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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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Borin GP, Oliveira JVDC. Assessing the intracellular primary metabolic profile of Trichoderma reesei and Aspergillus niger grown on different carbon sources. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:998361. [PMID: 37746225 PMCID: PMC10512294 DOI: 10.3389/ffunb.2022.998361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 09/26/2023]
Abstract
Trichoderma reesei and Aspergillus niger are efficient biological platforms for the production of various industrial products, including cellulases and organic acids. Nevertheless, despite the extensive research on these fungi, integrated analyses of omics-driven approaches are still missing. In this study, the intracellular metabolic profile of T. reesei RUT-C30 and A. niger N402 strains grown on glucose, lactose, carboxymethylcellulose (CMC), and steam-exploded sugarcane bagasse (SEB) as carbon sources for 48 h was analysed by proton nuclear magnetic resonance. The aim was to verify the changes in the primary metabolism triggered by these substrates and use transcriptomics data from the literature to better understand the dynamics of the observed alterations. Glucose and CMC induced higher fungal growth whereas fungi grown on lactose showed the lowest dry weight. Metabolic profile analysis revealed that mannitol, trehalose, glutamate, glutamine, and alanine were the most abundant metabolites in both fungi regardless of the carbon source. These metabolites are of particular interest for the mobilization of carbon and nitrogen, and stress tolerance inside the cell. Their concomitant presence indicates conserved mechanisms adopted by both fungi to assimilate carbon sources of different levels of recalcitrance. Moreover, the higher levels of galactose intermediates in T. reesei suggest its better adaptation in lactose, whereas glycolate and malate in CMC might indicate activation of the glyoxylate shunt. Glycerol and 4-aminobutyrate accumulated in A. niger grown on CMC and lactose, suggesting their relevant role in these carbon sources. In SEB, a lower quantity and diversity of metabolites were identified compared to the other carbon sources, and the metabolic changes and higher xylanase and pNPGase activities indicated a better utilization of bagasse by A. niger. Transcriptomic analysis supported the observed metabolic changes and pathways identified in this work. Taken together, we have advanced the knowledge about how fungal primary metabolism is affected by different carbon sources, and have drawn attention to metabolites still unexplored. These findings might ultimately be considered for developing more robust and efficient microbial factories.
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Affiliation(s)
- Gustavo Pagotto Borin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Juliana Velasco de Castro Oliveira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), São Paulo, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
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3
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Enzyme activity of Aspergillus section Nigri strains isolated from the Korean fermentation starter, nuruk. J Microbiol 2022; 60:998-1006. [DOI: 10.1007/s12275-022-2071-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 10/15/2022]
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Aspergillus Hydrophobins: Physicochemical Properties, Biochemical Properties, and Functions in Solid Polymer Degradation. Microorganisms 2022; 10:microorganisms10081498. [PMID: 35893556 PMCID: PMC9394342 DOI: 10.3390/microorganisms10081498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 01/27/2023] Open
Abstract
Hydrophobins are small amphipathic proteins conserved in filamentous fungi. In this review, the properties and functions of Aspergillus hydrophobins are comprehensively discussed on the basis of recent findings. Multiple Aspergillus hydrophobins have been identified and categorized in conventional class I and two non-conventional classes. Some Aspergillus hydrophobins can be purified in a water phase without organic solvents. Class I hydrophobins of Aspergilli self-assemble to form amphipathic membranes. At the air–liquid interface, RolA of Aspergillus oryzae self-assembles via four stages, and its self-assembled films consist of two layers, a rodlet membrane facing air and rod-like structures facing liquid. The self-assembly depends mainly on hydrophobin conformation and solution pH. Cys4–Cys5 and Cys7–Cys8 loops, disulfide bonds, and conserved Cys residues of RodA-like hydrophobins are necessary for self-assembly at the interface and for adsorption to solid surfaces. AfRodA helps Aspergillus fumigatus to evade recognition by the host immune system. RodA-like hydrophobins recruit cutinases to promote the hydrolysis of aliphatic polyesters. This mechanism appears to be conserved in Aspergillus and other filamentous fungi, and may be beneficial for their growth. Aspergilli produce various small secreted proteins (SSPs) including hydrophobins, hydrophobic surface–binding proteins, and effector proteins. Aspergilli may use a wide variety of SSPs to decompose solid polymers.
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Zhang J, Liu S, Sun H, Jiang Z, Xu Y, Mao J, Qian B, Wang L, Mao J. Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu. Food Res Int 2022; 152:110707. [PMID: 35181108 DOI: 10.1016/j.foodres.2021.110707] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/13/2021] [Accepted: 09/05/2021] [Indexed: 12/11/2022]
Abstract
Daqu and wheat Qu are saccharification and fermenting agents in Chinese huangjiu and baijiu production. This study aimed to investigate the difference between Daqu and wheat Qu in physicochemical indices, microbial communities, functional genes, and the metabolic network of key microbes responsible for flavor synthesis by whole-metagenome sequencing and metabolite analysis. Herein, physicochemical indices indicated that compared with wheat Qu, Daqu exhibited higher protease and cellulase activity and acidity, and lower glucoamylase and amylase enzyme activity. Metagenomic sequencing reveals that although Daqu and wheat Qu community composition have significant differences at species level, they have similar functional genes. Daqu were enriched in Pediococcus pentosaceus, Weissella paramesenteroides, Rasamsonia emersonii and Byssochlamys spectabilis (22.48% of the total abundance), while wheat Qu harbored greater abundances of Saccharopolyspora (54.78%, Saccharopolyspora rectivirgula, Saccharopolyspora shandongensis, Saccharopolyspora hirsuta, Saccharopolyspora spinose, and Saccharopolyspora erythraea). From a functional perspective, the important functions of Daqu and wheat Qu are both amino acid metabolism and carbohydrate metabolism. Meanwhile, a combined analysis among microbiota, functional genes, and dominant flavors indicated S. shandongensis, S. rectivirgula, and S. spinose might be the main contributor to the synthesis of flavor compounds in wheat Qu, while R. emersonii, W. paramesenteroides, Leuconostoc citreum, Leuconostoc mesenteroides, Weissella cibaria and P. pentosaceus may make the greatest contribution to flavor compounds synthesis in Daqu. This study reveals the microbial and functional dissimilarities of Daqu and wheat Qu, and helps elucidating different metabolic roles of microbes during flavor formation.
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Affiliation(s)
- Jing Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shuangping Liu
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 31200, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Hailong Sun
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhengfei Jiang
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuezheng Xu
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Jieqi Mao
- Department of Food Science and Technology, National University of Singapore, Science Drive 2, 117542, Singapore
| | - Bin Qian
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Lan Wang
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China
| | - Jian Mao
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, Zhejiang 31200, China; National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 31200, China.
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Procópio DP, Kendrick E, Goldbeck R, Damasio ARDL, Franco TT, Leak DJ, Jin YS, Basso TO. Xylo-Oligosaccharide Utilization by Engineered Saccharomyces cerevisiae to Produce Ethanol. Front Bioeng Biotechnol 2022; 10:825981. [PMID: 35242749 PMCID: PMC8886126 DOI: 10.3389/fbioe.2022.825981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/18/2022] [Indexed: 11/26/2022] Open
Abstract
The engineering of xylo-oligosaccharide-consuming Saccharomyces cerevisiae strains is a promising approach for more effective utilization of lignocellulosic biomass and the development of economic industrial fermentation processes. Extending the sugar consumption range without catabolite repression by including the metabolism of oligomers instead of only monomers would significantly improve second-generation ethanol production This review focuses on different aspects of the action mechanisms of xylan-degrading enzymes from bacteria and fungi, and their insertion in S. cerevisiae strains to obtain microbial cell factories able of consume these complex sugars and convert them to ethanol. Emphasis is given to different strategies for ethanol production from both extracellular and intracellular xylo-oligosaccharide utilization by S. cerevisiae strains. The suitability of S. cerevisiae for ethanol production combined with its genetic tractability indicates that it can play an important role in xylan bioconversion through the heterologous expression of xylanases from other microorganisms.
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Affiliation(s)
- Dielle Pierotti Procópio
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, Brazil
| | - Emanuele Kendrick
- Department of Biology and Biochemistry, Faculty of Sciences, University of Bath, Bath, United Kingdom
| | - Rosana Goldbeck
- School of Food Engineering, University of Campinas, Campinas, Brazil
| | | | - Telma Teixeira Franco
- Interdisciplinary Center of Energy Planning, University of Campinas, Campinas, Brazil
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | - David J. Leak
- Department of Biology and Biochemistry, Faculty of Sciences, University of Bath, Bath, United Kingdom
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Food Science and Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, Brazil
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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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Zhang T, Mai RM, Fang QQ, Ou JF, Mo LX, Tian D, Li CX, Gu LS, Luo XM, Feng JX, Zhao S. Regulatory function of the novel transcription factor CxrC in Penicillium oxalicum. Mol Microbiol 2021; 116:1512-1532. [PMID: 34797006 DOI: 10.1111/mmi.14843] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 10/24/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
Numerous transcription factors (TFs) in ascomycete fungi play crucial roles in cellular processes; however, how most of them function is poorly understood. Here, we identified and characterized a novel TF, CxrC (POX01387), acting downstream of the key TF CxrA, which is essential for plant-biomass-degrading-enzyme (PBDE) production in Penicillium oxalicum. Deletion of cxrC in P. oxalicum significantly affected the production of PBDEs, as well as mycelial growth and conidiospore production. CxrA directly repressed the expression of cxrC after about 12 hr following switch to Avicel culture. CxrC bound the promoters of major PBDE genes and genes involved in conidiospore development. CxrC was found to bind the TSSGTYR core sequence (S: C and G; Y: T and C; R: G and A) of the important cellulase genes cbh1 and eg1. Both N- and C-terminal peptides of CxrC and the CxrC phosphorylation were found to mediate its homodimerization. The conserved motif LPSVRSLLTP (65-74) in CxrC was found to be required for regulating cellulase production. This study reveals novel mechanisms of TF-mediated regulation of the expression of PBDE genes and genes involved in cellular processes in an ascomycete fungus.
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Affiliation(s)
- Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Rong-Ming Mai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Qi-Qi Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Jian-Feng Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Li-Xiang Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Di Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Li-Sha Gu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
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Heeger F, Bourne EC, Wurzbacher C, Funke E, Lipzen A, He G, Ng V, Grigoriev IV, Schlosser D, Monaghan MT. Evidence for Lignocellulose-Decomposing Enzymes in the Genome and Transcriptome of the Aquatic Hyphomycete Clavariopsis aquatica. J Fungi (Basel) 2021; 7:jof7100854. [PMID: 34682274 PMCID: PMC8537685 DOI: 10.3390/jof7100854] [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: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Fungi are ecologically outstanding decomposers of lignocellulose. Fungal lignocellulose degradation is prominent in saprotrophic Ascomycota and Basidiomycota of the subkingdom Dikarya. Despite ascomycetes dominating the Dikarya inventory of aquatic environments, genome and transcriptome data relating to enzymes involved in lignocellulose decay remain limited to terrestrial representatives of these phyla. We sequenced the genome of an exclusively aquatic ascomycete (the aquatic hyphomycete Clavariopsis aquatica), documented the presence of genes for the modification of lignocellulose and its constituents, and compared differential gene expression between C. aquatica cultivated on lignocellulosic and sugar-rich substrates. We identified potential peroxidases, laccases, and cytochrome P450 monooxygenases, several of which were differentially expressed when experimentally grown on different substrates. Additionally, we found indications for the regulation of pathways for cellulose and hemicellulose degradation. Our results suggest that C. aquatica is able to modify lignin to some extent, detoxify aromatic lignin constituents, or both. Such characteristics would be expected to facilitate the use of carbohydrate components of lignocellulose as carbon and energy sources.
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Affiliation(s)
- Felix Heeger
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Department Materials and Environment, Federal Institute for Material Research and Testing, 12203 Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Correspondence:
| | - Elizabeth C. Bourne
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany;
| | - Elisabeth Funke
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (A.L.); (G.H.); (V.N.); (I.V.G.)
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dietmar Schlosser
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany;
| | - Michael T. Monaghan
- Department Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany; (E.C.B.); (E.F.); (M.T.M.)
- Berlin Center for Genomics in Biodiversity Research, 14195 Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, 14195 Berlin, Germany
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10
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The F-box protein gene exo- 1 is a target for reverse engineering enzyme hypersecretion in filamentous fungi. Proc Natl Acad Sci U S A 2021; 118:2025689118. [PMID: 34168079 DOI: 10.1073/pnas.2025689118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Carbohydrate active enzymes (CAZymes) are vital for the lignocellulose-based biorefinery. The development of hypersecreting fungal protein production hosts is therefore a major aim for both academia and industry. However, despite advances in our understanding of their regulation, the number of promising candidate genes for targeted strain engineering remains limited. Here, we resequenced the genome of the classical hypersecreting Neurospora crassa mutant exo-1 and identified the causative point of mutation to reside in the F-box protein-encoding gene, NCU09899. The corresponding deletion strain displayed amylase and invertase activities exceeding those of the carbon catabolite derepressed strain Δcre-1, while glucose repression was still mostly functional in Δexo-1 Surprisingly, RNA sequencing revealed that while plant cell wall degradation genes are broadly misexpressed in Δexo-1, only a small fraction of CAZyme genes and sugar transporters are up-regulated, indicating that EXO-1 affects specific regulatory factors. Aiming to elucidate the underlying mechanism of enzyme hypersecretion, we found the high secretion of amylases and invertase in Δexo-1 to be completely dependent on the transcriptional regulator COL-26. Furthermore, misregulation of COL-26, CRE-1, and cellular carbon and nitrogen metabolism was confirmed by proteomics. Finally, we successfully transferred the hypersecretion trait of the exo-1 disruption by reverse engineering into the industrially deployed fungus Myceliophthora thermophila using CRISPR-Cas9. Our identification of an important F-box protein demonstrates the strength of classical mutants combined with next-generation sequencing to uncover unanticipated candidates for engineering. These data contribute to a more complete understanding of CAZyme regulation and will facilitate targeted engineering of hypersecretion in further organisms of interest.
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11
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From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi. Biotechnol Adv 2021; 50:107770. [PMID: 33989704 DOI: 10.1016/j.biotechadv.2021.107770] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/04/2021] [Accepted: 05/08/2021] [Indexed: 01/21/2023]
Abstract
In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.
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12
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Allison CL, Moskaluk A, VandeWoude S, Reynolds MM. Detection of glucosamine as a marker for Aspergillus niger: a potential screening method for fungal infections. Anal Bioanal Chem 2021; 413:2933-2941. [PMID: 33615396 PMCID: PMC8043943 DOI: 10.1007/s00216-021-03225-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/21/2021] [Accepted: 02/08/2021] [Indexed: 11/07/2022]
Abstract
Several species of fungus from the genus Aspergillus are implicated in pulmonary infections in immunocompromised patients. Broad screening methods for fungal infections are desirable, as cultures require a considerable amount of time to provide results. Herein, we developed degradation and detection methods to produce and detect D-glucosamine (GlcN) from Aspergillus niger, a species of filamentous fungus. Ultimately, these techniques hold the potential to contribute to the diagnosis of pulmonary fungal infections in immunocompromised patients. In the following studies, we produced GlcN from fungal-derived chitin to serve as a marker for Aspergillus niger. To accomplish this, A. niger cells were lysed and subjected to a hydrochloric acid degradation protocol. Products were isolated, reconstituted in aqueous solutions, and analyzed using hydrophilic interaction liquid chromatography (HILIC) in tandem with electrospray ionization time-of-flight mass spectrometry. Our results indicated that GlcN was produced from A. niger. To validate these results, products obtained via fungal degradation were compared to products obtained from the degradation of two chitin polymers. The observed retention times and mass spectral extractions provided a two-step validation confirming that GlcN was produced from fungal-derived chitin. Our studies qualitatively illustrate that GlcN can be produced from A. niger; applying these methods to a more diverse range of fungi offers the potential to render a broad screening method for fungal detection pertinent to diagnosis of fungal infections.
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Affiliation(s)
- Christopher L Allison
- Department of Chemistry, Colorado State University, 1801 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Alex Moskaluk
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Melissa M Reynolds
- Department of Chemistry, Colorado State University, 1801 Campus Delivery, Fort Collins, CO, 80523, USA.
- Department of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523, USA.
- School of Biomedical Engineering, Colorado State University, 1376 Campus Delivery, Fort Collins, CO, 80523, USA.
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13
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Demirci E, Arentshorst M, Yilmaz B, Swinkels A, Reid ID, Visser J, Tsang A, Ram AFJ. Genetic Characterization of Mutations Related to Conidiophore Stalk Length Development in Aspergillus niger Laboratory Strain N402. Front Genet 2021; 12:666684. [PMID: 33959152 PMCID: PMC8093798 DOI: 10.3389/fgene.2021.666684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Aspergillus niger is an important filamentous fungus in industrial biotechnology for the production of citric acid and enzymes. In the late 1980s, the A. niger N400/NRRL3 strain was selected for both fundamental and applied studies in relation to several processes including gluconic acid and protein production. To facilitate handling of A. niger, the N400 wild-type strain was UV mutagenized in two consecutive rounds to generate N401 and N402. N402 was used as a reference laboratory strain and exhibits the phenotypes with reduced conidiophore stalk length and reduced radial growth. The conidiophore stalk length and radial growth of A. niger strain N400 were determined and compared to N401 and N402. The length of N400 conidiophore stalks (2.52 ± 0.40 mm) was reduced in N401 and N402 to 0.66 ± 0.14 mm and 0.34 ± 0.06 mm, respectively. Whereas N400 reached a colony diameter of 6.7 ± 0.2 cm after 7 days, N401 and N402 displayed reduced radial growth phenotype (4.3 ± 0.1 and 4.1 ± 0.1, respectively). To identify the mutations (dubbed cspA and cspB) responsible for the phenotypes of N401 and N402, the genomes were sequenced and compared to the N400 genome sequence. A parasexual cross was performed between N400 and N402 derivatives to isolate segregants which allowed cosegregation analysis of single nucleotide polymorphisms and insertions and deletions among the segregants. The shorter conidiophore stalk and reduced radial growth in N401 (cspA) was found to be caused by a 9-kb deletion on chromosome III and was further narrowed down to a truncation of NRRL3_03857 which encodes a kinesin-like protein homologous to the A. nidulans UncA protein. The mutation responsible for the further shortening of conidiophore stalks in N402 (cspB) was found to be caused by a missense mutation on chromosome V in a hitherto unstudied C2H2 transcription factor encoded by the gene NRRL3_06646. The importance of these two genes in relation to conidiophore stalk length and radial growth was confirmed by single and double gene deletion studies. The mutations in the laboratory strain N402 should be taken into consideration when studying phenotypes in the N402 background.
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Affiliation(s)
- Ebru Demirci
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Mark Arentshorst
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Baran Yilmaz
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Aram Swinkels
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
| | - Ian D Reid
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Jaap Visser
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands.,Fungal Genetics and Technology Consultancy, Wageningen, Netherlands
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada
| | - Arthur F J Ram
- Institute of Biology Leiden, Microbial Sciences, Leiden University, Leiden, Netherlands
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14
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Li CX, Liao LS, Wan XD, Zhang FF, Zhang T, Luo XM, Zhao S, Feng JX. PoxCbh, a novel CENPB-type HTH domain protein, regulates cellulase and xylanase gene expression in Penicillium oxalicum. Mol Microbiol 2021; 116:140-153. [PMID: 33561892 DOI: 10.1111/mmi.14696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/08/2021] [Accepted: 02/06/2021] [Indexed: 01/10/2023]
Abstract
The essential transcription factor PoxCxrA is required for cellulase and xylanase gene expression in the filamentous fungus Penicillium oxalicum that is potentially applied in biotechnological industry as a result of the existence of the integrated cellulolytic and xylolytic system. However, the regulatory mechanism of cellulase and xylanase gene expression specifically associated with PoxCxrA regulation in fungi is poorly understood. In this study, the novel regulator PoxCbh (POX06865), containing a centromere protein B-type helix-turn-helix domain, was identified through screening for the PoxCxrA regulon under Avicel induction and genetic analysis. The mutant ∆PoxCbh showed significant reduction in cellulase and xylanase production, ranging from 28.4% to 59.8%. Furthermore, PoxCbh was found to directly regulate the expression of important cellulase and xylanase genes, as well as the known regulatory genes PoxNsdD and POX02484, and its expression was directly controlled by PoxCxrA. The PoxCbh-binding DNA sequence in the promoter region of the cellobiohydrolase 1 gene cbh1 was identified. These results expand our understanding of the diverse roles of centromere protein B-like protein, the regulatory network of cellulase and xylanase gene expression, and regulatory mechanisms in fungi.
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Affiliation(s)
- Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Xu-Dong Wan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Feng-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, People's Republic of China
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15
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Yamashita M, Tsujikami M, Murata S, Kobayashi T, Shimizu M, Kato M. Artificial AmyR::XlnR transcription factor induces α-amylase production in response to non-edible xylan-containing hemicellulosic biomass. Enzyme Microb Technol 2021; 145:109762. [PMID: 33750542 DOI: 10.1016/j.enzmictec.2021.109762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022]
Abstract
Filamentous fungi belonging to the Aspergillus genus are one of the most favored microorganisms for industrial enzyme production because they can secrete large amounts of proteins into the culture medium. α-Amylase, an enzyme produced by Aspergillus species, is important for food and industrial applications. The production of α-amylase is induced by starch, mainly obtained from the edible biomass; however, the increasing demand for foods is limiting the application of the latter. Therefore, it is expected that using the non-edible biomass, such as rice straw, could improve the competition for industrial application starch containing resources. The transcription factor AmyR activates the transcription of amylolytic enzyme genes, while the transcription factor XlnR activates the transcription of xylanolytic enzyme genes in response to xylose. In this study, we aimed to construct an artificial AmyR::XlnR transcription factor (AXTF) by replacing the DNA-binding domain (1-159 amino acids) of XlnR with that (1-68 aa) of AmyR, which is capable of inducing amylolytic enzyme production in response to xylan-containing hemicellulosic biomass. The chimeric transcription factor AXTF was constructed and expressed using the gapA promoter in the amyR-deficient mutant strain SA1. When the AXTF strain was cultured in the minimal medium containing xylose as the carbon source, the amyB, amyF, agdB, and agdE transcription levels were 41.1-, 11.3-, 37.9-, and 23.7-fold higher, respectively, than those of the wild-type strain. The α-amylase and α-glucosidase activities in the culture supernatant of the AXTF strain grown with xylose for 48 h were 696.6 and 536.1 U/mL, respectively, while these activities were not detected in the culture supernatant of the wild-type and SA1 strains. When rice straw hydrolysate was used as a carbon source, the α-amylase and α-glucosidase activities were 590.2 and 362.7 U/mL, respectively. Thus, we successfully generated an Aspergillus nidulans strain showing amylolytic enzyme production in response to non-edible xylan-containing hemicellulosic biomass by transforming it with the chimeric transcription factor AXTF. Furthermore, the use of genes encoding engineered transcription factors is advantageous because introducing such genes into an industrial Aspergillus strain has similar simultaneous effects on multiple amylase genes controlled by AmyR.
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Affiliation(s)
- Miharu Yamashita
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Masaya Tsujikami
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Shunsuke Murata
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Tetsuo Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Motoyuki Shimizu
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan
| | - Masashi Kato
- Faculty of Agriculture, Meijo University, Shiogamaguchi, Tenpaku-ku, Nagoya, Aichi, 468-8502, Japan.
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16
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Wu H, Nakazawa T, Xu H, Yang R, Bao D, Kawauchi M, Sakamoto M, Honda Y. Comparative transcriptional analyses of Pleurotus ostreatus mutants on beech wood and rice straw shed light on substrate-biased gene regulation. Appl Microbiol Biotechnol 2021; 105:1175-1190. [PMID: 33415371 DOI: 10.1007/s00253-020-11087-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/15/2020] [Accepted: 12/28/2020] [Indexed: 11/25/2022]
Abstract
Distinct wood degraders occupying their preferred habitats have biased enzyme repertoires that are well fitted to their colonized substrates. Pleurotus ostreatus, commonly found on wood, has evolved its own enzyme-producing traits. In our previous study, transcriptional shifts in several P. ostreatus delignification-defective mutants, including Δhir1 and Δgat1 strains, were analyzed, which revealed the downregulation of ligninolytic genes and the upregulation of cellulolytic and xylanolytic genes when compared to their parental strain 20b on beech wood sawdust medium (BWS). In this study, rice straw (RS) was used as an alternative substrate to examine the transcriptional responses of P. ostreatus to distinct substrates. The vp1 gene and a cupredoxin-encoding gene were significantly upregulated in the 20b strain on RS compared with that on BWS, reflecting their distinct regulation patterns. The overall expression level of genes encoding glucuronidases was also higher on RS than on BWS, showing a good correlation with the substrate composition. Transcriptional alterations in the mutants (Δhir1 or Δgat1 versus 20b strain) on RS were similar to those on BWS, and the extracellular lignocellulose-degrading enzyme activities and lignin-degrading ability of the mutants on RS were consistent with the transcriptional alterations of the corresponding enzyme-encoding genes. However, transcripts of specific genes encoding enzymes belonging to the same CAZyme family exhibited distinct alteration patterns in the mutant strains grown on RS compared to those grown on BWS. These findings provide new insights into the molecular mechanisms underlying the transcriptional regulation of lignocellulolytic genes in P. ostreatus.Key Points• P. ostreatus expressed variable enzymatic repertoire-related genes in response to distinct substrates.• A demand to upregulate the cellulolytic genes seems to be present in ligninolysis-deficient mutants.• The regulation of some specific genes probably driven by the demand is dependent on the substrate.
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Affiliation(s)
- Hongli Wu
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Haibo Xu
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ruiheng Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Moriyuki Kawauchi
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
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17
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Corrêa CL, Midorikawa GEO, Filho EXF, Noronha EF, Alves GSC, Togawa RC, Silva-Junior OB, Costa MMDC, Grynberg P, Miller RNG. Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation. Front Bioeng Biotechnol 2020; 8:564527. [PMID: 33123513 PMCID: PMC7573219 DOI: 10.3389/fbioe.2020.564527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
Given the global abundance of plant biomass residues, potential exists in biorefinery-based applications with lignocellulolytic fungi. Frequently isolated from agricultural cellulosic materials, Aspergillus terreus is a fungus efficient in secretion of commercial enzymes such as cellulases, xylanases and phytases. In the context of biomass saccharification, lignocellulolytic enzyme secretion was analyzed in a strain of A. terreus following liquid culture with sugarcane bagasse (SB) (1% w/v) and soybean hulls (SH) (1% w/v) as sole carbon source, in comparison to glucose (G) (1% w/v). Analysis of the fungal secretome revealed a maximum of 1.017 UI.mL–1 xylanases after growth in minimal medium with SB, and 1.019 UI.mL–1 after incubation with SH as carbon source. The fungal transcriptome was characterized on SB and SH, with gene expression examined in comparison to equivalent growth on G as carbon source. Over 8000 genes were identified, including numerous encoding enzymes and transcription factors involved in the degradation of the plant cell wall, with significant expression modulation according to carbon source. Eighty-nine carbohydrate-active enzyme (CAZyme)-encoding genes were identified following growth on SB, of which 77 were differentially expressed. These comprised 78% glycoside hydrolases, 8% carbohydrate esterases, 2.5% polysaccharide lyases, and 11.5% auxiliary activities. Analysis of the glycoside hydrolase family revealed significant up-regulation for genes encoding 25 different GH family proteins, with predominance for families GH3, 5, 7, 10, and 43. For SH, from a total of 91 CAZyme-encoding genes, 83 were also significantly up-regulated in comparison to G. These comprised 80% glycoside hydrolases, 7% carbohydrate esterases, 5% polysaccharide lyases, 7% auxiliary activities (AA), and 1% glycosyltransferases. Similarly, within the glycoside hydrolases, significant up-regulation was observed for genes encoding 26 different GH family proteins, with predominance again for families GH3, 5, 10, 31, and 43. A. terreus is a promising species for production of enzymes involved in the degradation of plant biomass. Given that this fungus is also able to produce thermophilic enzymes, this first global analysis of the transcriptome following cultivation on lignocellulosic carbon sources offers considerable potential for the application of candidate genes in biorefinery applications.
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Affiliation(s)
- Camila L Corrêa
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Glaucia E O Midorikawa
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | | | - Eliane Ferreira Noronha
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Gabriel S C Alves
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica - PqEB, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica - PqEB, Brasília, Brazil
| | - Robert N G Miller
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
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18
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van Munster JM, Daly P, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Arvas M, Raulo R, Pullan ST, Delmas S, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:69. [PMID: 32313551 PMCID: PMC7155255 DOI: 10.1186/s13068-020-01702-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. RESULTS We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. CONCLUSION In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
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Affiliation(s)
- Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Manchester Institute of Biotechnology (MIB) & School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | | | | | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT Espoo, Finland
| | - Roxane Raulo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Public Health England, National Infection Service, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, 75005 Paris, France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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19
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Lin H, Zhao J, Zhang Q, Cui S, Fan Z, Chen H, Tian C. Identification and Characterization of a Cellodextrin Transporter in Aspergillus niger. Front Microbiol 2020; 11:145. [PMID: 32117164 PMCID: PMC7020610 DOI: 10.3389/fmicb.2020.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/21/2020] [Indexed: 11/13/2022] Open
Abstract
Aspergillus niger produces a wide spectrum of extracellular polysaccharide hydrolases that hydrolyze cellulose into soluble glucose and cellodextrins. Transporters are essential for sugar uptake, yet it is not clear whether cellodextrin transporters exist in A. niger. Here, one cellulose inducible cellodextrin transporter CtA was identified in A. niger B2. It was found that CtA not only could transport cellobiose, but also cellotriose, cellotetraose, and cellopentaose. The yeast strain YPβG-CtA, expressing cellodextrin transporter CtA and an intracellular β-glucosidase, grew on cellobiose with the cell growth rate of 0.0830 ± 0.0113 h–1 under aerobic condition. Furthermore, the engineered yeast could produce 1.1 g/L ethanol anaerobically on cellobiose in 2 days. The identification of CtA provides evidence that the cellodextrin uptake is a complementary strategy of cellulose utilization in A. niger, and the CtA could be a strong transporter candidate for constructing engineered cellodextrin-utilizing microorganisms.
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Affiliation(s)
- Hui Lin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Zhao
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Qingqing Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Shixiu Cui
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhiliang Fan
- Department of Biological and Agricultural Engineering, University of California, Davis, Davis, CA, United States
| | - Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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20
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Torres-Barajas LR, Alvarez-Zúñiga MT, Mendoza-Hernández G, Aguilar-Osorio G. Analysis of polysaccharide hydrolases secreted by Aspergillus flavipes FP-500 on corn cobs and wheat bran as complex carbon sources. Prep Biochem Biotechnol 2019; 50:390-400. [DOI: 10.1080/10826068.2019.1700518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lizzete Ruth Torres-Barajas
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
| | - María Teresa Alvarez-Zúñiga
- Department of Food Science and Biotechnology, Faculty of Chemistry, National Autonomous University of Mexico, Coyoacan, Mexico
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21
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Khosravi C, Kowalczyk JE, Chroumpi T, Battaglia E, Aguilar Pontes MV, Peng M, Wiebenga A, Ng V, Lipzen A, He G, Bauer D, Grigoriev IV, de Vries RP. Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. BMC Genomics 2019; 20:853. [PMID: 31726994 PMCID: PMC6854810 DOI: 10.1186/s12864-019-6235-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/28/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Enzymatic plant biomass degradation by fungi is a highly complex process and one of the leading challenges in developing a biobased economy. Some industrial fungi (e.g. Aspergillus niger) have a long history of use with respect to plant biomass degradation and for that reason have become 'model' species for this topic. A. niger is a major industrial enzyme producer that has a broad ability to degrade plant based polysaccharides. A. niger wild-type, the (hemi-)cellulolytic regulator (xlnR) and xylulokinase (xkiA1) mutant strains were grown on a monocot (corn stover, CS) and dicot (soybean hulls, SBH) substrate. The xkiA1 mutant is unable to utilize the pentoses D-xylose and L-arabinose and the polysaccharide xylan, and was previously shown to accumulate inducers for the (hemi-)cellulolytic transcriptional activator XlnR and the arabinanolytic transcriptional activator AraR in the presence of pentoses, resulting in overexpression of their target genes. The xlnR mutant has reduced growth on xylan and down-regulation of its target genes. The mutants therefore have a similar phenotype on xylan, but an opposite transcriptional effect. D-xylose and L-arabinose are the most abundant monosaccharides after D-glucose in nearly all plant-derived biomass materials. In this study we evaluated the effect of the xlnR and xkiA1 mutation during growth on two pentose-rich substrates by transcriptome analysis. RESULTS Particular attention was given to CAZymes, metabolic pathways and transcription factors related to the plant biomass degradation. Genes coding for the main enzymes involved in plant biomass degradation were down-regulated at the beginning of the growth on CS and SBH. However, at a later time point, significant differences were found in the expression profiles of both mutants on CS compared to SBH. CONCLUSION This study demonstrates the high complexity of the plant biomass degradation process by fungi, by showing that mutant strains with fairly straightforward phenotypes on pure mono- and polysaccharides, have much less clear-cut phenotypes and transcriptomes on crude plant biomass.
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Affiliation(s)
- Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Joanna E. Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Tania Chroumpi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Maria-Victoria Aguilar Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
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22
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Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation. Biotechnol Adv 2019; 37:107361. [PMID: 30825514 DOI: 10.1016/j.biotechadv.2019.02.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Fungal strain engineering is commonly used in many areas of biotechnology, including the production of plant biomass degrading enzymes. Its aim varies from the production of specific enzymes to overall increased enzyme production levels and modification of the composition of the enzyme set that is produced by the fungus. Strain engineering involves a diverse range of methodologies, including classical mutagenesis, genetic engineering and genome editing. In this review, the main approaches for strain engineering of filamentous fungi in the field of plant biomass degradation will be discussed, including recent and not yet implemented methods, such as CRISPR/Cas9 genome editing and adaptive evolution.
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23
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The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum. N Biotechnol 2019; 51:57-66. [PMID: 30797054 DOI: 10.1016/j.nbt.2019.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/07/2018] [Accepted: 02/20/2019] [Indexed: 11/22/2022]
Abstract
Guar gum consists mainly of galactomannan and constitutes the endosperm of guar seeds that acts as a reserve polysaccharide for germination. Due to its molecular structure and physical properties, this biopolymer has been considered as one of the most important and widely used gums in industry. However, for many of these applications this (hemi-)cellulosic structure needs to be modified or (partially) depolymerized in order to customize and improve its physicochemical properties. In this study, transcriptome, exoproteome and enzyme activity analyses were employed to decipher the complete enzymatic arsenal for guar gum depolymerization by Aspergillus niger. This multi-omic analysis revealed a set of 46 genes encoding carbohydrate-active enzymes (CAZymes) responding to the presence of guar gum, including CAZymes not only with preferred activity towards galactomannan, but also towards (arabino-)xylan, cellulose, starch and pectin, likely due to trace components in guar gum. This demonstrates that the purity of substrates has a strong effect on the resulting enzyme mixture produced by A. niger and probably by other fungi as well, which has significant implications for the commercial production of fungal enzyme cocktails.
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24
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Tong Z, Zheng X, Tong Y, Shi YC, Sun J. Systems metabolic engineering for citric acid production by Aspergillus niger in the post-genomic era. Microb Cell Fact 2019; 18:28. [PMID: 30717739 PMCID: PMC6362574 DOI: 10.1186/s12934-019-1064-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/16/2019] [Indexed: 11/11/2022] Open
Abstract
Citric acid is the world’s largest consumed organic acid and is widely used in beverage, food and pharmaceutical industries. Aspergillus niger is the main industrial workhorse for citric acid production. Since the release of the genome sequence, extensive multi-omic data are being rapidly obtained, which greatly boost our understanding of the citric acid accumulation mechanism in A. niger to a molecular and system level. Most recently, the rapid development of CRISPR/Cas9 system facilitates highly efficient genome-scale genetic perturbation in A. niger. In this review, we summarize the impact of systems biology on the citric acid molecular regulatory mechanisms, the advances in metabolic engineering strategies for enhancing citric acid production and discuss the development and application of CRISPR/Cas9 systems for genome editing in A. niger. We believe that future systems metabolic engineering efforts will redesign and engineer A. niger as a highly optimized cell factory for industrial citric acid production.
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Affiliation(s)
- Zhenyu Tong
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS, 66506, USA
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Yi Tong
- COFCO Biochemical (Anhui) Co. Ltd, Bengbu, 233000, People's Republic of China
| | - Yong-Cheng Shi
- Department of Grain Science and Industry, Kansas State University, Manhattan, KS, 66506, USA
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
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25
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Llanos A, Déjean S, Neugnot-Roux V, François JM, Parrou JL. Carbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule. Microb Cell Fact 2019; 18:14. [PMID: 30691469 PMCID: PMC6348686 DOI: 10.1186/s12934-019-1062-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/13/2019] [Indexed: 11/19/2022] Open
Abstract
Background Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the XlnR/XYR1 transcriptional activator. The purpose of this study was to evaluate the specificities of the industrial fungus Talaromyces versatilis, getting clues into the role of XlnR and the importance of glucose repression at the transcriptional level, to provide further levers for cocktail production. Results By studying a set of 62 redundant genes representative of several categories of enzymes, our results underlined the huge plasticity of transcriptional responses when changing nutritional status. As a general trend, the more heterogeneous the substrate, the more efficient to trigger activation. Genetic modifications of xlnR led to significant reorganisation of transcriptional patterns. Just a minimal set of genes actually fitted in a simplistic model of regulation by a transcriptional activator, and this under specific substrates. On the contrary, the diversity of xlnR+ versus ΔxlnR responses illustrated the existence of complex and unpredicted patterns of co-regulated genes that were highly dependent on the culture condition, even between genes that encode members of a functional category of enzymes. They notably revealed a dual, substrate-dependant repressor-activator role of XlnR, with counter-intuitive transcripts regulations that targeted specific genes. About glucose, it appeared as a formal repressive sugar as we observed a massive repression of most genes upon glucose addition to the mycelium grown on wheat straw. However, we also noticed a positive role of this sugar on the basal expression of a few genes, (notably those encoding cellulases), showing again the strong dependence of these regulatory mechanisms upon promoter and nutritional contexts. Conclusions The diversity of transcriptional patterns appeared to be the rule, while common and stable behaviour, both within gene families and with fungal literature, the exception. The setup of a new biotechnological process to reach optimized, if not customized expression patterns of enzymes, hence appeared tricky just relying on published data that can lead, in the best scenario, to approximate trends. We instead encourage preliminary experimental assays, carried out in the context of interest to reassess gene responses, as a mandatory step before thinking in (genetic) strategies for the improvement of enzyme production in fungi.![]() Electronic supplementary material The online version of this article (10.1186/s12934-019-1062-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agustina Llanos
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.,Adisseo France S.A.S, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219-Université de Toulouse; CNRS-UPS, 31062, Toulouse Cedex 9, France
| | | | - Jean M François
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France
| | - Jean-Luc Parrou
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.
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26
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The repertoire of effector candidates in Colletotrichum lindemuthianum reveals important information about Colletotrichum genus lifestyle. Appl Microbiol Biotechnol 2019; 103:2295-2309. [DOI: 10.1007/s00253-019-09639-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 01/04/2023]
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27
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Liao LS, Li CX, Zhang FF, Yan YS, Luo XM, Zhao S, Feng JX. How an essential Zn2Cys6 transcription factor PoxCxrA regulates cellulase gene expression in ascomycete fungi? BIOTECHNOLOGY FOR BIOFUELS 2019; 12:105. [PMID: 31073329 PMCID: PMC6498484 DOI: 10.1186/s13068-019-1444-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 04/16/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Soil ascomycete fungi produce plant-biomass-degrading enzymes to facilitate nutrient and energy uptake in response to exogenous stress. This is controlled by a complex signal network, but the regulatory mechanisms are poorly understood. An essential Zn2Cys6 transcription factor (TF) PoxCxrA was identified to be required for cellulase and xylanase production in Penicillium oxalicum. The genome-wide regulon and DNA binding sequences of PoxCxrA were further identified through RNA-Sequencing, DNase I footprinting experiments and in vitro electrophoretic mobility shift assays. Moreover, a minimal DNA-binding domain in PoxCxrA was recognised. RESULTS A PoxCxrA regulon of 1970 members was identified in P. oxalicum, and it was displayed that PoxCxrA regulated the expression of genes encoding major plant cell wall-degrading enzymes, as well as important cellodextrin and/or glucose transporters. Interestingly, PoxCxrA positively regulated the expression of a known important TF PoxClrB. DNase I footprinting experiments and in vitro electrophoretic mobility shift assays further revealed that PoxCxrA directly bound the promoter regions of PoxClrB and a cellobiohydrolase gene cbh1 (POX05587/Cel7A-2) at different nucleic acid sequences. Remarkably, PoxCxrA autoregulated its own PoxCxrA gene expression. Additionally, a minimal 42-amino-acid PoxCxrA DNA-binding domain was identified. CONCLUSION PoxCxrA could directly regulate the expression of cellulase genes and the regulatory gene PoxClrB via binding their promoters at different nucleic acid sequences. This work expands the diversity of DNA-binding motifs known to be recognised by Zn2Cys6 TFs, and demonstrates novel regulatory mechanisms of fungal cellulase gene expression.
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Affiliation(s)
- Lu-Sheng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Cheng-Xi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Feng-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Yu-Si Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Xue-Mei Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004 Guangxi People’s Republic of China
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28
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Midorikawa GEO, Correa CL, Noronha EF, Filho EXF, Togawa RC, Costa MMDC, Silva-Junior OB, Grynberg P, Miller RNG. Analysis of the Transcriptome in Aspergillus tamarii During Enzymatic Degradation of Sugarcane Bagasse. Front Bioeng Biotechnol 2018; 6:123. [PMID: 30280097 PMCID: PMC6153317 DOI: 10.3389/fbioe.2018.00123] [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: 07/06/2018] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
The production of bioethanol from non-food agricultural residues represents an alternative energy source to fossil fuels for incorporation into the world's economy. Within the context of bioconversion of plant biomass into renewable energy using improved enzymatic cocktails, Illumina RNA-seq transcriptome profiling was conducted on a strain of Aspergillus tamarii, efficient in biomass polysaccharide degradation, in order to identify genes encoding proteins involved in plant biomass saccharification. Enzyme production and gene expression was compared following growth in liquid and semi-solid culture with steam-exploded sugarcane bagasse (SB) (1% w/v) and glucose (1% w/v) employed as contrasting sole carbon sources. Enzyme production following growth in liquid minimum medium supplemented with SB resulted in 0.626 and 0.711 UI.mL-1 xylanases after 24 and 48 h incubation, respectively. Transcriptome profiling revealed expression of over 7120 genes, with groups of genes modulated according to solid or semi-solid culture, as well as according to carbon source. Gene ontology analysis of genes expressed following SB hydrolysis revealed enrichment in xyloglucan metabolic process and xylan, pectin and glucan catabolic process, indicating up-regulation of genes involved in xylanase secretion. According to carbohydrate-active enzyme (CAZy) classification, 209 CAZyme-encoding genes were identified with significant differential expression on liquid or semi-solid SB, in comparison to equivalent growth on glucose as carbon source. Up-regulated CAZyme-encoding genes related to cellulases (CelA, CelB, CelC, CelD) and hemicellulases (XynG1, XynG2, XynF1, XylA, AxeA, arabinofuranosidase) showed up to a 10-fold log2FoldChange in expression levels. Five genes from the AA9 (GH61) family, related to lytic polysaccharide monooxygenase (LPMO), were also identified with significant expression up-regulation. The transcription factor gene XlnR, involved in induction of hemicellulases, showed up-regulation on liquid and semi-solid SB culture. Similarly, the gene ClrA, responsible for regulation of cellulases, showed increased expression on liquid SB culture. Over 150 potential transporter genes were also identified with increased expression on liquid and semi-solid SB culture. This first comprehensive analysis of the transcriptome of A. tamarii contributes to our understanding of genes and regulatory systems involved in cellulose and hemicellulose degradation in this fungus, offering potential for application in improved enzymatic cocktail development for plant biomass degradation in biorefinery applications.
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Affiliation(s)
| | - Camila Louly Correa
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | | | | | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Brazil
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29
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Higgins SA, Schadt CW, Matheny PB, Löffler FE. Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism. Genome Biol Evol 2018; 10:2474-2489. [PMID: 30165640 PMCID: PMC6161760 DOI: 10.1093/gbe/evy187] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/16/2022] Open
Abstract
Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet axenic fungal cultures do not couple N-oxyanion respiration to growth and these fungi produce only minor quantities of N2O. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying denitrification were examined in >700 fungal genomes. Of 167 p450nor—containing genomes identified, 0, 30, and 48 also harbored the denitrification genes narG, napA, or nirK, respectively. Compared with napA and nirK, p450nor was twice as abundant and exhibited 2–5-fold more gene duplications, losses, and transfers, indicating a disconnect between p450nor presence and denitrification potential. Furthermore, cooccurrence of p450nor with genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87, p = 1.6e−10) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11%) p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24%) genomes harbored genes nearby p450nor predicted to encode hallmark SM functions, providing additional contextual evidence linking p450nor to SM. These findings underscore the potential physiological implications of widespread p450nor gene transfer, support the undiscovered affiliation of p450nor with fungal SM, and challenge the hypothesis of p450nor’s primary role in denitrification.
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Affiliation(s)
- Steven A Higgins
- Department of Microbiology, University of Tennessee, Knoxville.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge
| | - Christopher W Schadt
- Department of Microbiology, University of Tennessee, Knoxville.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge.,University of Tennessee and Oak Ridge National Laboratory (UT-ORNL), Joint Institute for Biological Sciences (JIBS), Oak Ridge
| | - Patrick B Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge.,University of Tennessee and Oak Ridge National Laboratory (UT-ORNL), Joint Institute for Biological Sciences (JIBS), Oak Ridge.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville.,Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville.,Center for Environmental Biotechnology, University of Tennessee, Knoxville
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Wang L, Luo H, Hu W, Yang Y, Hong N, Wang G, Wang A, Wang L. De novo transcriptomic assembly and mRNA expression patterns of Botryosphaeria dothidea infection with mycoviruses chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1). Virol J 2018; 15:126. [PMID: 30103770 PMCID: PMC6088430 DOI: 10.1186/s12985-018-1033-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/27/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pear ring rot, caused by Botryosphaeria species, is responsible for substantial economic losses by causing severe recession of pear tree growth in China. Mycovirus-mediated hypovirulence in plant pathogenic fungi is a crucial biological method to control fungal diseases. METHODS We conducted a large-scale and comprehensive transcriptome analysis to identify mRNA in B. dothidea in response to mycovirus. De novo sequencing technology from four constructed libraries of LW-C (Botryosphaeria dothidea chrysovirus 1, BdCV1), LW-P (Botryosphaeria dothidea partitivirus 1, BdPV1), LW-CP (LW-1 strain infection with BdCV1 and BdPV1), and Mock (free virus) was used to investigate and compare gene expression changes in B.dothidea strains infected with mycovirus. RESULTS In total, 30,058 Unigenes with an average length of 2128 bp were obtained from 4 libraries of B. dothidea strains. These were annotated to specify their classified function. We demonstrate that mRNAs of B. dothidea strains in response to mycovirus are differentially expressed. In total, 5598 genes were up-regulated and 3298 were down-regulated in the LW-CP group, 4468 were up-regulated and 4291 down-regulated in the LW-C group, and 2590 were up-regulated and 2325 down-regulated in the LW-P group. RT-qPCR was used to validate the expression of 9 selected genes. The B. dothidea transcriptome was more affected by BdCV1 infection than BdPV1. We conducted GO enrichment analysis to characterize gene functions regulated by B. dothidea with mycovirus infection. These involved metabolic process, cellular process, catalytic activity, transporter activity, signaling, and other biological pathways. KEGG function analysis demonstrated that the enriched differentially expressed genes are involved in metabolism, transcription, signal transduction, and ABC transport. mRNA is therefore involved in the interaction between fungi and mycovirus. In addition, changes in differential accumulation levels of cp and RdRp of BdCV1 and BdPV1 in B. dothidea strains were evaluated, revealing that the accumulation of BdCV1 and BdPV1 is related to the phenotype and virulence of B. dothidea strain LW-1. CONCLUSIONS The identification and analysis of mRNAs from B. dothidea was first reported at the transcriptome level. Our analysis provides further insight into the interaction of B. dothidea strains infection with chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1) at the transcriptome level.
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Affiliation(s)
- Lihua Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Hui Luo
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Wangcheng Hu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Yuekun Yang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3 Canada
| | - Liping Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei 430070 People’s Republic of China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei 430070 People’s Republic of China
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31
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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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32
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Liu L, Gong W, Sun X, Chen G, Wang L. Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional Omics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:1285-1295. [PMID: 29334221 DOI: 10.1021/acs.jafc.7b05164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Byproducts of food processing can be utilized for the production of high-value-added enzyme cocktails. In this study, we utilized integrated functional omics technology to analyze composition and functional characteristics of extracellular enzymes produced by Aspergillus niger grown on food processing byproducts. The results showed that oligosaccharides constituted by arabinose, xylose, and glucose in wheat bran were able to efficiently induce the production of extracellular enzymes of A. niger. Compared with other substrates, wheat bran was more effective at inducing the secretion of β-glucosidases from GH1 and GH3 families, as well as >50% of proteases from A1-family aspartic proteases. Compared with proteins induced by single wheat bran or soybean dregs, the protein yield induced by their mixture was doubled, and the time required to reach peak enzyme activity was shortened by 25%. This study provided a technical platform for the complex formulation of various substrates and functional analysis of extracellular enzymes.
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Affiliation(s)
- Lin Liu
- State Key Laboratory of Microbial Technology, Shandong University , 27 Shandanan Road, Jinan 250100, China
- College of Marine Science, Shandong University , Weihai 264200, China
| | - Weili Gong
- State Key Laboratory of Microbial Technology, Shandong University , 27 Shandanan Road, Jinan 250100, China
| | - Xiaomeng Sun
- State Key Laboratory of Microbial Technology, Shandong University , 27 Shandanan Road, Jinan 250100, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University , 27 Shandanan Road, Jinan 250100, China
- College of Marine Science, Shandong University , Weihai 264200, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University , 27 Shandanan Road, Jinan 250100, China
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Adnan M, Zheng W, Islam W, Arif M, Abubakar YS, Wang Z, Lu G. Carbon Catabolite Repression in Filamentous Fungi. Int J Mol Sci 2017; 19:ijms19010048. [PMID: 29295552 PMCID: PMC5795998 DOI: 10.3390/ijms19010048] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Carbon Catabolite Repression (CCR) has fascinated scientists and researchers around the globe for the past few decades. This important mechanism allows preferential utilization of an energy-efficient and readily available carbon source over relatively less easily accessible carbon sources. This mechanism helps microorganisms to obtain maximum amount of glucose in order to keep pace with their metabolism. Microorganisms assimilate glucose and highly favorable sugars before switching to less-favored sources of carbon such as organic acids and alcohols. In CCR of filamentous fungi, CreA acts as a transcription factor, which is regulated to some extent by ubiquitination. CreD-HulA ubiquitination ligase complex helps in CreA ubiquitination, while CreB-CreC deubiquitination (DUB) complex removes ubiquitin from CreA, which causes its activation. CCR of fungi also involves some very crucial elements such as Hexokinases, cAMP, Protein Kinase (PKA), Ras proteins, G protein-coupled receptor (GPCR), Adenylate cyclase, RcoA and SnfA. Thorough study of molecular mechanism of CCR is important for understanding growth, conidiation, virulence and survival of filamentous fungi. This review is a comprehensive revision of the regulation of CCR in filamentous fungi as well as an updated summary of key regulators, regulation of different CCR-dependent mechanisms and its impact on various physical characteristics of filamentous fungi.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Arif
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Kowalczyk JE, Khosravi C, Purvine S, Dohnalkova A, Chrisler WB, Orr G, Robinson E, Zink E, Wiebenga A, Peng M, Battaglia E, Baker S, de Vries RP. High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger. Environ Microbiol 2017; 19:4587-4598. [PMID: 29027734 DOI: 10.1111/1462-2920.13923] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/18/2017] [Accepted: 08/30/2017] [Indexed: 11/28/2022]
Abstract
In A. niger, two transcription factors, AraR and XlnR, regulate the production of enzymes involved in degradation of arabinoxylan and catabolism of the released l-arabinose and d-xylose. Deletion of both araR and xlnR in leads to reduced production of (hemi)cellulolytic enzymes and reduced growth on arabinan, arabinogalactan and xylan. In this study, we investigated the colonization and degradation of wheat bran by the A. niger reference strain CBS 137562 and araR/xlnR regulatory mutants using high-resolution microscopy and exo-proteomics. We discovered that wheat bran flakes have a 'rough' and 'smooth' surface with substantially different affinity towards fungal hyphae. While colonization of the rough side was possible for all strains, the xlnR mutants struggled to survive on the smooth side of the wheat bran particles after 20 and 40 h post inoculation. Impaired colonization ability of the smooth surface of wheat bran was linked to reduced potential of ΔxlnR to secrete arabinoxylan and cellulose-degrading enzymes and indicates that XlnR is the major regulator that drives colonization of wheat bran in A. niger.
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Affiliation(s)
- Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Claire Khosravi
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Samuel Purvine
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Alice Dohnalkova
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - William B Chrisler
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Galya Orr
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Errol Robinson
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Erika Zink
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
| | - Scott Baker
- Department of Energy, Environmental Molecular Sciences Laboratory, Richland, WA, USA
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, the Netherlands
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Sui YF, Ouyang LM, Chu J, Cao WQ, liang LF, Zhuang YP, Cheng S, Norrman H, Zhang SL, zhang GY. Global transcriptional response of Aspergillus niger in the process of glucoamylase fermentation. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0160-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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Kowalczyk JE, Lubbers RJM, Peng M, Battaglia E, Visser J, de Vries RP. Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin. Sci Rep 2017; 7:12356. [PMID: 28955038 PMCID: PMC5617896 DOI: 10.1038/s41598-017-12362-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/07/2017] [Indexed: 01/06/2023] Open
Abstract
Aspergillus niger produces an arsenal of extracellular enzymes that allow synergistic degradation of plant biomass found in its environment. Pectin is a heteropolymer abundantly present in the primary cell wall of plants. The complex structure of pectin requires multiple enzymes to act together. Production of pectinolytic enzymes in A. niger is highly regulated, which allows flexible and efficient capture of nutrients. So far, three transcriptional activators have been linked to regulation of pectin degradation in A. niger. The L-rhamnose-responsive regulator RhaR controls the production of enzymes that degrade rhamnogalacturonan-I. The L-arabinose-responsive regulator AraR controls the production of enzymes that decompose the arabinan and arabinogalactan side chains of rhamnogalacturonan-II. The D-galacturonic acid-responsive regulator GaaR controls the production of enzymes that act on the polygalacturonic acid backbone of pectin. This project aims to better understand how RhaR, AraR and GaaR co-regulate pectin degradation. For that reason, we constructed single, double and triple disruptant strains of these regulators and analyzed their growth phenotype and pectinolytic gene expression in A. niger grown on sugar beet pectin.
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Affiliation(s)
- Joanna E Kowalczyk
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Ronnie J M Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
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Fungal lytic polysaccharide monooxygenases from family AA9: Recent developments and application in lignocelullose breakdown. Int J Biol Macromol 2017; 102:771-778. [DOI: 10.1016/j.ijbiomac.2017.04.077] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022]
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38
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Borin GP, Sanchez CC, de Santana ES, Zanini GK, Dos Santos RAC, de Oliveira Pontes A, de Souza AT, Dal'Mas RMMTS, Riaño-Pachón DM, Goldman GH, Oliveira JVDC. Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei. BMC Genomics 2017; 18:501. [PMID: 28666414 PMCID: PMC5493111 DOI: 10.1186/s12864-017-3857-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Background Second generation (2G) ethanol is produced by breaking down lignocellulosic biomass into fermentable sugars. In Brazil, sugarcane bagasse has been proposed as the lignocellulosic residue for this biofuel production. The enzymatic cocktails for the degradation of biomass-derived polysaccharides are mostly produced by fungi, such as Aspergillus niger and Trichoderma reesei. However, it is not yet fully understood how these microorganisms degrade plant biomass. In order to identify transcriptomic changes during steam-exploded bagasse (SEB) breakdown, we conducted a RNA-seq comparative transcriptome profiling of both fungi growing on SEB as carbon source. Results Particular attention was focused on CAZymes, sugar transporters, transcription factors (TFs) and other proteins related to lignocellulose degradation. Although genes coding for the main enzymes involved in biomass deconstruction were expressed by both fungal strains since the beginning of the growth in SEB, significant differences were found in their expression profiles. The expression of these enzymes is mainly regulated at the transcription level, and A. niger and T. reesei also showed differences in TFs content and in their expression. Several sugar transporters that were induced in both fungal strains could be new players on biomass degradation besides their role in sugar uptake. Interestingly, our findings revealed that in both strains several genes that code for proteins of unknown function and pro-oxidant, antioxidant, and detoxification enzymes were induced during growth in SEB as carbon source, but their specific roles on lignocellulose degradation remain to be elucidated. Conclusions This is the first report of a time-course experiment monitoring the degradation of pretreated bagasse by two important fungi using the RNA-seq technology. It was possible to identify a set of genes that might be applied in several biotechnology fields. The data suggest that these two microorganisms employ different strategies for biomass breakdown. This knowledge can be exploited for the rational design of enzymatic cocktails and 2G ethanol production improvement. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3857-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Camila Cristina Sanchez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Eliane Silva de Santana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Guilherme Keppe Zanini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Renato Augusto Corrêa Dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Angélica de Oliveira Pontes
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Aline Tieppo de Souza
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Roberta Maria Menegaldo Tavares Soares Dal'Mas
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.,Current address: Laboratório de Biologia de Sistemas Regulatórios, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748 - Butantã - São Paulo - SP, São Paulo, CEP 05508-000, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, Ribeirão Preto, CEP, São Paulo, 14040-903, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Campinas, São Paulo, Caixa Postal 6170, 13083-970, Brazil.
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Analysis of Light- and Carbon-Specific Transcriptomes Implicates a Class of G-Protein-Coupled Receptors in Cellulose Sensing. mSphere 2017; 2:mSphere00089-17. [PMID: 28497120 PMCID: PMC5425790 DOI: 10.1128/msphere.00089-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/14/2017] [Indexed: 01/16/2023] Open
Abstract
In fungi, most metabolic processes are subject to regulation by light. For Trichoderma reesei, light-dependent regulation of cellulase gene expression is specifically shown. Therefore, we intended to unravel the relationship between regulation of enzymes by the carbon source and regulation of enzymes by light. Our two-dimensional analysis included inducing and repressing carbon sources which we used to compare light-specific regulation to dark-specific regulation and to rule out effects specific for a single carbon source. We found close connections with respect to gene regulation as well as significant differences in dealing with carbon in the environment in light and darkness. Moreover, our analyses showed an intricate regulation mechanism for substrate degradation potentially involving surface sensing and provide a basis for knowledge-based screening for strain improvement. In fungi, most metabolic processes are subject to regulation by light. Trichoderma reesei is adapted to degradation of plant cell walls and regulates production of the required enzymes in a manner dependent on the nutrient source and the light status. Here we investigated the interrelated relevance of two regulation levels of the transcriptome of T. reesei: light regulation and carbon source-dependent control. We show that the carbon source (cellulose, lactose, sophorose, glucose, or glycerol) is the major source of variation, with light having a modulating effect on transcript regulation. A total of 907 genes were regulated under cellulase-inducing conditions in light, and 947 genes were regulated in darkness, with 530 genes overlapping (1,324 in total). Only 218 of the 1,324 induction-specific genes were independent of light and not regulated by the BLR1, BLR2, and ENV1 photoreceptors. Analysis of the genomic distribution of genes regulated by light upon growth on cellulose revealed considerable overlap of light-regulated clusters with induction-specific clusters and carbohydrate-active enzyme (CAZyme) clusters. Further, we found evidence for the operation of a sensing mechanism for solid cellulosic substrates, with regulation of genes such as swo1, cip1, and cip2 or of genes encoding hydrophobins which is related to the cyclic AMP (cAMP)-dependent regulatory output of ENV1. We identified class XIII G-protein-coupled receptors (GPCRs) CSG1 and CSG2 in T. reesei as putative cellulose/glucose-sensing GPCRs. Our data indicate that the cellulase regulation pathway is bipartite, comprising a section corresponding to transcriptional regulation and one corresponding to posttranscriptional regulation, with the two connected by the function of CSG1. IMPORTANCE In fungi, most metabolic processes are subject to regulation by light. For Trichoderma reesei, light-dependent regulation of cellulase gene expression is specifically shown. Therefore, we intended to unravel the relationship between regulation of enzymes by the carbon source and regulation of enzymes by light. Our two-dimensional analysis included inducing and repressing carbon sources which we used to compare light-specific regulation to dark-specific regulation and to rule out effects specific for a single carbon source. We found close connections with respect to gene regulation as well as significant differences in dealing with carbon in the environment in light and darkness. Moreover, our analyses showed an intricate regulation mechanism for substrate degradation potentially involving surface sensing and provide a basis for knowledge-based screening for strain improvement.
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van Munster JM, Thomas B, Riese M, Davis AL, Gray CJ, Archer DB, Flitsch SL. Application of carbohydrate arrays coupled with mass spectrometry to detect activity of plant-polysaccharide degradative enzymes from the fungus Aspergillus niger. Sci Rep 2017; 7:43117. [PMID: 28220903 PMCID: PMC5318901 DOI: 10.1038/srep43117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/19/2017] [Indexed: 01/25/2023] Open
Abstract
Renewables-based biotechnology depends on enzymes to degrade plant lignocellulose to simple sugars that are converted to fuels or high-value products. Identification and characterization of such lignocellulose degradative enzymes could be fast-tracked by availability of an enzyme activity measurement method that is fast, label-free, uses minimal resources and allows direct identification of generated products. We developed such a method by applying carbohydrate arrays coupled with MALDI-ToF mass spectrometry to identify reaction products of carbohydrate active enzymes (CAZymes) of the filamentous fungus Aspergillus niger. We describe the production and characterization of plant polysaccharide-derived oligosaccharides and their attachment to hydrophobic self-assembling monolayers on a gold target. We verify effectiveness of this array for detecting exo- and endo-acting glycoside hydrolase activity using commercial enzymes, and demonstrate how this platform is suitable for detection of enzyme activity in relevant biological samples, the culture filtrate of A. niger grown on wheat straw. In conclusion, this versatile method is broadly applicable in screening and characterisation of activity of CAZymes, such as fungal enzymes for plant lignocellulose degradation with relevance to biotechnological applications as biofuel production, the food and animal feed industry.
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Affiliation(s)
- Jolanda M van Munster
- Fungal Biology and Genetics, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Baptiste Thomas
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michel Riese
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Adrienne L Davis
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Christopher J Gray
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David B Archer
- Fungal Biology and Genetics, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Sabine L Flitsch
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:35. [PMID: 28184248 PMCID: PMC5294722 DOI: 10.1186/s13068-017-0700-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails. RESULTS We investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns. CONCLUSIONS The presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | | | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- TB Programme, Microbiology Services, Public Health England, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- UPMC, Univ. Paris 06, CNRS UMR7238, Sorbonne Universités, 15 rue de l’Ecole de Médecine, 75270 Paris, France
| | - Paul R. Waldron
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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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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Sugai-Guérios MH, Balmant W, Krieger N, Furigo Junior A, Mitchell DA. Colonization of solid particles by Rhizopus oligosporus and Aspergillus oryzae in solid-state fermentation involves two types of penetrative hyphae: A model-based study on how these hyphae grow. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wilkinson S, Smart KA, James S, Cook DJ. Bioethanol Production from Brewers Spent Grains Using a Fungal Consolidated Bioprocessing (CBP) Approach. BIOENERGY RESEARCH 2016; 10:146-157. [PMID: 32269706 PMCID: PMC7114960 DOI: 10.1007/s12155-016-9782-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Production of bioethanol from brewers spent grains (BSG) using consolidated bioprocessing (CBP) is reported. Each CBP system consists of a primary filamentous fungal species, which secretes the enzymes required to deconstruct biomass, paired with a secondary yeast species to ferment liberated sugars to ethanol. Interestingly, although several pairings of fungi were investigated, the sake fermentation system (A. oryzae and S. cerevisiae NCYC479) was found to yield the highest concentrations of ethanol (37 g/L of ethanol within 10 days). On this basis, 1 t of BSG (dry weight) would yield 94 kg of ethanol using 36 hL of water in the process. QRT-PCR analysis of selected carbohydrate degrading (CAZy) genes expressed by A. oryzae in the BSG sake system showed that hemicellulose was deconstructed first, followed by cellulose. One drawback of the CBP approach is lower ethanol productivity rates; however, it requires low energy and water inputs, and hence is worthy of further investigation and optimisation.
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Affiliation(s)
- Stuart Wilkinson
- Brewing Science Section, Division of Food Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Katherine A. Smart
- SABMiller Plc, SABMiller House, Church Street West, Woking, Surrey GU21 6HS UK
| | - Sue James
- SABMiller Plc, SABMiller House, Church Street West, Woking, Surrey GU21 6HS UK
| | - David J. Cook
- Brewing Science Section, Division of Food Sciences, The University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
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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: 13] [Impact Index Per Article: 1.6] [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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Brown NA, Ries LNA, Reis TF, Rajendran R, Corrêa dos Santos RA, Ramage G, Riaño-Pachón DM, Goldman GH. RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:145. [PMID: 27437031 PMCID: PMC4950808 DOI: 10.1186/s13068-016-0558-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/24/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Sugarcane is one of the world's most profitable crops. Waste steam-exploded sugarcane bagasse (SEB) is a cheap, abundant, and renewable lignocellulosic feedstock for the next-generation biofuels. In nature, fungi seldom exist as planktonic cells, similar to those found in the nutrient-rich environment created within an industrial fermenter. Instead, fungi predominantly form biofilms that allow them to thrive in hostile environments. RESULTS In turn, we adopted an RNA-sequencing approach to interrogate how the model fungus, Aspergillus nidulans, adapts to SEB, revealing the induction of carbon starvation responses and the lignocellulolytic machinery, in addition to morphological adaptations. Genetic analyses showed the importance of hydrophobins for growth on SEB. The major hydrophobin, RodA, was retained within the fungal biofilm on SEB fibres. The StuA transcription factor that regulates fungal morphology was up-regulated during growth on SEB and controlled hydrophobin gene induction. The absence of the RodA or DewC hydrophobins reduced biofilm formation. The loss of a RodA or a functional StuA reduced the retention of the hydrolytic enzymes within the vicinity of the fungus. Hence, hydrophobins promote biofilm formation on SEB, and may enhance lignocellulose utilisation via promoting a compact substrate-enzyme-fungus structure. CONCLUSION This novel study highlights the importance of hydrophobins to the formation of biofilms and the efficient deconstruction of lignocellulose.
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Affiliation(s)
- Neil Andrew Brown
- />Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Laure N. A. Ries
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila F. Reis
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Ranjith Rajendran
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, The University of Glasgow, Glasgow, UK
| | - Renato Augusto Corrêa dos Santos
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, SP CEP 13083-970 Brazil
| | - Gordon Ramage
- />Infection and Immunity Research Group, Glasgow Dental School, School of Medicine, College of Medical, Veterinary and Life Sciences, The University of Glasgow, Glasgow, UK
| | - Diego Mauricio Riaño-Pachón
- />Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192, Campinas, SP CEP 13083-970 Brazil
| | - Gustavo H. Goldman
- />Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
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Glass NL. The Enigmatic Universe of the Herbivore Gut. Trends Biochem Sci 2016; 41:561-562. [PMID: 27257096 DOI: 10.1016/j.tibs.2016.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 11/25/2022]
Abstract
The herbivore gut is a fascinating ecosystem exquisitely adapted to plant biomass degradation. Within this ecosystem, anaerobic fungi invade biomass and secrete hydrolytic enzymes. In a recent study, Solomon et al. characterized three anaerobic fungi by transcriptomics, proteomics, and functional analyses to identify novel components essential for plant biomass deconstruction.
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Affiliation(s)
- N Louise Glass
- Plant and Microbial Biology Department, Energy Biosciences Institute, The University of California, Berkeley, CA 94720-3102, USA.
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Mukherjee S, Chandrababunaidu MM, Panda A, Khowala S, Tripathy S. Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. Front Microbiol 2016; 7:596. [PMID: 27242677 PMCID: PMC4865484 DOI: 10.3389/fmicb.2016.00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/11/2016] [Indexed: 01/24/2023] Open
Abstract
This study catalogs production of industrially important enzymes and changes in transcript expression caused by 2-deoxy D-glucose (2-DG) treatment in Arthrinium malaysianum cultures. Carbon Catabolite Repression (CCR) induced by 2-DG in this species is cAMP independent unlike many other organisms. Higher levels of secreted endoglucanase (EG), β-glucosidase (BGL), β-xylosidase (BXL), and filter paper activity assay (FPase) enzymes under 2-DG treatment can be exploited for commercial purposes. An integrated RNA sequencing and quantitative proteomic analysis was performed to investigate the cellular response to 2-DG in A. malaysianum. Analysis of RNASeq data under 2-DG treated and control condition reveals that 56% of the unigenes do not have any known similarity to proteins in non-redundant database. Gene Ontology IDs were assigned to 36% of the transcripts (13260) and about 5207 (14%) were mapped to Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). About 1711 genes encoding 2691 transcripts were differentially expressed in treated vs. control samples. Out of the 2691 differentially expressed transcripts, only 582 have any known function. The most up regulated genes belonged to Pentose Phosphate Pathways and carbohydrate degradation class as expected. In addition, genes involved in protein folding, binding, catalytic activity, DNA repair, and secondary metabolites were up-regulated under 2-DG treatment. Whereas genes encoding glycosylation pathways, growth, nutrient reservoir activity was repressed. Gene ontology analysis of the differentially expressed genes indicates metabolic process (35%) is the pre-dominant class followed by carbohydrate degradation (11%), protein folding, and trafficking (6.2%) and transport (5.3%) classes. Unlike other organisms, conventional unfolded protein response (UPR) was not activated in either control or treated conditions. Major enzymes secreted by A. malaysianum are those degrading plant polysaccharides, the most dominant ones being β-glucosidase, as demonstrated by the 2D gel analysis. A set of 7 differentially expressed mRNAs were validated by qPCR. Transmission electron microscopy analyses demonstrated that the 2-DG treated cell walls of hyphae showed significant differences in the cell-wall thickness. Overall 2-DG treatment in A. malaysianum induced secretion of large amount of commercially viable enzymes compared to other known species.
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Affiliation(s)
- Soumya Mukherjee
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Mathu Malar Chandrababunaidu
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Arijit Panda
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Suman Khowala
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
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49
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Valette N, Benoit-Gelber I, Falco MD, Wiebenga A, de Vries RP, Gelhaye E, Morel-Rouhier M. Secretion of small proteins is species-specific within Aspergillus sp. Microb Biotechnol 2016; 10:323-329. [PMID: 27153937 PMCID: PMC5328806 DOI: 10.1111/1751-7915.12361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/27/2016] [Indexed: 01/01/2023] Open
Abstract
Small secreted proteins (SSP) have been defined as proteins containing a signal peptide and a sequence of less than 300 amino acids. In this analysis, we have compared the secretion pattern of SSPs among eight aspergilli species in the context of plant biomass degradation and have highlighted putative interesting candidates that could be involved in the degradative process or in the strategies developed by fungi to resist the associated stress that could be due to the toxicity of some aromatic compounds or reactive oxygen species released during degradation. Among these candidates, for example, some stress‐related superoxide dismutases or some hydrophobic surface binding proteins (HsbA) are specifically secreted according to the species . Since these latter proteins are able to recruit lytic enzymes to the surface of hydrophobic solid materials and promote their degradation, a synergistic action of HsbA with the degradative system may be considered and need further investigations. These SSPs could have great applications in biotechnology by optimizing the efficiency of the enzymatic systems for biomass degradation.
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Affiliation(s)
- Nicolas Valette
- Faculté des Sciences et Technologies BP 70239, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes", Université de Lorraine, Vandoeuvre-lès-Nancy Cedex, F-54506, France.,Faculté des Sciences et Technologies BP 70239, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes", INRA, Vandoeuvre-lès-Nancy Cedex, F-54506, France
| | - Isabelle Benoit-Gelber
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Marcos Di Falco
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
| | - Ad Wiebenga
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Eric Gelhaye
- Faculté des Sciences et Technologies BP 70239, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes", Université de Lorraine, Vandoeuvre-lès-Nancy Cedex, F-54506, France.,Faculté des Sciences et Technologies BP 70239, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes", INRA, Vandoeuvre-lès-Nancy Cedex, F-54506, France
| | - Mélanie Morel-Rouhier
- Faculté des Sciences et Technologies BP 70239, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes", Université de Lorraine, Vandoeuvre-lès-Nancy Cedex, F-54506, France.,Faculté des Sciences et Technologies BP 70239, UMR1136 INRA-Université de Lorraine "Interactions Arbres/Micro-organismes", INRA, Vandoeuvre-lès-Nancy Cedex, F-54506, France
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Daly P, van Munster JM, Kokolski M, Sang F, Blythe MJ, Malla S, Velasco de Castro Oliveira J, Goldman GH, Archer DB. Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression. Fungal Genet Biol 2016; 102:4-21. [PMID: 27150814 PMCID: PMC5476202 DOI: 10.1016/j.fgb.2016.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/20/2016] [Accepted: 04/29/2016] [Indexed: 12/15/2022]
Abstract
First genome-wide transcriptional response in fungal mixed species straw cultures. In mixed cultures, rRNA abundance was used to predict RNA-seq read abundance. Subset of P. chrysogenum CAZy with mixed cultures increased abundance pattern. Lack of overall higher CAZy transcripts/activities due to inter-species antagonism. Induction of secondary metabolite producing gene clusters in mixed cultures.
Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Jolanda M van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Fei Sang
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Martin J Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Sunir Malla
- Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK.
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro 10000, Campinas, São Paulo 13083-100, Brazil.
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, São Paulo 14040-903, Brazil.
| | - David B Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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