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Ashoor S, Mathew GM, Sukumaran RK. Rice straw hydrolysis using in-situ produced enzymes: Feedstock influences fungal enzyme composition and hydrolytic efficiency. Prep Biochem Biotechnol 2024:1-7. [PMID: 38327105 DOI: 10.1080/10826068.2024.2312458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Trichoderma reesei RUT-C30 was cultivated on differentially pretreated rice straw and pure cellulose as a carbon source/inducer for cellulase production, and the enzymes were evaluated for hydrolysis of sequential acid and alkali pretreated rice straw. Growth on pretreated rice straw enhanced protein secretion and cellulase activities compared to pure cellulose as a carbon source. The yield of cellulolytic enzymes was higher for alkali pretreated rice straw (ALP-RS), while H2O2-treated (HP-RS) could not induce cellulases to a larger level compared to pure cellulose. Protein concentration was 3.5-fold higher on ALP-RS as compared to pure cellulose, with a maximum filter-paper cellulase (FPase) activity of 1.76 IU/ml and carboxy-methyl cellulase (CMCase) activity of 40.16 IU/ml (2.18 fold higher). Beta-glucosidase (BGL) activity was more or less the same with the different substrates and supplementation of heterologous BGL could result in a quantum jump in hydrolytic efficiencies, which in the case of ALP-RS induced enzymes was 34% (increased from 69.26% to 92.51%). The use of lignocellulosic biomass (LCB) itself as a substrate for the production of cellulase is advantageous not only in terms of raw material costs but also for obtaining a more suitable enzyme profile for biomass hydrolysis.
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Affiliation(s)
- Selim Ashoor
- Department of Agricultural Microbiology, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Gincy Marina Mathew
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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2
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Nogueira KMV, Mendes V, Kamath KS, Cheruku A, Oshiquiri LH, de Paula RG, Carraro C, Pedersoli WR, Pereira LMS, Vieira LC, Steindorff AS, Amirkhani A, McKay MJ, Nevalainen H, Molloy MP, Silva RN. Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei. Microb Cell Fact 2024; 23:22. [PMID: 38229067 DOI: 10.1186/s12934-023-02279-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T. reesei remain poorly identified and characterized. RESULTS To address this gap, this study used temporal membrane proteomics analysis to identify five known and nine putative sugar transporters that may be involved in cellulose degradation by T. reesei. Docking analysis pointed out potential ligands for the putative sugar transporter Tr44175. Further functional validation of this transporter was carried out in Saccharomyces cerevisiae. The results showed that Tr44175 transports a variety of sugar molecules, including cellobiose, cellotriose, cellotetraose, and sophorose. CONCLUSION This study has unveiled a transporter Tr44175 capable of transporting cellobiose, cellotriose, cellotetraose, and sophorose. Our study represents the first inventory of T. reesei sugar transportome once exposed to cellulose, offering promising potential targets for strain engineering in the context of bioethanol production.
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Affiliation(s)
- Karoline Maria Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Vanessa Mendes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karthik Shantharam Kamath
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Anusha Cheruku
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Letícia Harumi Oshiquiri
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria, ES, 29047-105, Brazil
| | - Claudia Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Wellington Ramos Pedersoli
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Lucas Matheus Soares Pereira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Luiz Carlos Vieira
- Department of Molecular and Cell Biology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Helena Nevalainen
- Department of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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Yan S, Xu Y, Yu XW. Role of cellulose response transporter-like protein CRT2 in cellulase induction in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:118. [PMID: 37488642 PMCID: PMC10364367 DOI: 10.1186/s13068-023-02371-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Induction of cellulase in cellulolytic fungi Trichoderma reesei is strongly activated by cellulosic carbon sources. The transport of cellulosic inducer and the perception of inducing signal is generally considered as the critical process for cellulase induction, that the inducing signal would be perceived by a sugar transporter/transceptor in T. reesei. Several sugar transporters are coexpressed during the induction stage, but which function they serve and how they work collaboratively are still difficult to elucidate. RESULTS In this study, we found that the constitutive expression of the cellulose response transporter-like protein CRT2 (previously identified as putative lactose permease TRE77517) improves cellulase induction on a cellulose, cellobiose or lactose medium. Functional studies indicate that the membrane-bound CRT2 is not a transporter of cellobiose, lactose or glucose in a yeast system, and it also does not affect cellobiose and lactose utilization in T. reesei. Further study reveals that CRT2 has a slightly similar function to the cellobiose transporter CRT1 in cellulase induction. Overexpression of CRT2 led to upregulation of CRT1 and the key transcription factor XYR1. Moreover, overexpression of CRT2 could partially compensate for the function loss of CRT1 on cellulase induction. CONCLUSIONS Our study uncovers the novel function of CRT2 in cellulase induction collaborated with CRT1 and XYR1, possibly as a signal transductor. These results deepen the understanding of the influence of sugar transporters in cellulase production.
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Affiliation(s)
- Su Yan
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiao-Wei Yu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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Techno-Economic Analysis of an Integrated Bio-Refinery for the Production of Biofuels and Value-Added Chemicals from Oil Palm Empty Fruit Bunches. Processes (Basel) 2022. [DOI: 10.3390/pr10101965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lignocellulose-rich empty fruit bunches (EFBs) have high potential as feedstock for second-generation biofuel and biochemical production without compromising food security. Nevertheless, the major challenge of valorizing lignocellulose-rich EFB is its high pretreatment cost. In this study, the preliminary techno-economic feasibility of expanding an existing pellet production plant into an integrated bio-refinery plant to produce xylitol and bioethanol was investigated as a strategy to diversify the high production cost and leverage the high selling price of biofuel and biochemicals. The EFB feedstock was split into a pellet production stream and a xylitol and bioethanol production stream. Different economic performance metrics were used to compare the profitability at different splitting ratios of xylitol and bioethanol to pellet production. The analysis showed that an EFB splitting ratio below 40% for pellet production was economically feasible. A sensitivity analysis showed that xylitol price had the most significant impact on the economic performance metrics. Another case study on the coproduction of pellet and xylitol versus that of pellet and bioethanol concluded that cellulosic bioethanol production is yet to be market-ready, requiring a minimum selling price above the current market price to be feasible at 16% of the minimum acceptable return rate.
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Antoniêto ACC, Nogueira KMV, Mendes V, Maués DB, Oshiquiri LH, Zenaide-Neto H, de Paula RG, Gaffey J, Tabatabaei M, Gupta VK, Silva RN. Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products. Int J Biol Macromol 2022; 221:456-471. [PMID: 36070819 DOI: 10.1016/j.ijbiomac.2022.08.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022]
Abstract
Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.
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Affiliation(s)
- Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Vanessa Mendes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Letícia Harumi Oshiquiri
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Hermano Zenaide-Neto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES 29047-105, Brazil
| | - James Gaffey
- Circular Bioeconomy Research Group, Shannon Applied Biotechnology Centre, Munster Technological University, Kerry, Ireland; BiOrbic, Bioeconomy Research Centre, University College Dublin, Belfield, Dublin, Ireland
| | - Meisam Tabatabaei
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900, Brazil.
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Beier S, Stiegler M, Hitzenhammer E, Monika S. Screening for genes involved in cellulase regulation by expression under the control of a novel constitutive promoter in Trichoderma reesei. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Filho JAF, Rosolen RR, Almeida DA, de Azevedo PHC, Motta MLL, Aono AH, dos Santos CA, Horta MAC, de Souza AP. Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. 3 Biotech 2021; 11:475. [PMID: 34777932 PMCID: PMC8548487 DOI: 10.1007/s13205-021-03032-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Fungi are key players in biotechnological applications. Although several studies focusing on fungal diversity and genetics have been performed, many details of fungal biology remain unknown, including how cellulolytic enzymes are modulated within these organisms to allow changes in main plant cell wall compounds, cellulose and hemicellulose, and subsequent biomass conversion. With the advent and consolidation of DNA/RNA sequencing technology, different types of information can be generated at the genomic, structural and functional levels, including the gene expression profiles and regulatory mechanisms of these organisms, during degradation-induced conditions. This increase in data generation made rapid computational development necessary to deal with the large amounts of data generated. In this context, the origination of bioinformatics, a hybrid science integrating biological data with various techniques for information storage, distribution and analysis, was a fundamental step toward the current state-of-the-art in the postgenomic era. The possibility of integrating biological big data has facilitated exciting discoveries, including identifying novel mechanisms and more efficient enzymes, increasing yields, reducing costs and expanding opportunities in the bioprocess field. In this review, we summarize the current status and trends of the integration of different types of biological data through bioinformatics approaches for biological data analysis and enzyme selection.
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Affiliation(s)
- Jaire A. Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Rafaela R. Rosolen
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Deborah A. Almeida
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Paulo Henrique C. de Azevedo
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria Lorenza L. Motta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Alexandre H. Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Clelton A. dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP Brazil
| | - Maria Augusta C. Horta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Anete P. de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Institute of Biology, UNICAMP, Universidade Estadual de Campinas, Campinas, SP 13083-875 Brazil
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Yan S, Xu Y, Yu XW. From induction to secretion: a complicated route for cellulase production in Trichoderma reesei. BIORESOUR BIOPROCESS 2021; 8:107. [PMID: 38650205 PMCID: PMC10991602 DOI: 10.1186/s40643-021-00461-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/16/2021] [Indexed: 11/10/2022] Open
Abstract
The filamentous fungus Trichoderma reesei has been widely used for cellulase production that has extensive applications in green and sustainable development. Increasing costs and depletion of fossil fuels provoke the demand for hyper-cellulase production in this cellulolytic fungus. To better manipulate T. reesei for enhanced cellulase production and to lower the cost for large-scale fermentation, it is wise to have a comprehensive understanding of the crucial factors and complicated biological network of cellulase production that could provide new perspectives for further exploration and modification. In this review, we summarize recent progress and give an overview of the cellular process of cellulase production in T. reesei, including the carbon source-dependent cellulase induction, complicated transcriptional regulation network, and efficient protein assembly and trafficking. Among that, the key factors involved in cellulase production were emphasized, shedding light on potential perspectives for further engineering.
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Affiliation(s)
- Su Yan
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Xiao-Wei Yu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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Naher L, Fatin SN, Sheikh MAH, Azeez LA, Siddiquee S, Zain NM, Karim SMR. Cellulase Enzyme Production from Filamentous Fungi Trichoderma reesei and Aspergillus awamori in Submerged Fermentation with Rice Straw. J Fungi (Basel) 2021; 7:jof7100868. [PMID: 34682288 PMCID: PMC8539901 DOI: 10.3390/jof7100868] [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: 09/16/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/03/2022] Open
Abstract
Fungi are a diverse group of microorganisms that play many roles in human livelihoods. However, the isolation of potential fungal species is the key factor to their utilization in different sectors, including the enzyme industry. Hence, in this study, we used two different fungal repositories—soil and weed leaves—to isolate filamentous fungi and evaluate their potential to produce the cellulase enzyme. The fungal strains were isolated using dichloran rose bengal agar (DRBA) and potato dextrose agar (PDA). For cellulase enzyme production, a rice straw submerged fermentation process was used. The enzyme production was carried out at the different incubation times of 3, 5, and 7 days of culture in submerged conditions with rice straw. Fungal identification studies by morphological and molecular methods showed that the soil colonies matched with Trichoderma reesei, and the weed leaf colonies matched with Aspergillus awamori. These species were coded as T. reesei UMK04 and A. awamori UMK02, respectively. This is the first report of A. awamori UMK02 isolation in Malaysian agriculture. The results of cellulase production using the two fungi incorporated with rice straw submerged fermentation showed that T. reesei produced a higher amount of cellulase at Day 5 (27.04 U/mg of dry weight) as compared with A. awamori (15.19 U/mg of dry weight), and the concentration was significantly different (p < 0.05). Our results imply that T. reesei can be utilized for cellulase production using rice straw.
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Affiliation(s)
- Laila Naher
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia; (S.N.F.); (M.A.H.S.); (L.A.A.); (N.M.Z.)
- Institute of Food Security and Sustainable Agriculture, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia
- Institute of Research and Poverty Management (InsPek), Universiti Malaysia Kelantan Bachok, Bachok 16400, Malaysia
- Correspondence:
| | - Siti Noor Fatin
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia; (S.N.F.); (M.A.H.S.); (L.A.A.); (N.M.Z.)
| | - Md Abdul Halim Sheikh
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia; (S.N.F.); (M.A.H.S.); (L.A.A.); (N.M.Z.)
| | - Lateef Adebola Azeez
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia; (S.N.F.); (M.A.H.S.); (L.A.A.); (N.M.Z.)
- Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin 240003, Nigeria
| | - Shaiquzzaman Siddiquee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Malaysia;
| | - Norhafizah Md Zain
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia; (S.N.F.); (M.A.H.S.); (L.A.A.); (N.M.Z.)
- Institute of Food Security and Sustainable Agriculture, Universiti Malaysia Kelantan Jeli Campus, Jeli 17600, Malaysia
- Institute of Research and Poverty Management (InsPek), Universiti Malaysia Kelantan Bachok, Bachok 16400, Malaysia
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Sarangi S, Swain H, Adak T, Bhattacharyya P, Mukherjee AK, Kumar G, Mehetre ST. Trichoderma-mediated rice straw compost promotes plant growth and imparts stress tolerance. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:44014-44027. [PMID: 33846916 DOI: 10.1007/s11356-021-13701-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Rice straw burning is causing huge economic losses and environmental hazards. Microbial mediated ex situ composting could be a viable solution which would not only reduce the straw burning but also will enrich nutrition to the soil. Strains of Trichoderma isolated from tree bark were tested to decompose rice straw efficiently, and the Trichoderma-mediated rice straw compost was used subsequently to improve rice growth. Two isolates of Trichoderma reesei (NRRIT-26 and NRRIT-27) decomposed the straw by producing higher decomposing enzymes, like total cellulase (≥ 1.87 IU mL-1), endoglucanase (≥ 0.75 IU mL-1), xylanase (≥ 163.49 nkat mL-1), and laccase (≥ 11.75 IU mL-1). Trichoderma decomposed rice straw compost had higher nutrient contents (1.97% N, 2.04% K, and 0.88% P) and optimum C/N ratio (28:2) as compared to control. The Trichoderma decomposed rice straw as a nutrient reduced the mean germination time (2.2 days as compared to 4 days in control) and enhanced the seedling vigor and total chlorophyll content in rice. Expression of defense enzymes, like catalase (≥ 200% both in shoot and root), peroxidase (≥ 180% in root and ≥ 300% in shoot), and superoxide dismutase (≥ 160% in root and ≥ 90% in shoot), were higher in treated plants as compared to control indicating higher stress tolerance ability to crops. We conclude that the Trichoderma-mediated rice straw management is a viable option and has the potential to reduce straw burning, and at the same time, the compost could enrich soil fertility and impart intrinsic stress tolerance to rice.
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Affiliation(s)
- Sarmistha Sarangi
- Molecular Plant Pathology Laboratory, Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Harekrushna Swain
- Molecular Plant Pathology Laboratory, Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Totan Adak
- Molecular Plant Pathology Laboratory, Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Pratap Bhattacharyya
- Division of Crop Production, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Arup K Mukherjee
- Molecular Plant Pathology Laboratory, Division of Crop Protection, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
| | - Gaurav Kumar
- Division of Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Sayaji T Mehetre
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
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11
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Pedersoli WR, de Paula RG, Antoniêto ACC, Carraro CB, Taveira IC, Maués DB, Martins MP, Ribeiro LFC, Damasio ARDL, Silva-Rocha R, Filho AR, Silva RN. Analysis of the phosphorylome of trichoderma reesei cultivated on sugarcane bagasse suggests post-translational regulation of the secreted glycosyl hydrolase Cel7A. ACTA ACUST UNITED AC 2021; 31:e00652. [PMID: 34258241 PMCID: PMC8254082 DOI: 10.1016/j.btre.2021.e00652] [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: 08/24/2020] [Revised: 05/05/2021] [Accepted: 06/16/2021] [Indexed: 11/27/2022]
Abstract
Phosphorylome of Trichoderma reesei reveals phosphosites in some glycosyl hydrolases. Phosphoserine and phosphothreonine is the major phosphosites identified. Protein Kinase C is the most frequently predicted kinase in phosphorylome. The cellulase Cel7A activity is affected by dephosphorylation.
Trichoderma reesei is one of the major producers of holocellulases. It is known that in T. reesei, protein production patterns can change in a carbon source-dependent manner. Here, we performed a phosphorylome analysis of T. reesei grown in the presence of sugarcane bagasse and glucose as carbon source. In presence of sugarcane bagasse, a total of 114 phosphorylated proteins were identified. Phosphoserine and phosphothreonine corresponded to 89.6% of the phosphosites and 10.4% were related to phosphotyrosine. Among the identified proteins, 65% were singly phosphorylated, 19% were doubly phosphorylated, 12% were triply phosphorylated, and 4% displayed even higher phosphorylation. Seventy-five kinases were predicted to phosphorylate the sites identified in this work, and the most frequently predicted serine/threonine kinase was PKC1. Among phosphorylated proteins, four glycosyl hydrolases were predicted to be secreted. Interestingly, Cel7A activity, the most secreted protein, was reduced to approximately 60% after in vitro dephosphorylation, suggesting that phosphorylation might alter Cel7A structure, substrate affinity, and targeting of the substrate to its carbohydrate-binding domain. These results suggest a novel post-translational regulation of Cel7A.
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Affiliation(s)
- Wellington Ramos Pedersoli
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.,Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitória, ES, 29047-105, Brazil
| | - Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Cláudia Batista Carraro
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Iasmin Cartaxo Taveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - David Batista Maués
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Maíra Pompeu Martins
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - André Ricardo de Lima Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, 13083-970, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, 14049-900, Brazil
| | - Antônio Rossi Filho
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
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12
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Lopes DCB, Carraro CB, Silva RN, de Paula RG. Molecular Characterization of Xyloglucanase cel74a from Trichoderma reesei. Int J Mol Sci 2021; 22:ijms22094545. [PMID: 33925273 PMCID: PMC8123685 DOI: 10.3390/ijms22094545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei is used on an industrial scale to produce enzymes of biotechnological interest. This fungus has a complex cellulolytic system involved in the degradation of lignocellulosic biomass. However, several aspects related to the regulation of the expression of holocellulolytic genes and the production of cellulases by this fungus are still understood. METHODS Here, we constructed a null mutant strain for the xyloglucanase cel74a gene and performed the characterization of the Δcel74a strain to evaluate the genetic regulation of the holocellulases during sugarcane bagasse (SCB) cultivation. RESULTS Our results demonstrate that the deletion of xyloglucanase cel74a may impact the regulation of holocellulase expression during SCB cultivation. The expression of cellulases cel7a, cel7b, and cel6a was reduced in Δcel74a strain, while the hemicellulases xyn1 and xyn2 were increased in the presence of SCB. The cel74a mutation also affected the xyloglucan hydrolysis patterns. In addition, CEL74A activity was modulated in the presence of calcium, suggesting that this ion may be required for efficient degradation of xyloglucan. CONCLUSIONS CEL74A affects the regulation of holocellulolytic genes and the efficient degradation of SCB in T. reesei. This data makes a significant contribution to our understanding of the carbon utilization of fungal strains as a whole.
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Affiliation(s)
- Douglas Christian Borges Lopes
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
| | - Cláudia Batista Carraro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
| | - Roberto Nascimento Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
- Correspondence:
| | - Renato Graciano de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto 14049-900, SP, Brazil; (D.C.B.L.); (C.B.C.); (R.G.d.P.)
- Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria 29047-105, ES, Brazil
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13
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Novy V, Nielsen F, Cullen D, Sabat G, Houtman CJ, Hunt CG. The characteristics of insoluble softwood substrates affect fungal morphology, secretome composition, and hydrolytic efficiency of enzymes produced by Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:105. [PMID: 33902680 PMCID: PMC8074412 DOI: 10.1186/s13068-021-01955-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/11/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND On-site enzyme production using Trichoderma reesei can improve yields and lower the overall cost of lignocellulose saccharification by exploiting the fungal gene regulatory mechanism that enables it to continuously adapt enzyme secretion to the substrate used for cultivation. To harness this, the interrelation between substrate characteristics and fungal response must be understood. However, fungal morphology or gene expression studies often lack structural and chemical substrate characterization. Here, T. reesei QM6a was cultivated on three softwood substrates: northern bleached softwood Kraft pulp (NBSK) and lodgepole pine pretreated either by dilute-acid-catalyzed steam pretreatment (LP-STEX) or mild alkaline oxidation (LP-ALKOX). With different pretreatments of similar starting materials, we presented the fungus with systematically modified substrates. This allowed the elucidation of substrate-induced changes in the fungal response and the testing of the secreted enzymes' hydrolytic strength towards the same substrates. RESULTS Enzyme activity time courses correlated with hemicellulose content and cellulose accessibility. Specifically, increased amounts of side-chain-cleaving hemicellulolytic enzymes in the protein produced on the complex substrates (LP-STEX; LP-ALKOX) was observed by secretome analysis. Confocal laser scanning micrographs showed that fungal micromorphology responded to changes in cellulose accessibility and initial culture viscosity. The latter was caused by surface charge and fiber dimensions, and likely restricted mass transfer, resulting in morphologies of fungi in stress. Supplementing a basic cellulolytic enzyme mixture with concentrated T. reesei supernatant improved saccharification efficiencies of the three substrates, where cellulose, xylan, and mannan conversion was increased by up to 27, 45, and 2800%, respectively. The improvement was most pronounced for proteins produced on LP-STEX and LP-ALKOX on those same substrates, and in the best case, efficiencies reached those of a state-of-the-art commercial enzyme preparation. CONCLUSION Cultivation of T. reesei on LP-STEX and LP-ALKOX produced a protein mixture that increased the hydrolytic strength of a basic cellulase mixture to state-of-the-art performance on softwood substrates. This suggests that the fungal adaptation mechanism can be exploited to achieve enhanced performance in enzymatic hydrolysis without a priori knowledge of specific substrate requirements.
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Affiliation(s)
- Vera Novy
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA.
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden.
| | - Fredrik Nielsen
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Daniel Cullen
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Grzegorz Sabat
- University of Wisconsin Biotechnology Center, Madison, WI, 53706, USA
| | - Carl J Houtman
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Christopher G Hunt
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
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14
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Karuppiah V, Zhixiang L, Liu H, Vallikkannu M, Chen J. Co-culture of Vel1-overexpressed Trichoderma asperellum and Bacillus amyloliquefaciens: An eco-friendly strategy to hydrolyze the lignocellulose biomass in soil to enrich the soil fertility, plant growth and disease resistance. Microb Cell Fact 2021; 20:57. [PMID: 33653343 PMCID: PMC7927390 DOI: 10.1186/s12934-021-01540-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Retention of agricultural bio-mass residues without proper treatment could affect the subsequent plant growth. In the present investigation, the co-cultivation of genetically engineered T. asperellum and B. amyloliquefaciens has been employed for multiple benefits including the enrichment of lignocellulose biodegradation, plant growth, defense potential and disease resistance. Results The Vel1 gene predominantly regulates the secondary metabolites, sexual and asexual development as well as cellulases and polysaccharide hydrolases productions. Overexpression mutant of the Trichoderma asperellum Vel1 locus (TA OE-Vel1) enhanced the activity of FPAase, CMCase, PNPCase, PNPGase, xylanase I, and xylanase II through the regulation of transcription regulating factors and the activation of cellulase and xylanase encoding genes. Further, these genes were induced upon co-cultivation with Bacillus amyloliquefaciens (BA). The co-culture of TA OE-Vel1 + BA produced the best composition of enzymes and the highest biomass hydrolysis yield of 89.56 ± 0.61%. The co-culture of TA OE-Vel1 + BA increased the corn stover degradation by the secretion of cellulolytic enzymes and maintained the C/N ratio of the corn stover amended soil. Moreover, the TA OE-Vel1 + BA increased the maize plant growth, expression of defense gene and disease resistance against Fusarium verticillioides and Cohilohorus herostrophus. Conclusion The co-cultivation of genetically engineered T. asperellum and B. amyloliquefaciens could be utilized as a profound and meaningful technique for the retention of agro residues and subsequent plant growth.
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Affiliation(s)
- Valliappan Karuppiah
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Lu Zhixiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Murugappan Vallikkannu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China.,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800, Dongchuan Road, Minhang, Shanghai, 200240, PR China. .,The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, PR China.
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15
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Ghosh S, Godoy L, Anchang KY, Achilonu CC, Gryzenhout M. Fungal Cellulases: Current Research and Future Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Effect of Oligosaccharide Degree of Polymerization on the Induction of Xylan-Degrading Enzymes by Fusarium oxysporum f. sp. Lycopersici. Molecules 2020; 25:molecules25245849. [PMID: 33322262 PMCID: PMC7764074 DOI: 10.3390/molecules25245849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 01/15/2023] Open
Abstract
Xylan is one of the most abundant carbohydrates on Earth. Complete degradation of xylan is achieved by the collaborative action of endo-β-1,4-xylanases and β-d-xylosidases and a number of accessories enzymes. In filamentous fungi, the xylanolytic system is controlled through induction and repression. However, the exact mechanism remains unclear. Substrates containing xylan promote the induction of xylanases, which release xylooligosaccharides. These, in turn, induce expression of xylanase-encoding genes. Here, we aimed to determine which xylan degradation products acted as inducers, and whether the size of the released oligomer correlated with its induction strength. To this end, we compared xylanase production by different inducers, such as sophorose, lactose, cellooligosaccharides, and xylooligosaccharides in Fusarium oxysporum f. sp. lycopersici. Results indicate that xylooligosaccharides are more effective than other substrates at inducing endoxylanase and β-xylosidases. Moreover, we report a correlation between the degree of xylooligosaccharide polymerization and induction efficiency of each enzyme. Specifically, xylotetraose is the best inducer of endoxylanase, xylohexaose of extracellular β-xylosidase, and xylobiose of cell-bound β-xylosidase.
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17
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Martins-Santana L, Paula RGD, Silva AG, Lopes DCB, Silva RDN, Silva-Rocha R. CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a. Genet Mol Biol 2020; 43:e20190244. [PMID: 32384133 PMCID: PMC7212764 DOI: 10.1590/1678-4685-gmb-2019-0244] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023] Open
Abstract
Trichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Here we investigated the role of CRZ1 and Ca2+signaling in the fungus T. reesei QM6a concerning holocellulases production. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reeseiAcrz1 strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, highlighting the role of the major regulator Ca2+ on the signaling for holocellulases transcriptional control in the most part of cellulases genes here investigated. This work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport.
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Affiliation(s)
- Leonardo Martins-Santana
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Laboratório de Biologia Sistêmica e Sintética, Ribeirão Preto, SP, Brazil.,Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | - Renato Graciano de Paula
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil.,Universidade Federal do Espírito Santo, Centro de Ciências da Saúde, Departamento de Ciências Fisiológicas, Vitória, ES, Brazil
| | - Adriano Gomes Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Laboratório de Biologia Sistêmica e Sintética, Ribeirão Preto, SP, Brazil
| | - Douglas Christian Borges Lopes
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | - Roberto do Nascimento Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Bioquímica e Imunologia, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Laboratório de Biologia Sistêmica e Sintética, Ribeirão Preto, SP, Brazil
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18
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Cellulases Production by a Trichoderma sp. Using Food Manufacturing Wastes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9204419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The cost of cellulase enzymes is a main contributor to the operational cost of a biorefinery producing ethanol from lignocellulosic material. Therefore, onsite production of enzymes using low-value substrates might be an option to make a bio-based facility more economical, while improving environmental sustainability. Food manufacturing wastes (FMWs), such as olive mill solids, tomato pomace, and grape pomace, are some of the main wastes produced by the food industry in Chile. FMWs are mostly composed of lignocellulosic material, which is primarily made of cellulose. A fungal strain obtained from olive stones was identified as a Trichoderma sp. and characterized by molecular and morphological techniques. This strain was able to grow on three FMWs in both liquid and solid cultures. In liquid cultures, cellulase and β-glucosidase activities from the culture supernatants were quantified. Identification of extracellular proteins using mass spectrometry revealed the presence of endoglucanases, exoglucanases, and β-glucosidases. Cellulase production from agroindustrial residues could be an excellent opportunity to utilize FMWs as well as decrease enzyme production costs in biorefinery processes.
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19
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Novy V, Nielsen F, Seiboth B, Nidetzky B. The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:238. [PMID: 31624500 PMCID: PMC6781402 DOI: 10.1186/s13068-019-1571-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/21/2023]
Abstract
Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the feedstock used. As summarized in this review, techno-economic studies suggest co-localization and integration of enzyme manufacturing with the cellulosic biorefinery as the most promising alternative to alleviate this problem. Thus, cultivation of Trichoderma reesei, the principal producer of lignocellulolytic enzymes, on the lignocellulosic biomass processed on-site can reduce the cost of enzyme manufacturing. Further, due to a complex gene regulation machinery, the fungus can adjust the gene expression of the lignocellulolytic enzymes towards the characteristics of the feedstock, increasing the hydrolytic efficiency of the produced enzyme cocktail. Despite extensive research over decades, the underlying regulatory mechanisms are not fully elucidated. One aspect that has received relatively little attention in literature is the influence the characteristics of a lignocellulosic substrate, i.e., its chemical and physical composition, has on the produced enzyme mixture. Considering that the fungus is dependent on efficient enzymatic degradation of the lignocellulose for continuous supply of carbon and energy, a relationship between feedstock characteristics and secretome composition can be expected. The aim of this review was to systematically collect, appraise, and aggregate data and integrate results from studies analyzing enzyme production by T. reesei on insoluble cellulosic model substrates and lignocellulosic biomass. The results show that there is a direct effect of the substrate's complexity (rated by structure, composition of the lignin-carbohydrate complex, and recalcitrance in enzymatic saccharification) on enzyme titers and the composition of specific activities in the secretome. It further shows that process-related factors, such as substrate loading and cultivation set-up, are direct targets for increasing enzyme yields. The literature on transcriptome and secretome composition further supports the proposed influence of substrate-related factors on the expression of lignocellulolytic enzymes. This review provides insights into the interrelation between the characteristics of the substrate and the enzyme production by T. reesei, which may help to advance integrated enzyme manufacturing of substrate-specific enzymes cocktails at scale.
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Affiliation(s)
- Vera Novy
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Fredrik Nielsen
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Bernhard Seiboth
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
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20
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Derntl C, Mach RL, Mach-Aigner AR. Fusion transcription factors for strong, constitutive expression of cellulases and xylanases in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:231. [PMID: 31583017 PMCID: PMC6767844 DOI: 10.1186/s13068-019-1575-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/22/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The filamentous ascomycete T. reesei is industrially used to produce cellulases and xylanases. Cost-effective production of cellulases is a bottleneck for biofuel production. Previously, different strain and process optimizations were deployed to enhance enzyme production rates. One approach is the overexpression of the main activator Xyr1 and a second is the construction of synthetic transcription factors. Notably, these genetic manipulations were introduced into strains bearing the wild-type xyr1 gene and locus. RESULTS Here, we constructed a Xyr1-deficient strain expressing a non-functional truncated version of Xyr1. This strain was successfully used as platform strain for overexpression of Xyr1, which enhanced the cellulase and xylanase production rates under inducing conditions, with the exception of lactose-there the cellulase production was severely reduced. Further, we introduced fusion transcription factors consisting of the DNA-binding domain of Xyr1 and the transactivation domain of either Ypr1 or Ypr2 (regulators of the sorbicillinoid biosynthesis gene cluster). The fusion of Xyr1 and Ypr2 yielded a moderately transactivating transcription factor, whereas the fusion of Xyr1 and Ypr1 yielded a highly transactivating transcription factor that induced xylanases and cellulases nearly carbon source independently. Especially, high production levels of xylanases were achieved on glycerol. CONCLUSION During this study, we constructed a Xyr1-deficient strain that can be fully reconstituted, which makes it an ideal platform strain for Xyr1-related studies. The mere overexpression of Xyr1 turned out not to be a successful strategy for overall enhancement of the enzyme production rates. We gained new insights into the regulatory properties of transcription factors by constructing respective fusion proteins. The Xyr1-Ypr1-fusion transcription factor could induce xylanase production rates on glycerol to outstanding extents, and hence could be deployed in the future to utilize crude glycerol, the main co-product of the biodiesel production process.
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Affiliation(s)
- Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Strasse 1a, 1060 Vienna, Austria
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21
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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22
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Thornbury M, Sicheri J, Slaine P, Getz LJ, Finlayson-Trick E, Cook J, Guinard C, Boudreau N, Jakeman D, Rohde J, McCormick C. Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics. PLoS One 2019; 14:e0209221. [PMID: 30601862 PMCID: PMC6314593 DOI: 10.1371/journal.pone.0209221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022] Open
Abstract
Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5–7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.
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Affiliation(s)
- Mackenzie Thornbury
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jacob Sicheri
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Patrick Slaine
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Landon J. Getz
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Emma Finlayson-Trick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Caroline Guinard
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nicholas Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David Jakeman
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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23
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de Paula RG, Antoniêto ACC, Nogueira KMV, Ribeiro LFC, Rocha MC, Malavazi I, Almeida F, Silva RN. Extracellular vesicles carry cellulases in the industrial fungus Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:146. [PMID: 31223336 PMCID: PMC6570945 DOI: 10.1186/s13068-019-1487-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Trichoderma reesei is the most important industrial producer of lignocellulolytic enzymes. These enzymes play an important role in biomass degradation leading to novel applications of this fungus in the biotechnology industry, specifically biofuel production. The secretory pathway of fungi is responsible for transporting proteins addressed to different cellular locations involving some cellular endomembrane systems. Although protein secretion is an extremely efficient process in T. reesei, the mechanisms underlying protein secretion have remained largely uncharacterized in this organism. RESULTS Here, we report for the first time the isolation and characterization of T. reesei extracellular vesicles (EVs). Using proteomic analysis under cellulose culture condition, we have confidently identified 188 vesicular proteins belonging to different functional categories. Also, we characterized EVs production using transmission electron microscopy in combination with light scattering analysis. Biochemical assays revealed that T. reesei extracellular vesicles have an enrichment of filter paper (FPase) and β-glucosidase activities in purified vesicles from 24, 72 and 96, and 72 and 96 h, respectively. Furthermore, our results showed that there is a slight enrichment of small RNAs inside the vesicles after 96 h and 120 h, and presence of hsp proteins inside the vesicles purified from T. reesei grown in the presence of cellulose. CONCLUSIONS This work points to important insights into a better understanding of the cellular mechanisms underlying the regulation of cellulolytic enzyme secretion in this fungus.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Amanda Cristina Campos Antoniêto
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Marina Campos Rocha
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Paulo, Brazil
| | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, São Paulo, 14049-900 Brazil
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