, University of York, York, United Kingdom
| | - Andre Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Wu X, Zhang S, Zhao S, Dai L, Huang S, Liu X, Yu J, Wang L. Functional Specificity of Three α-Arabinofuranosidases from Different Glycoside Hydrolase Families in Aspergillus niger An76. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5039-5048. [PMID: 35420820 DOI: 10.1021/acs.jafc.1c08388] [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] [Indexed: 05/15/2023]
Abstract
α-l-Arabinofuranosidase (Abf), a debranching enzyme that can remove arabinose substituents from arabinoxylan, promotes the hydrolysis of hemicellulose in plant biomass. However, the functional specificity of Abfs from different glycoside hydrolase (GH) families on the digestion of arabinoxylan and their synergistic interaction with xylanase have not been systematically studied. In this work, we characterized three Abfs (AxhA, AbfB, and AbfC) from GH62, GH54, and GH51 families in Aspergillus niger An76. Quantitative transcriptional analysis showed that expression of the axhA gene was upregulated as a result of induction by xylose substrates, whereas expression of the abfB gene was mainly induced by arabinose. Recombinant AxhA, AbfB, and AbfC exhibited different hydrolytic performances. AxhA showed the highest catalytic activity toward wheat arabinoxylan (WAX) and tended to hydrolyze monosubstituted arabinofuranose units, whereas AbfB had higher catalytic activity on AN and debranched arabinan (DAN), having the ability to cope with mono- and disubstituted arabinofuranose units. Furthermore, AbfC had greater arabinofuranosidase activity on p-nitrophenyl-α-l-arabinofuranoside (pNP-AraF) than on other substrates. Moreover, three Abfs displayed obvious synergistic action with GH11 xylanase XynB against WAX and barley husk residues. The elucidation of the degradation mechanisms of Abfs will lay a theoretical foundation for the efficient industrialized transformation of arabinoxylans.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao 266000, Shandong, China
| | - Shu Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Lin Dai
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Shuxia Huang
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao 266000, Shandong, China
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, Shandong, China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao 266000, Shandong, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
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Gila BC, Antal K, Birkó Z, Keserű JS, Pócsi I, Emri T. Strategies Shaping the Transcription of Carbohydrate-Active Enzyme Genes in Aspergillus nidulans. J Fungi (Basel) 2022; 8:jof8010079. [PMID: 35050018 PMCID: PMC8780418 DOI: 10.3390/jof8010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Understanding the coordinated regulation of the hundreds of carbohydrate-active enzyme (CAZyme) genes occurring in the genomes of fungi has great practical importance. We recorded genome-wide transcriptional changes of Aspergillus nidulans cultivated on glucose, lactose, or arabinogalactan, as well as under carbon-starved conditions. We determined both carbon-stress-specific changes (weak or no carbon source vs. glucose) and carbon-source-specific changes (one type of culture vs. all other cultures). Many CAZyme genes showed carbon-stress-specific and/or carbon-source-specific upregulation on arabinogalactan (138 and 62 genes, respectively). Besides galactosidase and arabinan-degrading enzyme genes, enrichment of cellulolytic, pectinolytic, mannan, and xylan-degrading enzyme genes was observed. Fewer upregulated genes, 81 and 107 carbon stress specific, and 6 and 16 carbon source specific, were found on lactose and in carbon-starved cultures, respectively. They were enriched only in galactosidase and xylosidase genes on lactose and rhamnogalacturonanase genes in both cultures. Some CAZyme genes (29 genes) showed carbon-source-specific upregulation on glucose, and they were enriched in β-1,4-glucanase genes. The behavioral ecological background of these characteristics was evaluated to comprehensively organize our knowledge on CAZyme production, which can lead to developing new strategies to produce enzymes for plant cell wall saccharification.
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Affiliation(s)
- Barnabás Cs. Gila
- Department of Molecular Biotechnology and Microbiology, Faculty of Sciences and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (B.C.G.); (I.P.)
- Doctoral School of Nutrition and Food Sciences, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Károly Antal
- Department of Zoology, Eszterházy Károly Catholic University, Eszterházy tér 1, 3300 Eger, Hungary;
| | - Zsuzsanna Birkó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.B.); (J.S.K.)
| | - Judit Sz. Keserű
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (Z.B.); (J.S.K.)
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, Faculty of Sciences and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (B.C.G.); (I.P.)
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Faculty of Sciences and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; (B.C.G.); (I.P.)
- Correspondence:
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Bioconversion of Lignocellulosic Biomass into Value Added Products under Anaerobic Conditions: Insight into Proteomic Studies. Int J Mol Sci 2021; 22:ijms222212249. [PMID: 34830131 PMCID: PMC8624197 DOI: 10.3390/ijms222212249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 01/14/2023] Open
Abstract
Production of biofuels and other value-added products from lignocellulose breakdown requires the coordinated metabolic activity of varied microorganisms. The increasing global demand for biofuels encourages the development and optimization of production strategies. Optimization in turn requires a thorough understanding of the microbial mechanisms and metabolic pathways behind the formation of each product of interest. Hydrolysis of lignocellulosic biomass is a bottleneck in its industrial use and often affects yield efficiency. The accessibility of the biomass to the microorganisms is the key to the release of sugars that are then taken up as substrates and subsequently transformed into the desired products. While the effects of different metabolic intermediates in the overall production of biofuel and other relevant products have been studied, the role of proteins and their activity under anaerobic conditions has not been widely explored. Shifts in enzyme production may inform the state of the microorganisms involved; thus, acquiring insights into the protein production and enzyme activity could be an effective resource to optimize production strategies. The application of proteomic analysis is currently a promising strategy in this area. This review deals on the aspects of enzymes and proteomics of bioprocesses of biofuels production using lignocellulosic biomass as substrate.
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Planifilum fulgidum Is the Dominant Functional Microorganism in Compost Containing Spent Mushroom Substrate. SUSTAINABILITY 2021. [DOI: 10.3390/su131810002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The extensive accumulation of spent mushroom substrate (SMS) owing to the large-scale production of edible fungi is causing environmental problems that cannot be ignored. Co-composting is a promising method for agricultural and animal husbandry waste disposal. In this study, the composition and function of microbial communities in the process of cattle manure–maize straw composting with SMS addition were compared through an integrated meta-omics approach. The results showed that irrespective of SMS addition, the predominant fungi were Ascomycota, while the dominant bacteria were Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. High temperature promoted the evolution from Gram-negative bacteria (Bacteroides, Proteobacteria) to Gram-positive bacteria (Firmicutes, Actinomycetes). The composting process was accelerated by SMS addition, and the substrate was effectively degraded in 14 days. Metaproteomics results showed that the dominant microorganism, Planifilum fulgidum, secreted large amounts of S8, M17, and M32 proteases that could degrade macromolecular protein substrates in the presence of SMS. Planifilum fulgidum, along with Thermobifida fusca and Melanocarpus albomyces, synergistically degraded hemicellulose, cellulose, and protein. In addition, the dominant microorganisms related to the initial raw materials such as Pichia, Lactobacillus in the microbial agent and Hypsizygus in SMS could not adapt to the high-temperature environment (>60 °C) and were replaced by thermophilic bacteria after 5 days of composting.
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Ali A, Ellinger B, Brandt SC, Betzel C, Rühl M, Wrenger C, Schlüter H, Schäfer W, Brognaro H, Gand M. Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass. Microorganisms 2021; 9:1581. [PMID: 34442660 PMCID: PMC8398502 DOI: 10.3390/microorganisms9081581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Staphylotrichum longicolleum FW57 (DSM105789) is a prolific chitinolytic fungus isolated from wood, with a chitinase activity of 0.11 ± 0.01 U/mg. We selected this strain for genome sequencing and annotation, and compiled its growth characteristics on four different chitinous substrates as well as two agro-industrial waste products. We found that the enzymatic mixture secreted by FW57 was not only able to digest pre-treated sugarcane bagasse, but also untreated sugarcane bagasse and maize leaves. The efficiency was comparable to a commercial enzymatic cocktail, highlighting the potential of the S. longicolleum enzyme mixture as an alternative pretreatment method. To further characterize the enzymes, which efficiently digested polymers such as cellulose, hemicellulose, pectin, starch, and lignin, we performed in-depth mass spectrometry-based secretome analysis using tryptic peptides from in-gel and in-solution digestions. Depending on the growth conditions, we were able to detect from 442 to 1092 proteins, which were annotated to identify from 134 to 224 putative carbohydrate-active enzymes (CAZymes) in five different families: glycoside hydrolases, auxiliary activities, carbohydrate esterases, polysaccharide lyases, glycosyl transferases, and proteins containing a carbohydrate-binding module, as well as combinations thereof. The FW57 enzyme mixture could be used to replace commercial enzyme cocktails for the digestion of agro-residual substrates.
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Affiliation(s)
- Arslan Ali
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
- Institute of Clinical Chemistry and Laboratory Medicine, Diagnostic Center, Section Mass Spectrometry & Proteomics, Campus Research, Martinistr. 2, N27, Medical Center Hamburg-Eppendorf, Universität Hamburg, 20246 Hamburg, Germany
| | - Bernhard Ellinger
- Department ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany;
| | - Sophie C. Brandt
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Department Biology and Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany;
| | - Carsten Wrenger
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Biomedical Science Institute, University of São Paulo, Av. Lineu Prestes, 2415, São Paulo CEP 05508-900, Brazil
| | - Hartmut Schlüter
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Institute of Clinical Chemistry and Laboratory Medicine, Diagnostic Center, Section Mass Spectrometry & Proteomics, Campus Research, Martinistr. 2, N27, Medical Center Hamburg-Eppendorf, Universität Hamburg, 20246 Hamburg, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Biomedical Science Institute, University of São Paulo, Av. Lineu Prestes, 2415, São Paulo CEP 05508-900, Brazil
| | - Martin Gand
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
- Institute of Food Chemistry and Food Biotechnology, Department Biology and Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany;
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9
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Brandt SC, Brognaro H, Ali A, Ellinger B, Maibach K, Rühl M, Wrenger C, Schlüter H, Schäfer W, Betzel C, Janssen S, Gand M. Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:74. [PMID: 33743779 PMCID: PMC7981871 DOI: 10.1186/s13068-021-01927-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The transition to a biobased economy involving the depolymerization and fermentation of renewable agro-industrial sources is a challenge that can only be met by achieving the efficient hydrolysis of biomass to monosaccharides. In nature, lignocellulosic biomass is mainly decomposed by fungi. We recently identified six efficient cellulose degraders by screening fungi from Vietnam. RESULTS We characterized a high-performance cellulase-producing strain, with an activity of 0.06 U/mg, which was identified as a member of the Fusarium solani species complex linkage 6 (Fusarium metavorans), isolated from mangrove wood (FW16.1, deposited as DSM105788). The genome, representing nine potential chromosomes, was sequenced using PacBio and Illumina technology. In-depth secretome analysis using six different synthetic and artificial cellulose substrates and two agro-industrial waste products identified 500 proteins, including 135 enzymes assigned to five different carbohydrate-active enzyme (CAZyme) classes. The F. metavorans enzyme cocktail was tested for saccharification activity on pre-treated sugarcane bagasse, as well as untreated sugarcane bagasse and maize leaves, where it was complemented with the commercial enzyme mixture Accellerase 1500. In the untreated sugarcane bagasse and maize leaves, initial cell wall degradation was observed in the presence of at least 196 µg/mL of the in-house cocktail. Increasing the dose to 336 µg/mL facilitated the saccharification of untreated sugarcane biomass, but had no further effect on the pre-treated biomass. CONCLUSION Our results show that F. metavorans DSM105788 is a promising alternative pre-treatment for the degradation of agro-industrial lignocellulosic materials. The enzyme cocktail promotes the debranching of biopolymers surrounding the cellulose fibers and releases reduced sugars without process disadvantages or loss of carbohydrates.
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Affiliation(s)
- Sophie C Brandt
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Hévila Brognaro
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, CEP, 05508-000, Brazil
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Arslan Ali
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi, 75270, Pakistan
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, Campus Research. Martinistr. 52, N27, 20246, Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Department ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Katharina Maibach
- Department Biology and Chemistry, Algorithmic Bioinformatics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392, Gießen, Germany
| | - Martin Rühl
- Department Biology and Chemistry, Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, CEP, 05508-000, Brazil
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
- Institute of Clinical Chemistry and Laboratory Medicine Diagnostic Center, Campus Research. Martinistr. 52, N27, 20246, Hamburg, Germany
| | - Wilhelm Schäfer
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146, Hamburg, Germany
| | - Stefan Janssen
- Department Biology and Chemistry, Algorithmic Bioinformatics, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392, Gießen, Germany
| | - Martin Gand
- Faculty of Mathematics, Computer Science and Natural Science, Department of Biology, Biozentrum Klein Flottbek, Molecular Phytopathology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
- Department Biology and Chemistry, Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany.
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10
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Díaz GV, Coniglio RO, Alvarenga AE, Zapata PD, Villalba LL, Fonseca MI. Secretomic analysis of cheap enzymatic cocktails of Aspergillus niger LBM 134 grown on cassava bagasse and sugarcane bagasse. Mycologia 2020; 112:663-676. [PMID: 32574526 DOI: 10.1080/00275514.2020.1763707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Currently, agroindustrial wastes are little used for generating value-added products; hence, their use of these waste to produce enzymatic cocktails for the conversion of lignocellulosic biomass to fermentable sugars is a very interesting alternative in the second-generation bioethanol process. The Ascomycota fungus Aspergillus niger LBM 134 produces hydrolytic enzymes in large proportions. In this work, A. niger LBM 134 was grown on sugarcane and cassava bagasses under optimized conditions. To identify the extracellular enzymes involved in the degradation of these agroindustrial wastes, the secretomes of the culture supernatants of the fungus were analyzed and validated by biochemical assays of the enzymatic activities. A. niger LBM 134 secreted higher quantities of xylanases and accessory hemicellulases when it grew on sugarcane bagasse, whereas more cellulases, amylases, and pectinases were secreted when it grew on cassava bagasse. These findings suggest two promising enzyme cocktails for the hydrolysis of lignocellulose carbohydrate polymers to fermentable sugars. These bioinformatic analysis were functional validates through enzymatic biochemical assays that confirm the biotechnological potential of A. niger LBM 134 for the bioconversion of hemicellulosic substrates such as sugarcane and cassava bagasses.
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Affiliation(s)
- Gabriela Verónica Díaz
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Romina Olga Coniglio
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Adriana Elizabet Alvarenga
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Pedro Darío Zapata
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - Laura Lidia Villalba
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
| | - María Isabel Fonseca
- Laboratorio de Biotecnología Molecular, Instituto de Biotecnología Misiones "María Ebe Reca" CONICET, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones , Ruta 12 km 7.5, C.P. 3300, Posadas, Argentina
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11
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Jagadeeswaran G, Gainey L, Mort AJ. An AA9-LPMO containing a CBM1 domain in Aspergillus nidulans is active on cellulose and cleaves cello-oligosaccharides. AMB Express 2018; 8:171. [PMID: 30328527 PMCID: PMC6192940 DOI: 10.1186/s13568-018-0701-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/10/2018] [Indexed: 11/14/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper dependent enzymes that carry out oxidative cleavage of cellulose and other polysaccharides. Aspergillus nidulans, an ascomycete fungus that contains multiple AA9 LPMOs in the genome, offers an excellent model system to study their activity during the oxidative degradation of biomass. AN1602, a dual domain AA9-LPMO in A. nidulans appended with a carbohydrate-binding module, CBM1, was expressed in Pichia pastoris for analyzing oxidative cleavage on cellulosic substrates. The mass spectral and HPAEC analyses showed that the enzyme cleaves phosphoric acid swollen cellulose (PASC) in the presence of a reducing agent, yielding a range of cello-oligosaccharides. In addition to the polymeric substrate cellulose, AN1602 is also active on soluble cellohexaose, a property that is restricted to only a few characterized LPMOs. Product analysis of AN1602 cleaved cellohexaose revealed that C4 was the sole site of oxidation. The sequence and predicted structure of the catalytic domain of AN1602 matched very closely to known C4 cellohexaose active enzymes.
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12
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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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13
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Mäkelä M, DiFalco M, McDonnell E, Nguyen T, Wiebenga A, Hildén K, Peng M, Grigoriev I, Tsang A, de Vries R. Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli. Stud Mycol 2018; 91:79-99. [PMID: 30487660 PMCID: PMC6249967 DOI: 10.1016/j.simyco.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.
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Affiliation(s)
- M.R. Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - M. DiFalco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - E. McDonnell
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - T.T.M. Nguyen
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - A. Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - K. Hildén
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - M. Peng
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - I.V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - A. Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B1R6, Canada
| | - R.P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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14
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Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. Sci Rep 2018; 8:6617. [PMID: 29700415 PMCID: PMC5919931 DOI: 10.1038/s41598-018-25016-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022] Open
Abstract
Aspergillus fumigatus and multiple other Aspergillus species cause a wide range of lung infections, collectively termed aspergillosis. Aspergilli are ubiquitous in environment with healthy immune systems routinely eliminating inhaled conidia, however, Aspergilli can become an opportunistic pathogen in immune-compromised patients. The aspergillosis mortality rate and emergence of drug-resistance reveals an urgent need to identify novel targets. Secreted and cell membrane proteins play a critical role in fungal-host interactions and pathogenesis. Using a computational pipeline integrating data from high-throughput experiments and bioinformatic predictions, we have identified secreted and cell membrane proteins in ten Aspergillus species known to cause aspergillosis. Small secreted and effector-like proteins similar to agents of fungal-plant pathogenesis were also identified within each secretome. A comparison with humans revealed that at least 70% of Aspergillus secretomes have no sequence similarity with the human proteome. An analysis of antigenic qualities of Aspergillus proteins revealed that the secretome is significantly more antigenic than cell membrane proteins or the complete proteome. Finally, overlaying an expression dataset, four A. fumigatus proteins upregulated during infection and with available structures, were found to be structurally similar to known drug target proteins in other organisms, and were able to dock in silico with the respective drug.
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15
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de Gouvêa PF, Bernardi AV, Gerolamo LE, de Souza Santos E, Riaño-Pachón DM, Uyemura SA, Dinamarco TM. Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. BMC Genomics 2018; 19:232. [PMID: 29614953 PMCID: PMC5883313 DOI: 10.1186/s12864-018-4627-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS. RESULTS The maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome. CONCLUSIONS This is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.
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Affiliation(s)
- Paula Fagundes de Gouvêa
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Aline Vianna Bernardi
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luis Eduardo Gerolamo
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Emerson de Souza Santos
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory, Campinas, São Paulo, Brazil
- Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sergio Akira Uyemura
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Taisa Magnani Dinamarco
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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16
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Gong W, Dai L, Zhang H, Zhang L, Wang L. A Highly Efficient Xylan-Utilization System in Aspergillus niger An76: A Functional-Proteomics Study. Front Microbiol 2018; 9:430. [PMID: 29623069 PMCID: PMC5874446 DOI: 10.3389/fmicb.2018.00430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/26/2018] [Indexed: 11/23/2022] Open
Abstract
Xylan constituted with β-1,4-D-xylose linked backbone and diverse substituted side-chains is the most abundant hemicellulose component of biomass, which can be completely and rapidly degraded into fermentable sugars by Aspergillus niger. This is of great value for obtaining renewable biofuels and biochemicals. To clarify the underlying mechanisms associated with highly efficient xylan degradation, assimilation, and metabolism by A. niger, we utilized functional proteomics to analyze the secreted proteins, sugar transporters, and intracellular proteins of A. niger An76 grown on xylan-based substrates. Results demonstrated that the complete xylanolytic enzyme system required for xylan degradation and composed of diverse isozymes was secreted in a sequential order. Xylan-backbone-degrading enzymes were preferentially induced by xylose or other soluble sugars, which efficiently produced large amounts of xylooligosaccharides (XOS) and xylose; however, XOS was more efficient than xylose in triggering the expression of the key transcription activator XlnR, resulting in higher xylanase activity and shortening xylanase-production time. Moreover, the substituted XOS was responsible for improving the abundance of side-chain-degrading enzymes, specific transporters, and key reductases and dehydrogenases in the pentose catabolic pathway. Our findings indicated that industries might be able to improve the species and concentrations of xylan-degrading enzymes and shorten fermentation time by adding abundant intermediate products of natural xylan (XOS) to cultures of filamentous fungi.
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Affiliation(s)
- Weili Gong
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lin Dai
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Huaiqiang Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lili Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.,State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
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17
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Secretome profiling reveals temperature-dependent growth of Aspergillus fumigatus. SCIENCE CHINA-LIFE SCIENCES 2017; 61:578-592. [PMID: 29067645 DOI: 10.1007/s11427-017-9168-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/29/2017] [Indexed: 12/11/2022]
Abstract
Aspergillus fumigatus is a ubiquitous opportunistic fungus. In this study, systematic analyses were carried out to study the temperature adaptability of A. fumigatus. A total of 241 glycoside hydrolases and 69 proteases in the secretome revealed the strong capability of A. fumigatus to degrade plant biomass and protein substrates. In total, 129 pathogenesis-related proteins detected in the secretome were strongly correlated with glycoside hydrolases and proteases. The variety and abundance of proteins remained at temperatures of 34°C-45°C. The percentage of endo-1,4-xylanase increased when the temperature was lowered to 20°C, while the percentage of cellobiohydrolase increased as temperature was increased, suggesting that the strain obtains carbon mainly by degrading xylan and cellulose, and the main types of proteases in the secretome were aminopeptidases and carboxypeptidases. Only half of the proteins were retained and their abundance declined to 9.7% at 55°C. The activities of the remaining β-glycosidases and proteases were merely 35% and 24%, respectively, when the secretome was treated at 60°C for 2 h. Therefore, temperatures >60°C restrict the growth of A. fumigatus.
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18
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Contesini FJ, Liberato MV, Rubio MV, Calzado F, Zubieta MP, Riaño-Pachón DM, Squina FM, Bracht F, Skaf MS, Damasio AR. Structural and functional characterization of a highly secreted α-l-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1758-1769. [PMID: 28890404 DOI: 10.1016/j.bbapap.2017.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 12/30/2022]
Abstract
Carbohydrate-Active Enzymes are key enzymes for biomass-to-bioproducts conversion. α-l-Arabinofuranosidases that belong to the Glycoside Hydrolase family 62 (GH62) have important applications in biofuel production from plant biomass by hydrolyzing arabinoxylans, found in both the primary and secondary cell walls of plants. In this work, we identified a GH62 α-l-arabinofuranosidase (AnAbf62Awt) that was highly secreted when Aspergillus nidulans was cultivated on sugarcane bagasse. The gene AN7908 was cloned and transformed in A. nidulans for homologous production of AnAbf62Awt, and we confirmed that the enzyme is N-glycosylated at asparagine 83 by mass spectrometry analysis. The enzyme was also expressed in Escherichia coli and the studies of circular dichroism showed that the melting temperature and structural profile of AnAbf62Awt and the non-glycosylated enzyme from E. coli (AnAbf62Adeglyc) were highly similar. In addition, the designed glycomutant AnAbf62AN83Q presented similar patterns of secretion and activity to the AnAbf62Awt, indicating that the N-glycan does not influence the properties of this enzyme. The crystallographic structure of AnAbf62Adeglyc was obtained and the 1.7Å resolution model showed a five-bladed β-propeller fold, which is conserved in family GH62. Mutants AnAbf62AY312F and AnAbf62AY312S showed that Y312 was an important substrate-binding residue. Molecular dynamics simulations indicated that the loop containing Y312 could access different conformations separated by moderately low energy barriers. One of these conformations, comprising a local minimum, is responsible for placing Y312 in the vicinity of the arabinose glycosidic bond, and thus, may be important for catalytic efficiency.
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Affiliation(s)
- Fabiano Jares Contesini
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil; Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil
| | - Marcelo Vizoná Liberato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil
| | - Marcelo Ventura Rubio
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil
| | - Felipe Calzado
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil
| | | | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Caixa Postal 6192, 13083-970, Brazil; Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, CEP: 05508-000, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, (UNISO), Sorocaba, SP, CEP 18023-000, Brazil
| | - Fabricio Bracht
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP CEP: 13084-862, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP CEP: 13084-862, Brazil
| | - André Ricardo Damasio
- Institute of Biology, University of Campinas - UNICAMP, Campinas, SP CEP 13083-862, Brazil.
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Zeiner CA, Purvine SO, Zink EM, Paša-Tolić L, Chaput DL, Wu S, Santelli CM, Hansel CM. Quantitative iTRAQ-based secretome analysis reveals species-specific and temporal shifts in carbon utilization strategies among manganese(II)-oxidizing Ascomycete fungi. Fungal Genet Biol 2017; 106:61-75. [DOI: 10.1016/j.fgb.2017.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 01/05/2023]
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Berrin JG, Rosso MN, Abou Hachem M. Fungal secretomics to probe the biological functions of lytic polysaccharide monooxygenases. Carbohydr Res 2017; 448:155-160. [DOI: 10.1016/j.carres.2017.05.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/29/2022]
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21
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Genetics, Molecular, and Proteomics Advances in Filamentous Fungi. Curr Microbiol 2017; 74:1226-1236. [PMID: 28733909 DOI: 10.1007/s00284-017-1308-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Filamentous fungi play a dynamic role in health and the environment. In addition, their unique and complex hyphal structures are involved in their morphogenesis, integrity, synthesis, and degradation, according to environmental and physiological conditions and resource availability. However, in biotechnology, it has a great value in the production of enzymes, pharmaceuticals, and food ingredients. The beginning of nomenclature of overall fungi started in early 1990 after which the categorization, interior and exterior mechanism, function, molecular and genetics study took pace. This mini-review has emphasized some of the important aspects of filamentous fungi, their pattern of life cycle, history, and development of different strategic methods applied to exploit this unique organism. New trends and concepts that have been applied to overcome obstacle because of their basic structure related to genomics and systems biology has been presented. Furthermore, the future aspects and challenges that need to be deciphered to get a bigger and better picture of filamentous fungi have been discussed.
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Itoh E, Odakura R, Oinuma KI, Shimizu M, Masuo S, Takaya N. Sirtuin E is a fungal global transcriptional regulator that determines the transition from the primary growth to the stationary phase. J Biol Chem 2017; 292:11043-11054. [PMID: 28465348 PMCID: PMC5491787 DOI: 10.1074/jbc.m116.753772] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 04/20/2017] [Indexed: 11/06/2022] Open
Abstract
In response to limited nutrients, fungal cells exit the primary growth phase, enter the stationary phase, and cease proliferation. Although fundamental to microbial physiology in many environments, the regulation of this transition is poorly understood but likely involves many transcriptional regulators. These may include the sirtuins, which deacetylate acetyllysine residues of histones and epigenetically regulate global transcription. Therefore, we investigated the role of a nuclear sirtuin, sirtuin E (SirE), from the ascomycete fungus Aspergillus nidulans An A. nidulans strain with a disrupted sirE gene (SirEΔ) accumulated more acetylated histone H3 during the stationary growth phase when sirE was expressed at increased levels in the wild type. SirEΔ exhibited decreased mycelial autolysis, conidiophore development, sterigmatocystin biosynthesis, and production of extracellular hydrolases. Moreover, the transcription of the genes involved in these processes was also decreased, indicating that SirE is a histone deacetylase that up-regulates these activities in the stationary growth phase. Transcriptome analyses indicated that SirE repressed primary carbon and nitrogen metabolism and cell-wall synthesis. Chromatin immunoprecipitation demonstrated that SirE deacetylates acetylated Lys-9 residues in histone H3 at the gene promoters of α-1,3-glucan synthase (agsB), glycolytic phosphofructokinase (pfkA), and glyceraldehyde 3-phosphate (gpdA), indicating that SirE represses the expression of these primary metabolic genes. In summary, these results indicate that SirE facilitates the metabolic transition from the primary growth phase to the stationary phase. Because the observed gene expression profiles in stationary phase matched those resulting from carbon starvation, SirE appears to control this metabolic transition via a mechanism associated with the starvation response.
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Affiliation(s)
- Eriko Itoh
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Rika Odakura
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ken-Ichi Oinuma
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Motoyuki Shimizu
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Shunsuke Masuo
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Naoki Takaya
- From the Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Proteomics as a Tool to Identify New Targets Against Aspergillus and Scedosporium in the Context of Cystic Fibrosis. Mycopathologia 2017; 183:273-289. [PMID: 28484941 DOI: 10.1007/s11046-017-0139-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/25/2017] [Indexed: 12/26/2022]
Abstract
Cystic fibrosis (CF) is a genetic disorder that increases the risk of suffering microbial, including fungal, infections. In this paper, proteomics-based information was collated relating to secreted and cell wall proteins with potential medical applications from the most common filamentous fungi in CF, i.e., Aspergillus and Scedosporium/Lomentospora species. Among the Aspergillus fumigatus secreted allergens, β-1,3-endoglucanase, the alkaline protease 1 (Alp1/oryzin), Asp f 2, Asp f 13/15, chitinase, chitosanase, dipeptidyl-peptidase V (DppV), the metalloprotease Asp f 5, mitogillin/Asp f 1, and thioredoxin reductase receive a special mention. In addition, the antigens β-glucosidase 1, catalase, glucan endo-1,3-β-glucosidase EglC, β-1,3-glucanosyltransferases Gel1 and Gel2, and glutaminase A were also identified in secretomes of other Aspergillus species associated with CF: Aspergillus flavus, Aspergillus niger, Aspergillus nidulans, and Aspergillus terreus. Regarding cell wall proteins, cytochrome P450 and eEF-3 were proposed as diagnostic targets, and alkaline protease 2 (Alp2), Asp f 3 (putative peroxiredoxin pmp20), probable glycosidases Asp f 9/Crf1 and Crf2, GPI-anchored protein Ecm33, β-1,3-glucanosyltransferase Gel4, conidial hydrophobin Hyp1/RodA, and secreted aspartyl protease Pep2 as protective vaccines in A. fumigatus. On the other hand, for Scedosporium/Lomentospora species, the heat shock protein Hsp70 stands out as a relevant secreted and cell wall antigen. Additionally, the secreted aspartyl proteinase and an ortholog of Asp f 13, as well as the cell wall endo-1,3-β-D-glucosidase and 1,3-β-glucanosyl transferase, were also found to be significant proteins. In conclusion, proteins mentioned in this review may be promising candidates for developing innovative diagnostic and therapeutic tools for fungal infections in CF patients.
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Immobilization of indigenous holocellulase on iron oxide (Fe 2 O 3 ) nanoparticles enhanced hydrolysis of alkali pretreated paddy straw. Int J Biol Macromol 2017; 96:538-549. [DOI: 10.1016/j.ijbiomac.2016.11.109] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/26/2016] [Accepted: 11/28/2016] [Indexed: 11/19/2022]
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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26
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Damasio ARDL, Rubio MV, Gonçalves TA, Persinoti GF, Segato F, Prade RA, Contesini FJ, de Souza AP, Buckeridge MS, Squina FM. Xyloglucan breakdown by endo-xyloglucanase family 74 from Aspergillus fumigatus. Appl Microbiol Biotechnol 2016; 101:2893-2903. [PMID: 28013403 DOI: 10.1007/s00253-016-8014-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 11/09/2016] [Accepted: 11/12/2016] [Indexed: 12/30/2022]
Abstract
Xyloglucan is the most abundant hemicellulose in primary walls of spermatophytes except for grasses. Xyloglucan-degrading enzymes are important in lignocellulosic biomass hydrolysis because they remove xyloglucan, which is abundant in monocot-derived biomass. Fungal genomes encode numerous xyloglucanase genes, belonging to at least six glycoside hydrolase (GH) families. GH74 endo-xyloglucanases cleave xyloglucan backbones with unsubstituted glucose at the -1 subsite or prefer xylosyl-substituted residues in the -1 subsite. In this work, 137 GH74-related genes were detected by examining 293 Eurotiomycete genomes and Ascomycete fungi contained one or no GH74 xyloglucanase gene per genome. Another interesting feature is that the triad of tryptophan residues along the catalytic cleft was found to be widely conserved among Ascomycetes. The GH74 from Aspergillus fumigatus (AfXEG74) was chosen as an example to conduct comprehensive biochemical studies to determine the catalytic mechanism. AfXEG74 has no CBM and cleaves the xyloglucan backbone between the unsubstituted glucose and xylose-substituted glucose at specific positions, along the XX motif when linked to regions deprived of galactosyl branches. It resembles an endo-processive activity, which after initial random hydrolysis releases xyloglucan-oligosaccharides as major reaction products. This work provides insights on phylogenetic diversity and catalytic mechanism of GH74 xyloglucanases from Ascomycete fungi.
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Affiliation(s)
- André Ricardo de Lima Damasio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Marcelo Ventura Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Thiago Augusto Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Gabriela Felix Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Fernando Segato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Fabiano Jares Contesini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Amanda Pereira de Souza
- Laboratório de Fisiologia e Ecologia de Plantas (LAFIECO), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia e Ecologia de Plantas (LAFIECO), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.
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Sharma Ghimire P, Ouyang H, Wang Q, Luo Y, Shi B, Yang J, Lü Y, Jin C. Insight into Enzymatic Degradation of Corn, Wheat, and Soybean Cell Wall Cellulose Using Quantitative Secretome Analysis of Aspergillus fumigatus. J Proteome Res 2016; 15:4387-4402. [PMID: 27618962 DOI: 10.1021/acs.jproteome.6b00465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lignocelluloses contained in animal forage cannot be digested by pigs or poultry with 100% efficiency. On contrary, Aspergillus fumigatus, a saprophytic filamentous fungus, is known to harbor 263 glycoside hydrolase encoding genes, suggesting that A. fumigatus is an efficient lignocellulose degrader. Hence the present study uses corn, wheat, or soybean as a sole carbon source to culture A. fumigatus under animal physiological condition to understand how cellulolytic enzymes work together to achieve an efficient degradation of lignocellulose. Our results showed that A. fumigatus produced different sets of enzymes to degrade lignocelluloses derived from corn, wheat, or soybean cell wall. In addition, the cellulolytic enzymes produced by A. fumigatus were stable under acidic condition or at higher temperatures. Using isobaric tags for a relative and absolute quantification (iTRAQ) approach, a total of ∼600 extracellular proteins were identified and quantified, in which ∼50 proteins were involved in lignocellulolysis, including cellulases, hemicellulases, lignin-degrading enzymes, and some hypothetical proteins. Data are available via ProteomeXchange with identifier PXD004670. On the basis of quantitative iTRAQ results, 14 genes were selected for further confirmation by RT-PCR. Taken together, our results indicated that the expression and regulation of lignocellulolytic proteins in the secretome of A. fumigatus were dependent on both nature and complexity of cellulose, thus suggesting that a different enzyme system is required for degradation of different lignocelluloses derived from plant cells. Although A. fumigatus is a pathogenic fungus and cannot be directly used as an enzyme source, as an efficient lignocellulose degrader its strategy to synergistically degrade various lignocelluloses with different enzymes can be used to design enzyme combination for optimal digestion and absorption of corn, wheat, or soybean that are used as forage of pig and poultry.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100101, China
- Himalayan Environment Research Institute (HERI) , Bouddha-6, Kathmandu, Nepal
| | - Haomiao Ouyang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Qian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Bo Shi
- Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081, China
| | - Jinghua Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yang Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Cheng Jin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100101, China
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Effect of glucose as a carbon repressor on the extracellular proteome of Aspergillus niger during the production of amylases by solid state cultivation. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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dos Santos HB, Bezerra TMS, Pradella JGC, Delabona P, Lima D, Gomes E, Hartson SD, Rogers J, Couger B, Prade R. Myceliophthora thermophila M77 utilizes hydrolytic and oxidative mechanisms to deconstruct biomass. AMB Express 2016; 6:103. [PMID: 27807811 PMCID: PMC5093097 DOI: 10.1186/s13568-016-0276-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 12/23/2022] Open
Abstract
Biomass is abundant, renewable and useful for biofuel production as well as chemical priming for plastics and composites. Deconstruction of biomass by enzymes is perceived as recalcitrant while an inclusive breakdown mechanism remains to be discovered. Fungi such as Myceliophthora thermophila M77 appear to decompose natural biomass sources quite well. This work reports on this fungus fermentation property while producing cellulolytic enzymes using natural biomass substrates. Little hydrolytic activity was detected, insufficient to explain the large amount of biomass depleted in the process. Furthermore, this work makes a comprehensive account of extracellular proteins and describes how secretomes redirect their qualitative protein content based on the nature and chemistry of the nutritional source. Fungus grown on purified cellulose or on natural biomass produced secretomes constituted by: cellobiohydrolases, cellobiose dehydrogenase, β-1,3 glucanase, β-glucosidases, aldose epimerase, glyoxal oxidase, GH74 xyloglucanase, galactosidase, aldolactonase and polysaccharide monooxygenases. Fungus grown on a mixture of purified hemicellulose fractions (xylans, arabinans and arabinoxylans) produced many enzymes, some of which are listed here: xylosidase, mixed β-1,3(4) glucanase, β-1,3 glucanases, β-glucosidases, β-mannosidase, β-glucosidases, galactosidase, chitinases, polysaccharide lyase, endo β-1,6 galactanase and aldose epimerase. Secretomes produced on natural biomass displayed a comprehensive set of enzymes involved in hydrolysis and oxidation of cellulose, hemicellulose-pectin and lignin. The participation of oxidation reactions coupled to lignin decomposition in the breakdown of natural biomass may explain the discrepancy observed for cellulose decomposition in relation to natural biomass fermentation experiments.
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Affiliation(s)
- Hévila Brognaro dos Santos
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
| | - Thaís Milena Souza Bezerra
- Laboratório de Enzimologia, Instituto de Química, UNESP, Araraquara, São Paulo Brazil
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
| | - José G. C. Pradella
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
| | - Priscila Delabona
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
| | - Deise Lima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
| | - Eleni Gomes
- Laboratório de Microbiologia e Bioquímica Aplicada, Departamento de Biologia, IBILCE/UNESP, Rua Cristovão Colombo, 2265 Bairro Jd. Nazareth, São José do Rio Preto, SP CEP 15054-000 Brazil
| | - Steve D. Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
| | - Rolf Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
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30
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Rubio MV, Zubieta MP, Franco Cairo JPL, Calzado F, Paes Leme AF, Squina FM, Prade RA, de Lima Damásio AR. Mapping N-linked glycosylation of carbohydrate-active enzymes in the secretome of Aspergillus nidulans grown on lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:168. [PMID: 27508003 PMCID: PMC4977673 DOI: 10.1186/s13068-016-0580-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/27/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND The genus Aspergillus includes microorganisms that naturally degrade lignocellulosic biomass, secreting large amounts of carbohydrate-active enzymes (CAZymes) that characterize their saprophyte lifestyle. Aspergillus has the capacity to perform post-translational modifications (PTM), which provides an additional advantage for the use of these organisms as a host for the production of heterologous proteins. In this study, the N-linked glycosylation of CAZymes identified in the secretome of Aspergillus nidulans grown on lignocellulose was mapped. RESULTS Aspergillus nidulans was grown in glucose, xylan and pretreated sugarcane bagasse (SCB) for 96 h, after which glycoproteomics and glycomics were carried out on the extracellular proteins (secretome). A total of 265 proteins were identified, with 153, 210 and 182 proteins in the glucose, xylan and SCB substrates, respectively. CAZymes corresponded to more than 50 % of the total secretome in xylan and SCB. A total of 182 N-glycosylation sites were identified, of which 121 were detected in 67 CAZymes. A prevalence of the N-glyc sequon N-X-T (72.2 %) was observed in N-glyc sites compared with N-X-S (27.8 %). The amino acids flanking the validated N-glyc sites were mainly composed of hydrophobic and polar uncharged amino acids. Selected proteins were evaluated for conservation of the N-glyc sites in Aspergilli homologous proteins, but a pattern of conservation was not observed. A global analysis of N-glycans released from the proteins secreted by A. nidulans was also performed. While the proportion of N-glycans with Hex5 to Hex9 was similar in the xylan condition, a prevalence of Hex5 was observed in the SCB and glucose conditions. CONCLUSIONS The most common and frequent N-glycosylated motifs, an overview of the N-glycosylation of the CAZymes and the number of mannoses found in N-glycans were analyzed. There are many bottlenecks in protein production by filamentous fungi, such as folding, transport by vesicles and secretion, but N-glycosylation in the correct context is a fundamental event for defining the high levels of secretion of target proteins. A comprehensive analysis of the protein glycosylation processes in A. nidulans will assist with a better understanding of glycoprotein structures, profiles, activities and functions. This knowledge can help in the optimization of heterologous expression and protein secretion in the fungal host.
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Affiliation(s)
- Marcelo Ventura Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Mariane Paludetti Zubieta
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - João Paulo Lourenço Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Felipe Calzado
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK USA
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
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Zeiner CA, Purvine SO, Zink EM, Paša-Tolić L, Chaput DL, Haridas S, Wu S, LaButti K, Grigoriev IV, Henrissat B, Santelli CM, Hansel CM. Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi. PLoS One 2016; 11:e0157844. [PMID: 27434633 PMCID: PMC4951024 DOI: 10.1371/journal.pone.0157844] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/06/2016] [Indexed: 01/08/2023] Open
Abstract
Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
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Affiliation(s)
- Carolyn A. Zeiner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Erika M. Zink
- Biological Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Dominique L. Chaput
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257, Centre National de la Recherche Scientifique and Aix-Marseille Université, 13288 Marseille Cedex 9, France
- Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
| | - Cara M. Santelli
- Department of Earth Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Colleen M. Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
- * E-mail:
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Jagadeeswaran G, Gainey L, Prade R, Mort AJ. A family of AA9 lytic polysaccharide monooxygenases in Aspergillus nidulans is differentially regulated by multiple substrates and at least one is active on cellulose and xyloglucan. Appl Microbiol Biotechnol 2016; 100:4535-47. [DOI: 10.1007/s00253-016-7505-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/21/2016] [Accepted: 03/24/2016] [Indexed: 02/03/2023]
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Schneider WDH, Gonçalves TA, Uchima CA, Couger MB, Prade R, Squina FM, Dillon AJP, Camassola M. Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:66. [PMID: 26989443 PMCID: PMC4794826 DOI: 10.1186/s13068-016-0476-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/02/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND The enzymatic degradation of lignocellulosic materials by fungal enzyme systems has been extensively studied due to its effectiveness in the liberation of fermentable sugars for bioethanol production. Recently, variants of the fungus Penicillium echinulatum have been described as a great producer of cellulases and considered a promising strain for the bioethanol industry. RESULTS Penicillium echinulatum, wild-type 2HH and its mutant strain S1M29, were grown on four different carbon sources: cellulose, sugar cane bagasse pretreated by steam explosion (SCB), glucose, and glycerol for 120 h. Samples collected at 24, 96, and 120 h were used for enzymatic measurement, and the 96-h one was also used for secretome analysis by 1D-PAGE LC-MS/MS. A total of 165 proteins were identified, and more than one-third of these proteins belong to CAZy families. Glycosyl hydrolases (GH) are the most abundant group, being represented in larger quantities by GH3, 5, 17, 43, and 72. Cellobiohydrolases, endoglucanases, β-glycosidases, xylanases, β-xylosidases, and mannanases were found, and in minor quantities, pectinases, ligninases, and amylases were also found. Swollenin and esterases were also identified. CONCLUSIONS Our study revealed differences in the two strains of P. echinulatum in several aspects in which the mutation improved the production of enzymes related to lignocellulosic biomass deconstruction. Considering the spectral counting analysis, the mutant strain S1M29 was more efficient in the production of enzymes involved in cellulose and hemicellulose degradation, despite having a nearly identical CAZy enzymatic repertoire. Moreover, S1M29 secretes more quantities of protein on SCB than on cellulose, relevant information when considering the production of cellulases using raw materials at low cost. Glucose, and especially glycerol, were used mainly for the production of amylases and ligninases.
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Affiliation(s)
- Willian Daniel Hahn Schneider
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
| | - Thiago Augusto Gonçalves
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
- />Department of Biochemistry, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo Brazil
| | - Cristiane Akemi Uchima
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
| | - Matthew Brian Couger
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way, Stillwater, OK 74078 USA
| | - Rolf Prade
- />Department of Microbiology and Molecular Genetics, Oklahoma State University, 1110 South Innovation Way, Stillwater, OK 74078 USA
| | - Fabio Marcio Squina
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Giuseppe Maximo Scolfaro 10.000, Campinas, São Paulo 13083-970 Brazil
| | - Aldo José Pinheiro Dillon
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
| | - Marli Camassola
- />Enzymes and Biomass Laboratory, Institute of Biotechnology, University of Caxias do Sul, Francisco Getúlio Vargas Street 1130, Caxias Do Sul, RS 95070-560 Brazil
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Ribeiro LF, Tullman J, Nicholes N, Silva SRB, Vieira DS, Ostermeier M, Ward RJ. A xylose-stimulated xylanase-xylose binding protein chimera created by random nonhomologous recombination. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:119. [PMID: 27274356 PMCID: PMC4896006 DOI: 10.1186/s13068-016-0529-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Saccharification of lignocellulosic material by xylanases and other glycoside hydrolases is generally conducted at high concentrations of the final reaction products, which frequently inhibit the enzymes used in the saccharification process. Using a random nonhomologous recombination strategy, we have fused the GH11 xylanase from Bacillus subtilis (XynA) with the xylose binding protein from Escherichia coli (XBP) to produce an enzyme that is allosterically stimulated by xylose. RESULTS The pT7T3GFP_XBP plasmid containing the XBP coding sequence was randomly linearized with DNase I, and ligated with the XynA coding sequence to create a random XynA-XBP insertion library, which was used to transform E. coli strain JW3538-1 lacking the XBP gene. Screening for active XBP was based on the expression of GFP from the pT7T3GFP_XBP plasmid under the control of a xylose inducible promoter. In the presence of xylose, cells harboring a functional XBP domain in the fusion protein (XBP+) showed increased GFP fluorescence and were selected using FACS. The XBP+ cells were further screened for xylanase activity by halo formation around xylanase producing colonies (XynA+) on LB-agar-xylan media after staining with Congo red. The xylanase activity ratio with xylose/without xylose in supernatants from the XBP+/XynA+ clones was measured against remazol brilliant blue xylan. A clone showing an activity ratio higher than 1.3 was selected where the XynA was inserted after the asparagine 271 in the XBP, and this chimera was denominated as XynA-XBP271. The XynA-XBP271 was more stable than XynA at 55 °C, and in the presence of xylose the catalytic efficiency was ~3-fold greater than the parental xylanase. Molecular dynamics simulations predicted the formation of an extended protein-protein interface with coupled movements between the XynA and XBP domains. In the XynA-XBP271 with xylose bound to the XBP domain, the mobility of a β-loop in the XynA domain results in an increased access to the active site, and may explain the observed allosteric activation. CONCLUSIONS The approach presented here provides an important advance for the engineering enzymes that are stimulated by the final product.
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Affiliation(s)
- Lucas Ferreira Ribeiro
- />Johns Hopkins University, Baltimore, MD USA
- />Departamento de Bioquímica e Imunologia, FMRP-Universidade de São Paulo-USP, Ribeirão Preto, SP Brazil
| | - Jennifer Tullman
- />Johns Hopkins University, Baltimore, MD USA
- />Institute for Bioscience and Biotechnology Research, Rockville, MD USA
| | | | | | | | | | - Richard John Ward
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol-CTBE, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP Brazil
- />Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Ribeirão Preto, SP 14040-901 Brazil
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Nekiunaite L, Arntzen MØ, Svensson B, Vaaje-Kolstad G, Abou Hachem M. Lytic polysaccharide monooxygenases and other oxidative enzymes are abundantly secreted by Aspergillus nidulans grown on different starches. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:187. [PMID: 27588040 PMCID: PMC5007996 DOI: 10.1186/s13068-016-0604-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/24/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Starch is the second most abundant plant-derived biomass and a major feedstock in non-food industrial applications and first generation biofuel production. In contrast to lignocellulose, detailed insight into fungal degradation of starch is currently lacking. This study explores the secretomes of Aspergillus nidulans grown on cereal starches from wheat and high-amylose (HA) maize, as well as legume starch from pea for 5 days. RESULTS Aspergillus nidulans grew efficiently on cereal starches, whereas growth on pea starch was poor. The secretomes at days 3-5 were starch-type dependent as also reflected by amylolytic activity measurements. Nearly half of the 312 proteins in the secretomes were carbohydrate-active enzymes (CAZymes), mostly glycoside hydrolases (GHs) and oxidative auxiliary activities (AAs). The abundance of the GH13 α-amylase (AmyB) decreased with time, as opposed to other starch-degrading enzymes, e.g., the GH13 AmyF, GH15 glucoamylases (GlaA and GlaB), and the GH31 α-glucosidase (AgdE). Two AA13 LPMOs displayed similar secretion patterns as amylolytic hydrolases and were among the most abundant CAZymes. The starch-active AnLPMO13A that possesses a CBM20 carbohydrate-binding module dominated the starch-binding secretome fraction. A striking observation is the co-secretion of several redox-active enzymes with the starch-active AA13 LPMOs and GHs, some at high abundance. Notably nine AA9 LPMOs, six AA3 sub-family 2 (AA_2) oxidoreductases, and ten AA7 glyco-oligosaccharide oxidases were identified in the secretomes in addition to other non-CAZyme oxidoreductases. CONCLUSIONS The co-secretion and high abundance of AA13 LPMOs are indicative of a key role in starch granule deconstruction. The increase in AA13 LPMO abundance with culture time may reflect accumulation of a more resistant starch fraction towards the later stages of the culture. The identification of AmyR sites upstream AA13 LPMOs unveils co-regulation of LPMOs featuring in starch utilization. Differential deployment of amylolytic hydrolases and LPMOs over time suggests additional regulatory mechanisms. The abundant co-secretion of distinct AA3 and AA7 oxidoreductases merits further studies into their roles and possible interplay with LPMOs and other enzymes in the deconstruction of starchy substrates. The study reports for the first time the biological significance of LPMOs in starch degradation and the temporal interplay between these and amylolytic hydrolases.
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Affiliation(s)
- Laura Nekiunaite
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Elektrovej 375, 2800 Kgs Lyngby, Denmark
| | - Magnus Ø. Arntzen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Elektrovej 375, 2800 Kgs Lyngby, Denmark
| | - Gustav Vaaje-Kolstad
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Elektrovej 375, 2800 Kgs Lyngby, Denmark
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Zhu N, Liu J, Yang J, Lin Y, Yang Y, Ji L, Li M, Yuan H. Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:42. [PMID: 26900401 PMCID: PMC4761152 DOI: 10.1186/s13068-016-0461-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/11/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND The genome of Schizophyllum commune encodes a diverse repertoire of degradative enzymes for plant cell wall breakdown. Recent comparative genomics study suggests that this wood decayer likely has a mode of biodegradation distinct from the well-established white-rot/brown-rot models. However, much about the extracellular enzyme system secreted by S. commune during lignocellulose deconstruction remains unknown and the underlying mechanism is poorly understood. In this study, extracellular proteins of S. commune colonizing Jerusalem artichoke stalk were analyzed and compared with those of two white-rot fungi Phanerochaete chrysosporium and Ceriporiopsis subvermispora and a brown-rot fungus Gloeophyllum trabeum. RESULTS Under solid-state fermentation (SSF) conditions, S. commune displayed considerably higher levels of hydrolytic enzyme activities in comparison with those of P. chrysosporium, C. subvermispora and G. trabeum. During biodegradation process, this fungus modified the lignin polymer in a way which was consistent with a hydroxyl radical attack, similar to that of G. trabeum. The crude enzyme cocktail derived from S. commune demonstrated superior performance over a commercial enzyme preparation from Trichoderma longibrachiatum in the hydrolysis of pretreated lignocellulosic biomass at low enzyme loadings. Secretomic analysis revealed that compared with three other fungi, this species produced a higher diversity of carbohydrate-degrading enzymes, especially hemicellulases and pectinases acting on polysaccharide backbones and side chains, and a larger set of enzymes potentially supporting the generation of hydroxyl radicals. In addition, multiple non-hydrolytic proteins implicated in enhancing polysaccharide accessibility were identified in the S. commune secretome, including lytic polysaccharide monooxygenases (LPMOs) and expansin-like proteins. CONCLUSIONS Plant lignocellulose degradation by S. commune involves a hydroxyl radical-mediated mechanism for lignocellulose modification in parallel with the synergistic system of various polysaccharide-degrading enzymes. Furthermore, the complex enzyme system of S. commune holds significant potential for application in biomass saccharification. These discoveries will help unveil the diversity of natural lignocellulose-degrading mechanisms, and advance the design of more efficient enzyme mixtures for the deconstruction of lignocellulosic feedstocks.
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Affiliation(s)
- Ning Zhu
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Jiawen Liu
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Jinshui Yang
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yujian Lin
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Yi Yang
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Lei Ji
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Meng Li
- />National Energy R&D Center for Non-food Biomass, China Agricultural University, 100193 Beijing, China
| | - Hongli Yuan
- />State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
- />National Energy R&D Center for Non-food Biomass, China Agricultural University, 100193 Beijing, China
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Zhang L, Ma H, Zhang H, Xun L, Chen G, Wang L. Thermomyces lanuginosus is the dominant fungus in maize straw composts. BIORESOURCE TECHNOLOGY 2015; 197:266-75. [PMID: 26342338 DOI: 10.1016/j.biortech.2015.08.089] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 05/22/2023]
Abstract
The microbial community composition and function of three self-heating maize straw composts were compared by integrated meta-omics. The results revealed that the fungal communities were primarily dominated by the phylum Ascomycota (>90%) regardless of different nitrogen sources, which were exclusively composed of the Thermomyces, a genus of hemicellulose degraders. The bacterial community composition was affected by the addition of nitrogen sources, as the abundance of the Actinobacteria increased, while the Proteobacteria and Bacteroidetes decreased. Various hemicellulases and cellulases were detected in the composts, and the major xylanase secreted by Thermomyces lanuginosus was always present, revealing that it was the dominant fungus in hemicellulose hydrolysis and that bacteria and fungi might synergistically degrade lignocellulose. Thus, microbial communities in composts may develop a simple and stable structure of a dominant fungal species and limited numbers of bacterial species under the selective pressure of high temperature and maize straw as starting materials.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Haixia Ma
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Huaiqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.
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Madhavan A, Sukumaran RK. Signal peptides from filamentous fungi efficiently mediate the secretion of recombinant proteins in Kluyveromyces lactis. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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39
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Comparative Secretome Analysis of Aspergillus niger, Trichoderma reesei, and Penicillium oxalicum During Solid-State Fermentation. Appl Biochem Biotechnol 2015; 177:1252-71. [DOI: 10.1007/s12010-015-1811-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
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Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
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Spitzmüller Z, Kwon NJ, Szilágyi M, Keserű J, Tóth V, Yu JH, Pócsi I, Emri T. γ-Glutamyl transpeptidase (GgtA) of Aspergillus nidulans is not necessary for bulk degradation of glutathione. Arch Microbiol 2014; 197:285-97. [PMID: 25519188 DOI: 10.1007/s00203-014-1057-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/31/2022]
Abstract
Aspergillus nidulans exhibited high γ-glutamyl transpeptidase (γGT) activity in both carbon-starved and carbon-limited cultures. Glucose repressed, but casein peptone increased γGT production. Null mutation of creA did not influence γGT formation, but the functional meaB was necessary for the γGT induction. Deletion of the AN10444 gene (ggtA) completely eliminated the γGT activity, and the mRNA levels of ggtA showed strong correlation with the observed γGT activities. While ggtA does not contain a canonical signal sequence, the γGT activity was detectable both in the fermentation broth and in the hyphae. Deletion of the ggtA gene did not prevent the depletion of glutathione observed in carbon-starved and carbon-limited cultures. Addition of casein peptone to carbon-starved cultures lowered the formation of reactive species (RS). Deletion of ggtA could hinder this decrease and resulted in elevated RS formation. This effect of γGT on redox homeostasis may explain the reduced cleistothecia formation of ΔggtA strains in surface cultures.
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Affiliation(s)
- Zsolt Spitzmüller
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H4032, Hungary
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Winger AM, Heazlewood JL, Chan LJG, Petzold CJ, Permaul K, Singh S. Secretome analysis of the thermophilic xylanase hyper-producer Thermomyces lanuginosus SSBP cultivated on corn cobs. J Ind Microbiol Biotechnol 2014; 41:1687-96. [PMID: 25223615 DOI: 10.1007/s10295-014-1509-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022]
Abstract
Thermomyces lanuginosus is a thermophilic fungus known for its ability to produce industrially important enzymes including large amounts of xylanase, the key enzyme in hemicellulose hydrolysis. The secretome of T. lanuginosus SSBP was profiled by shotgun proteomics to elucidate important enzymes involved in hemicellulose saccharification and to characterise the presence of other industrially interesting enzymes. This study reproducibly identified a total of 74 proteins in the supernatant following growth on corn cobs. An analysis of proteins revealed nine glycoside hydrolase (GH) enzymes including xylanase GH11, β-xylosidase GH43, β-glucosidase GH3, α-galactosidase GH36 and trehalose hydrolase GH65. Two commercially produced Thermomyces enzymes, lipase and amylase, were also identified. In addition, other industrially relevant enzymes not currently explored in Thermomyces were identified including glutaminase, fructose-bisphosphate aldolase and cyanate hydratase. Overall, these data provide insight into the novel ability of a cellulase-free fungus to utilise lignocellulosic material, ultimately producing a number of enzymes important to various industrial processes.
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Affiliation(s)
- A M Winger
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4001, South Africa
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Budak SO, Zhou M, Brouwer C, Wiebenga A, Benoit I, Di Falco M, Tsang A, de Vries RP. A genomic survey of proteases in Aspergilli. BMC Genomics 2014; 15:523. [PMID: 24965873 PMCID: PMC4102723 DOI: 10.1186/1471-2164-15-523] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 06/18/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Proteases can hydrolyze peptides in aqueous environments. This property has made proteases the most important industrial enzymes by taking up about 60% of the total enzyme market. Microorganisms are the main sources for industrial protease production due to their high yield and a wide range of biochemical properties. Several Aspergilli have the ability to produce a variety of proteases, but no comprehensive comparative study has been carried out on protease productivity in this genus so far. RESULTS We have performed a combined analysis of comparative genomics, proteomics and enzymology tests on seven Aspergillus species grown on wheat bran and sugar beet pulp. Putative proteases were identified by homology search and Pfam domains. These genes were then clusters based on orthology and extracellular proteases were identified by protein subcellular localization prediction. Proteomics was used to identify the secreted enzymes in the cultures, while protease essays with and without inhibitors were performed to determine the overall protease activity per protease class. All this data was then integrated to compare the protease productivities in Aspergilli. CONCLUSIONS Genomes of Aspergillus species contain a similar proportion of protease encoding genes. According to comparative genomics, proteomics and enzymatic experiments serine proteases make up the largest group in the protease spectrum across the species. In general wheat bran gives higher induction of proteases than sugar beet pulp. Interesting differences of protease activity, extracellular enzyme spectrum composition, protein occurrence and abundance were identified for species. By combining in silico and wet-lab experiments, we present the intriguing variety of protease productivity in Aspergilli.
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Affiliation(s)
- Sebnem Ozturkoglu Budak
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Faculty of Agriculture, Department of Dairy Technology, University of Ankara, Ankara, Turkey
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miaomiao Zhou
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Carlo Brouwer
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
| | - Ad Wiebenga
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Marcos Di Falco
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Adrian Tsang
- />Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Ronald P de Vries
- />CBS-KNAW Fungal Biodiversity Center, Uppsalalaan 8, Utrecht, 3584 CT The Netherlands
- />Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
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Kolbusz MA, Di Falco M, Ishmael N, Marqueteau S, Moisan MC, Baptista CDS, Powlowski J, Tsang A. Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila. Fungal Genet Biol 2014; 72:10-20. [PMID: 24881579 DOI: 10.1016/j.fgb.2014.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 11/29/2022]
Abstract
Myceliophthora thermophila is a thermophilic fungus whose genome encodes a wide range of carbohydrate-active enzymes (CAZymes) involved in plant biomass degradation. Such enzymes have potential applications in turning different kinds of lignocellulosic feedstock into sugar precursors for biofuels and chemicals. The present study examined and compared the transcriptomes and exoproteomes of M. thermophila during cultivation on different types of complex biomass to gain insight into how its secreted enzymatic machinery varies with different sources of lignocellulose. In the transcriptome analysis three monocot (barley, oat, triticale) and three dicot (alfalfa, canola, flax) plants were used whereas in the proteome analysis additional substrates, i.e. wood and corn stover pulps, were included. A core set of 59 genes encoding CAZymes was up-regulated in response to both monocot and dicot straws, including nine polysaccharide monooxygenases and GH10, but not GH11, xylanases. Genes encoding additional xylanolytic enzymes were up-regulated during growth on monocot straws, while genes encoding additional pectinolytic enzymes were up-regulated in response to dicot biomass. Exoproteome analysis was generally consistent with the conclusions drawn from transcriptome analysis, but additional CAZymes that accumulated to high levels were identified. Despite the wide variety of biomass sources tested some CAZy family members were not expressed under any condition. The results of this study provide a comprehensive view from both transcriptome and exoproteome levels, of how M. thermophila responds to a wide range of biomass sources using its genomic resources.
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Affiliation(s)
- Magdalena Anna Kolbusz
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Nadeeza Ishmael
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Sandrine Marqueteau
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Marie-Claude Moisan
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Cassio da Silva Baptista
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Justin Powlowski
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada; Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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Liao H, Li S, Wei Z, Shen Q, Xu Y. Insights into high-efficiency lignocellulolytic enzyme production by Penicillium oxalicum GZ-2 induced by a complex substrate. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:162. [PMID: 25419234 PMCID: PMC4239378 DOI: 10.1186/s13068-014-0162-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/21/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND Agricultural residue is more efficient than purified cellulose at inducing lignocellulolytic enzyme production in Penicillium oxalicum GZ-2, but in Trichoderma reesei RUT-C30, cellulose induces a more efficient response. To understand the reasons, we designed an artificially simulated plant biomass (cellulose plus xylan) to study the roles and relationships of each component in the production of lignocellulolytic enzymes by P. oxalicum GZ-2. RESULTS The changes in lignocellulolytic enzyme activity, gene expression involving (hemi)cellulolytic enzymes, and the secretome of cultures grown on Avicel (A), xylan (X), or a mixture of both (AX) were studied. The addition of xylan to the cellulose culture did not affect fungal growth but significantly increased the activity of cellulase and hemicellulase. In the AX treatment, the transcripts of cellulase genes (egl1, egl2, egl3, sow, and cbh2) and hemicellulase genes (xyl3 and xyl4) were significantly upregulated (P <0.05). The proportion of biomass-degrading proteins in the secretome was altered; in particular, the percentage of cellulases and hemicellulases was increased. The percentage of cellulases and hemicellulases in the AX secretome increased from 4.5% and 7.6% to 10.3% and 21.8%, respectively, compared to the secretome of the A treatment. Cellobiohydrolase II (encoded by cbh2) and xylanase II (encoded by xyl2) were the main proteins in the secretome, and their corresponding genes (cbh2 and xyl2) were transcripted at the highest levels among the cellulolytic and xylanolytic genes. Several important proteins such as swollenin, cellobiohydrolase, and endo-beta-1,4-xylanase were only induced by AX. Bray-Curtis similarity indices, a dendrogram analysis, and a diversity index all demonstrated that the secretome produced by P. oxalicum GZ-2 depended on the substrate and that strain GZ-2 directionally adjusted the compositions of lignocellulolytic enzymes in its secretome to preferably degrade a complex substrate. CONCLUSION The addition of xylan to the cellulose medium not only induces more hemicellulases but also strongly activates cellulase production. The proportion of the biomass-degrading proteins in the secretome was altered significantly, with the proportion of cellulases and hemicellulases especially increased. Xylan and cellulose have positively synergistic effects, and they play a key role in the induction of highly efficient lignocellulolytic enzymes.
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Affiliation(s)
- Hanpeng Liao
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shuixian Li
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhong Wei
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qirong Shen
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yangchun Xu
- National Enginnering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095 China
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Martins I, Garcia H, Varela A, Núñez O, Planchon S, Galceran MT, Renaut J, Rebelo LPN, Silva Pereira C. Investigating Aspergillus nidulans secretome during colonisation of cork cell walls. J Proteomics 2013; 98:175-88. [PMID: 24316358 DOI: 10.1016/j.jprot.2013.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 10/30/2013] [Accepted: 11/23/2013] [Indexed: 11/19/2022]
Abstract
UNLABELLED Cork, the outer bark of Quercus suber, shows a unique compositional structure, a set of remarkable properties, including high recalcitrance. Cork colonisation by Ascomycota remains largely overlooked. Herein, Aspergillus nidulans secretome on cork was analysed (2DE). Proteomic data were further complemented by microscopic (SEM) and spectroscopic (ATR-FTIR) evaluation of the colonised substrate and by targeted analysis of lignin degradation compounds (UPLC-HRMS). Data showed that the fungus formed an intricate network of hyphae around the cork cell walls, which enabled polysaccharides and lignin superficial degradation, but probably not of suberin. The degradation of polysaccharides was suggested by the identification of few polysaccharide degrading enzymes (β-glucosidases and endo-1,5-α-l-arabinosidase). Lignin degradation, which likely evolved throughout a Fenton-like mechanism relying on the activity of alcohol oxidases, was supported by the identification of small aromatic compounds (e.g. cinnamic acid and veratrylaldehyde) and of several putative high molecular weight lignin degradation products. In addition, cork recalcitrance was corroborated by the identification of several protein species which are associated with autolysis. Finally, stringent comparative proteomics revealed that A. nidulans colonisation of cork and wood share a common set of enzymatic mechanisms. However the higher polysaccharide accessibility in cork might explain the increase of β-glucosidase in cork secretome. BIOLOGICAL SIGNIFICANCE Cork degradation by fungi remains largely overlook. Herein we aimed at understanding how A. nidulans colonise cork cell walls and how this relates to wood colonisation. To address this, the protein species consistently present in the secretome were analysed, as well as major alterations occurring in the substrate, including lignin degradation compounds being released. The obtained data demonstrate that this fungus has superficially attacked the cork cell walls apparently by using both enzymatic and Fenton-like reactions. Only a few polysaccharide degrading enzymes could be detected in the secretome which was dominated by protein species associated with autolysis. Lignin degradation was corroborated by the identification of some degradation products, but the suberin barrier in the cell wall remained virtually intact. Comparative proteomics revealed that cork and wood colonisation share a common set of enzymatic mechanisms.
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Affiliation(s)
- Isabel Martins
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Apartado 12, 2781-901 Oeiras, Portugal
| | - Helga Garcia
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Adélia Varela
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Instituto Nacional de Investigação Agrária e Veterinária, (INIAV), Av. da República, Quinta do Marquês, 2784-505 Oeiras, Portugal
| | - Oscar Núñez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
| | - Sébastien Planchon
- Proteomics Platform, Centre de Recherche Public -Gabriel Lippmann, Belvaux, Luxembourg
| | - Maria Teresa Galceran
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
| | - Jenny Renaut
- Proteomics Platform, Centre de Recherche Public -Gabriel Lippmann, Belvaux, Luxembourg
| | - Luís P N Rebelo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal; Instituto de Biologia Experimental e Tecnológica (IBET), Apartado 12, 2781-901 Oeiras, Portugal.
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An Acidic Thermostable Recombinant Aspergillus nidulans Endoglucanase Is Active towards Distinct Agriculture Residues. Enzyme Res 2013; 2013:287343. [PMID: 23936633 PMCID: PMC3723094 DOI: 10.1155/2013/287343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 11/18/2022] Open
Abstract
Aspergillus nidulans is poorly exploited as a source of enzymes for lignocellulosic residues degradation for biotechnological purposes. This work describes the A. nidulans Endoglucanase A heterologous expression in Pichia pastoris, the purification and biochemical characterization of the recombinant enzyme. Active recombinant endoglucanase A (rEG A) was efficiently secreted as a 35 kDa protein which was purified through a two-step chromatography procedure. The highest enzyme activity was detected at 50°C/pH 4. rEG A retained 100% of activity when incubated at 45 and 55°C for 72 h. Purified rEG A kinetic parameters towards CMC were determined as K m = 27.5 ± 4.33 mg/mL, V max = 1.185 ± 0.11 mmol/min, and 55.8 IU (international units)/mg specific activity. Recombinant P. pastoris supernatant presented hydrolytic activity towards lignocellulosic residues such as banana stalk, sugarcane bagasse, soybean residues, and corn straw. These data indicate that rEG A is suitable for plant biomass conversion into products of commercial importance, such as second-generation fuel ethanol.
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Lan TQ, Wei D, Yang ST, Liu X. Enhanced cellulase production by Trichoderma viride in a rotating fibrous bed bioreactor. BIORESOURCE TECHNOLOGY 2013; 133:175-182. [PMID: 23428816 DOI: 10.1016/j.biortech.2013.01.088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/17/2013] [Accepted: 01/19/2013] [Indexed: 06/01/2023]
Abstract
Filamentous fungi are widely used to produce cellulase, but how the fermentation conditions affect their production is not well known. In this study, cellulase production by Trichoderma viride in submerged fermentations with free cells in a stirred-tank reactor (STR) and immobilized cells in a rotating fibrous-bed bioreactor (RFBB) were investigated. Compared to free-cell fermentation, immobilized-cell fermentation gave 35.5% higher FPase activity and 69.7% higher saccharification yield of sugarcane bagasse (SCB). The secretory proteins in the fermentation broths were analyzed with two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF mass spectrometry, which identified 24 protein spots with differential expression levels. Among them, cellobiohydrolase CBH II and endoglucanase EG II were highly expressed and secreted in the immobilized-cell fermentation, while the free-cell fermentation produced more CBH І and EG ІV. These results showed that immobilized-cell fermentation with T. viride in the RFBB was advantageous for cellulase production.
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Affiliation(s)
- Tian-Qing Lan
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, PR China
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Liu G, Qin Y, Li Z, Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol Adv 2013; 31:962-75. [PMID: 23507038 DOI: 10.1016/j.biotechadv.2013.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/09/2013] [Accepted: 03/10/2013] [Indexed: 11/19/2022]
Abstract
The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.
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Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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Znameroski EA, Glass NL. Using a model filamentous fungus to unravel mechanisms of lignocellulose deconstruction. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:6. [PMID: 23339486 PMCID: PMC3598899 DOI: 10.1186/1754-6834-6-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/18/2013] [Indexed: 05/07/2023]
Abstract
Filamentous fungi are the main source of enzymes used to degrade lignocellulose to fermentable sugars for the production of biofuels. While the most commonly used organism for the production of cellulases in an industrial setting is Trichoderma reesei (Hypocrea jecorina), recent work in the model filamentous fungus Neurospora crassa has shown that the variety of molecular, genetic and biochemical techniques developed for this organism can expedite analyses of the complexities involved in the utilization of lignocellulose as a source of carbon. These include elucidating regulatory networks associated with plant cell wall deconstruction, the identification of signaling molecules necessary for induction of the expression of genes encoding lignocellulolytic enzymes and the characterization of new cellulolytic enzymatic activities. In particular, the availability of a full genome deletion strain set for N. crassa has expedited high throughput screening for mutants that display a cellulolytic phenotype. This review summarizes the key findings of several recent studies using N. crassa to further understanding the mechanisms of plant cell wall deconstruction by filamentous fungi.
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Affiliation(s)
- Elizabeth A Znameroski
- Department of Molecular and Cell Biology, University of California, 94720, Berkeley, CA, USA
- Current address: Novozymes, 1445 Drew Avenue, 95618, Davis, CA, USA
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, 94720, Berkeley, CA, USA
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