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Cachafeiro L, Heiss-Blanquet S, Hudebine D. An experimental and modeling approach to describe the deactivation of cellulases at the air-liquid interface. Biotechnol Bioeng 2024; 121:1927-1936. [PMID: 38501733 DOI: 10.1002/bit.28698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/15/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024]
Abstract
Understanding the reaction mechanisms involved in the enzymatic hydrolysis of cellulose is important because it is kinetically the most limiting step of the bioethanol production process. The present work focuses on the enzymatic deactivation at the air-liquid interface, which is one of the aspects contributing to this global deactivation. This phenomenon has already been experimentally proven, but this is the first time that a model has been proposed to describe it. Experiments were performed by incubating Celluclast cocktail solutions on an orbital stirring system at different enzyme concentrations and different surface-to-volume ratios. A 5-day follow-up was carried out by measuring the global FPase activity of cellulases for each condition tested. The activity loss was proven to depend on both the air-liquid surface area and the enzyme concentration. Both observations suggest that the loss of activity takes place at the air-liquid surface, the total amount of enzymes varying with volume or enzyme concentration. Furthermore, tests performed using five individual enzymes purified from a Trichoderma reesei cocktail showed that the only cellulase that is deactivated at the air-liquid interface is cellobiohydrolase II. From the experimental data collected by varying the initial enzyme concentration and the ratio surface to volume, it was possible to develop, for the first time, a model that describes the loss of activity at the air-liquid interface for this configuration.
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2
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Mittermeier F, Fischer F, Hauke S, Hirschmann P, Weuster-Botz D. Valorization of Wheat Bran by Co-Cultivation of Fungi with Integrated Hydrolysis to Provide Sugars and Animal Feed. BIOTECH 2024; 13:15. [PMID: 38804297 PMCID: PMC11130873 DOI: 10.3390/biotech13020015] [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: 04/10/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
The enzymatic hydrolysis of agricultural residues like wheat bran enables the valorization of otherwise unused carbon sources for biotechnological processes. The co-culture of Aspergillus niger and Trichoderma reesei with wheat bran particles as substrate produces an enzyme set consisting of xylanases, amylases, and cellulases that is suitable to degrade lignocellulosic biomass to sugar monomers (D-glucose, D-xylose, and L-arabinose). An integrated one-pot process for enzyme production followed by hydrolysis in stirred tank bioreactors resulted in hydrolysates with overall sugar concentrations of 32.3 g L-1 and 24.4 g L-1 at a 25 L and a 1000 L scale, respectively, within 86 h. Furthermore, the residual solid biomass consisting of fermented wheat bran with protein-rich fungal mycelium displays improved nutritional properties for usage as animal feed due to its increased content of sugars, protein, and fat.
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Affiliation(s)
- Fabian Mittermeier
- Chair of Biochemical Engineering, Technical University of Munich, 85748 Garching, Germany
| | - Fabienne Fischer
- Chair of Biochemical Engineering, Technical University of Munich, 85748 Garching, Germany
| | - Sebastian Hauke
- Chair of Biochemical Engineering, Technical University of Munich, 85748 Garching, Germany
| | - Peter Hirschmann
- Bavarian Milling Confederation (Bayerischer Müllerbund e.V.), 80333 Munich, Germany
| | - Dirk Weuster-Botz
- Chair of Biochemical Engineering, Technical University of Munich, 85748 Garching, Germany
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3
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Ji W, Xu L, Sun X, Xu X, Zhang H, Luo H, Yao B, Zhang W, Su X, Huang H. Exploiting Systematic Engineering of the Expression Cassette as a Powerful Tool to Enhance Heterologous Gene Expression in Trichoderma reesei. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5307-5317. [PMID: 38426871 DOI: 10.1021/acs.jafc.3c07988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Many endeavors in expressing a heterologous gene in microbial hosts rely on simply placing the gene of interest between a selected pair of promoters and terminator. However, although the expression efficiency could be improved by engineering the host cell, how modifying the expression cassette itself systematically would affect heterologous gene expression remains largely unknown. As the promoter and terminator bear plentiful cis-elements, herein using the Aspergillus niger mannanase with high application value in animal feeds and the eukaryotic filamentous fungus workhorse Trichoderma reesei as a model gene/host, systematic engineering of an expression cassette was investigated to decipher the effect of its mutagenesis on heterologous gene expression. Modifying the promoter, signal peptide, the eukaryotic-specific Kozak sequence, and the 3'-UTR could stepwise improve extracellular mannanase production from 17 U/mL to an ultimate 471 U/mL, representing a 27.7-fold increase in expression. The strategies can be generally applied in improving the production of heterologous proteins in eukaryotic microbial hosts.
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Affiliation(s)
- Wangli Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Li Xu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Xianhua Sun
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Haidian District, Beijing 100081, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing 100193, China
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4
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Zhao Q, Yang Z, Xiao Z, Zhang Z, Xing J, Liang H, Gao L, Zhao J, Qu Y, Liu G. Structure-guided engineering of transcriptional activator XYR1 for inducer-free production of lignocellulolytic enzymes in Trichoderma reesei. Synth Syst Biotechnol 2023; 8:732-740. [PMID: 38187093 PMCID: PMC10770280 DOI: 10.1016/j.synbio.2023.11.005] [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: 09/11/2023] [Revised: 10/29/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
The filamentous fungus Trichoderma reesei is widely used for the production of lignocellulolytic enzymes in industry. XYR1 is the major transcriptional activator of cellulases and hemicellulases in T. reesei. However, rational engineering of XYR1 for improved lignocellulolytic enzymes production has been limited by the lack of structure information. Here, alanine 873 was identified as a new potential target for the engineering of XYR1 based on its structure predicted by AlphaFold2. The mutation of this residue to tyrosine enabled significantly enhanced production of xylanolytic enzymes in the medium with cellulose as the carbon source. Moreover, xylanase and cellulase production increased by 56.7- and 3.3-fold, respectively, when glucose was used as the sole carbon source. Under both conditions, the improvements of lignocellulolytic enzyme production were higher than those in the previously reported V821F mutant. With the enriched hemicellulases and cellulases, the crude enzymes secreted by the A873Y mutant strain produced 51 % more glucose and 52 % more xylose from pretreated corn stover than those of the parent strain. The results provide a novel strategy for engineering the lignocellulolytic enzyme-producing capacity of T. reesei, and would be helpful for understanding the molecular mechanisms of XYR1 regulation.
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Affiliation(s)
- Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zezheng Yang
- Taishan College, Shandong University, Qingdao, 266237, China
| | - Ziyang Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jing Xing
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Huiqi Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Liwei Gao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Taishan College, Shandong University, Qingdao, 266237, China
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5
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Giwa AS, Ali N, Akhter MS. Cellulose Degradation Enzymes in Filamentous Fungi, A Bioprocessing Approach Towards Biorefinery. Mol Biotechnol 2023:10.1007/s12033-023-00900-1. [PMID: 37839042 DOI: 10.1007/s12033-023-00900-1] [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: 03/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023]
Abstract
The economic exploration of renewable energy resources has hot fundamentals among the countries besides dwindling energy resources and increasing public pressure. Cellulose accumulation is a major bio-natural resource from agricultural waste. Cellulases are the most potential enzymes that systematically degrade cellulosic biomass into monomers which could be further processed into several efficient value-added products via chemical and biological reactions including useful biomaterial for human benefits. This could lower the environmental risks problems followed by an energy crisis. Cellulases are mainly synthesized by special fungal genotypes. The strain Trichoderma orientalis could highly express cellulases and was regarded as an ideal strain for further research, as the genetic tools have found compatibility for cellulose breakdown by producing effective cellulose-degrading enzymes. This strain has found a cellulase production of about 35 g/L that needs further studies for advancement. The enzyme activity of strain Trichoderma orientalis needed to be further improved from a molecular level which is one of the important methods. Considering synthetic biological approaches to unveil the genetic tools will boost the knowledge about commercial cellulases bioproduction. Several genetic transformation methods were significantly cited in this study. The transformation approaches that are currently researchers are exploring is transcription regulatory factors that are deeply explained in this study, that are considered essential regulators of gene expression.
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Affiliation(s)
- Abdulmoseen Segun Giwa
- School of Environment and Civil Engineering, Nanchang Institute of Science and Technology, Nanchang, 330108, China
| | - Nasir Ali
- Institute of Biotechnology Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - Mohammed Salim Akhter
- Department of Chemistry, College of Science, University of Bahrain, Sakheer Campus Bahrain, Zallaq, Bahrain
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6
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Salazar-Cerezo S, de Vries RP, Garrigues S. Strategies for the Development of Industrial Fungal Producing Strains. J Fungi (Basel) 2023; 9:834. [PMID: 37623605 PMCID: PMC10455633 DOI: 10.3390/jof9080834] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands (R.P.d.V.)
| | - Sandra Garrigues
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, VLC, Spain
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7
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Quintero-García OJ, Pérez-Soler H, Amezcua-Allieri MA. Enzymatic Treatments for Biosolids: An Outlook and Recent Trends. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:4804. [PMID: 36981713 PMCID: PMC10049663 DOI: 10.3390/ijerph20064804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
Wastewaters are nutrient-rich organic materials containing significant concentrations of different nutrients, dissolved and particulate matter, microorganisms, solids, heavy metals, and organic pollutants, including aromatic xenobiotics. This variety makes wastewater treatment a technological challenge. As a result of wastewater treatment, biosolids are generated. Biosolids, commonly called sewage sludge, result from treating and processing wastewater residuals. Increased biosolids, or activated sludge, from wastewater treatment is a major environmental and social problem. Therefore, sustainable and energy-efficient wastewater treatment systems must address the water crisis and environmental deterioration. Although research on wastewater has received increasing attention worldwide, the significance of biosolids treatments and valorization is still poorly understood in terms of obtaining value-added products. Hence, in this review, we established some leading technologies (physical, chemical, and biological) for biosolids pretreatment. Later, the research focuses on natural treatment by fungal enzymes to end with lignocellulosic materials and xenobiotic compounds (polyaromatic hydrocarbons) as a carbon source to obtain biobased chemicals. Finally, this review discussed some recent trends and promising renewable resources within the biorefinery approach for bio-waste conversion to value-added by-products.
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Affiliation(s)
- Omar J. Quintero-García
- Nanotechnology Division, CINVESTAV-IPN, Avenida Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Heilyn Pérez-Soler
- Nanotechnology Division, CINVESTAV-IPN, Avenida Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City 07360, Mexico
| | - Myriam A. Amezcua-Allieri
- Biomass Conversion Division, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, San Bartolo Atepehuacan, Mexico City 07730, Mexico
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8
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Mittermeier F, Hafner N, XypoliaVasila K, Weuster‐Botz D. Co‐Cultivation of
Aspergillus niger
and
Trichoderma reesei
Enables Efficient Production of Enzymes for the Hydrolysis of Wheat Bran. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Fabian Mittermeier
- Technical University of Munich Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design Garching Germany
| | - Nathalie Hafner
- Technical University of Munich Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design Garching Germany
| | - Konstantina XypoliaVasila
- Technical University of Munich Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design Garching Germany
| | - Dirk Weuster‐Botz
- Technical University of Munich Chair of Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design Garching Germany
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9
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Noguchi T, Nishiyama R, Shimokawa T, Yamada K, Kagawa Y. Simultaneous production of cellobiose and xylobiose from alkali-treated bagasse using cellulase secreted by Fe-ion-irradiated Trichoderma reesei mutant. J Biosci Bioeng 2022; 134:491-495. [PMID: 36220721 DOI: 10.1016/j.jbiosc.2022.09.002] [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: 06/21/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Cellobiose and xylobiose are disaccharides composed of two glucose or xylose units with β-1,4 linkages. This study aimed to isolate a Trichoderma reesei mutant that lacks β-glucosidase and β-xylosidase activities for the simultaneous production of these disaccharides. Mutagenesis using Fe-ion beam resulted in a mutant strain, T. reesei T1640; the cellulase production in this strain was as high as that in the parent strain. Genomic analysis revealed that T1640 lost both the β-glucosidase and β-xylosidase activities owing to the translocation of the responsible genes. Hydrolysis of alkali-treated bagasse using the enzymes from T1640 leads to high yields (365 mg/g-biomass) and ratios (72.7% of the total sugars) of cellobiose and xylobiose.
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Affiliation(s)
- Takuya Noguchi
- New Frontiers Research Laboratory, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura, Kanagawa 248-8555, Japan
| | - Ryuji Nishiyama
- New Frontiers Research Laboratory, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura, Kanagawa 248-8555, Japan
| | - Takashi Shimokawa
- National Institutes of Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage, Chiba 263-8555, Japan
| | - Katsushige Yamada
- New Frontiers Research Laboratory, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura, Kanagawa 248-8555, Japan
| | - Yusuke Kagawa
- New Frontiers Research Laboratory, Toray Industries, Inc., 6-10-1 Tebiro, Kamakura, Kanagawa 248-8555, Japan.
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10
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Jiang S, Wang Y, Liu Q, Zhao Q, Gao L, Song X, Li X, Qu Y, Liu G. Genetic engineering and raising temperature enhance recombinant protein production with the cdna1 promoter in Trichoderma reesei. BIORESOUR BIOPROCESS 2022; 9:113. [PMID: 38647824 PMCID: PMC10991654 DOI: 10.1186/s40643-022-00607-2] [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: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022] Open
Abstract
The fungus Trichoderma reesei is a powerful host for secreted production of proteins. The promoter of cdna1 gene, which encodes a small basic protein of unknown function and high expression, is commonly used for constitutive protein production in T. reesei. Nevertheless, the production level of proteins driven by this promoter still needs to be improved. Here, we identified that the region 600- to 700-bp upstream of the start codon is critical for the efficiency of the cdna1 promoter. Increasing the copy number of this region to three improved the production of a heterologous β-mannanase by 37.5%. Screening of several stressful conditions revealed that the cdna1 promoter is heat inducible. Cultivation at 37 °C significantly enhanced the production of β-mannanase as well as a polygalacturonase with the cdna1 promoter compared with those at 30 °C. Combing the strategies of promoter engineering, multi-copy gene insertion, and control of cultivation temperature, β-mannanase of 199.85 U/mL and relatively high purity was produced in shake flask, which was 6.6 times higher than that before optimization. Taken together, the results advance the understanding of the widely used cdna1 promoter and provide effective strategies for enhancing the production of recombinant proteins in T. reesei.
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Affiliation(s)
- Shanshan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Yue Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Qin Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Liwei Gao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 11 Keyuanjingsi Road, Qingdao, 266101, China.
| | - Xin Song
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao, 266237, China.
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11
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Sohail M, Barzkar N, Michaud P, Tamadoni Jahromi S, Babich O, Sukhikh S, Das R, Nahavandi R. Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications. Molecules 2022; 27:3783. [PMID: 35744909 PMCID: PMC9229053 DOI: 10.3390/molecules27123783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.
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Affiliation(s)
- Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan;
| | - Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 3995, Iran
| | - Philippe Michaud
- Institute Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, F-63000 Clermont-Ferrand, France;
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 3995, Iran
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Rakesh Das
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), 1433 Aas, Norway;
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj 8361, Iran;
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12
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Pang AP, Luo Y, Hu X, Zhang F, Wang H, Gao Y, Durrani S, Li C, Shi X, Wu FG, Li BZ, Lu Z, Lin F. Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei. Microb Cell Fact 2022; 21:90. [PMID: 35590356 PMCID: PMC9118834 DOI: 10.1186/s12934-022-01809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown. Results We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose. Conclusions Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01809-1.
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Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaotong Shi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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Raheja Y, Singh V, Kaur B, Basotra N, Di Falco M, Tsang A, Singh Chadha B. Combination of system biology and classical approaches for developing biorefinery relevant lignocellulolytic Rasamsonia emersonii strain. BIORESOURCE TECHNOLOGY 2022; 351:127039. [PMID: 35318142 DOI: 10.1016/j.biortech.2022.127039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The objective of this study was to develop thermophilic fungus Rasamsonia emersonii using integrated system biology tools (genomics, proteomics and transcriptional analysis) in combination with classical strain breeding approaches. Developed hyper cellulolytic mutant strain M36 showed endoglucanase (476.35 U/ml), β-glucosidase (70.54 U/ml), cellobiohydrolase (15.17 U/ml), FPase (4.89 U/ml) and xylanase (485.21 U/ml) on cellulose/gram flour based production medium. Comparison of the expression profile at proteome and transcriptional level of the developed strain and wild type parent gave detailed insight into the up-regulation of different CAZymes including glycosyl hydrolases (GH5, GH6, GH7, GH3, GH10) and auxiliary enzymes (lytic polysaccharide monooxygenase, swollenin) at system level. Furthermore, the potential of lignocellulolytic enzyme produced by the developed strain and custom designed cocktail spiked with heterologously expressed lytic polysaccharide monooxygenase from Mycothermus thermophiloides were analyzed for the hydrolysis of biorefinery relevant unwashed pretreated rice straw slurry (PRAJ and IOCL) @17% substrate loading rate.
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Affiliation(s)
- Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Baljit Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Marcos Di Falco
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec H4B 1R6, Canada
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14
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Chai S, Zhu Z, Tian E, Xiao M, Wang Y, Zou G, Zhou Z. Building a Versatile Protein Production Platform Using Engineered Trichoderma reesei. ACS Synth Biol 2022; 11:486-496. [PMID: 34928572 DOI: 10.1021/acssynbio.1c00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trichoderma reesei has an extremely high capacity for synthesizing and secreting proteins, thus exhibiting promise as an expression platform for heterologous proteins. However, T. reesei secretes large amounts of native proteins, which hinders its widespread application for heterologous protein production. Here, we designed and built a series of T. reesei chassis using an iterative gene deletion approach based on an efficient genome editing system. Donor DNAs with specially designed construct facilitated screening of positive deletion strains without ectopic insertion. Finally, marker-free T. reesei chassis with lower rates of native protein secretion and low levels of extracellular protease activity were constructed after 11 consecutive rounds of gene deletion. Higher production levels of three heterologous proteins─a bacterial xylanase XYL7, a fungal immunomodulatory protein LZ8, and the human serum albumin HSA─were achieved with these chassis using the cbh1 promoter. It is possible that diverse high-value proteins might be produced at a high yield using this engineered platform.
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Affiliation(s)
- Shunxing Chai
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Zhihua Zhu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Ernuo Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Meili Xiao
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- University of Chinese Academy of Sciences, 19(A) Yuquan Rd, Beijing 100049, China
| | - Yan Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
| | - Gen Zou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, 1000 Jinqi Rd, Shanghai 201403, China
| | - Zhihua Zhou
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
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15
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Zhang W, Guo J, Wu X, Ren Y, Li C, Meng X, Liu W. Reformulating the Hydrolytic Enzyme Cocktail of Trichoderma reesei by Combining XYR1 Overexpression and Elimination of Four Major Cellulases to Improve Saccharification of Corn Fiber. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:211-222. [PMID: 34935374 DOI: 10.1021/acs.jafc.1c05946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The industrial fungus Trichoderma reesei has an outstanding capability of secreting an enzyme cocktail comprising multiple plant biomass-degrading enzymes. Herein, the overexpression of XYR1, the master transactivator controlling (hemi)cellulase gene expression, was performed in T. reesei lacking four main cellulase-encoding genes. The resultant strain Δ4celOExyr1 was able to produce a dramatically different profile of secretory proteins on soluble glucose or lactose compared with that of the wild-type T. reesei. The Δ4celOExyr1 secretome included cellulases EGIII and BGLI as well as several hemicellulases and nonhydrolytic cellulose degradation-associated proteins that are not preferentially induced in the wild-type T. reesei strain. Δ4celOExyr1 produced a significant amount of α-arabinofuranosidase I on lactose, and the crude enzyme cocktail of Δ4celOExyr1 not only released a considerable quantity of glucose but also exhibited remarkable performance in the hydrolytic release of xylose, arabinose, and mannose from un-pretreated corn fiber. These results showed that the engineered T. reesei strain holds great potential for improving the saccharification efficiency of the hemicellulosic constituents within corn fiber.
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Affiliation(s)
- Weixin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Junqi Guo
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiaoxiao Wu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Yajing Ren
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Chunyan Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
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Lee DS, Song Y, Lee YG, Bae HJ. Comparative Evaluation of Adsorption of Major Enzymes in a Cellulase Cocktail Obtained from Trichoderma reesei onto Different Types of Lignin. Polymers (Basel) 2022; 14:polym14010167. [PMID: 35012188 PMCID: PMC8747337 DOI: 10.3390/polym14010167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
Cellulase adsorption onto lignin decreases the productivity of enzymatic hydrolysis of lignocellulosic biomass. Here, adsorption of enzymes onto different types of lignin was investigated, and the five major enzymes—cellobiohydrolases (CBHs), endoglucanase (Cel7B), β-glucosidase (Cel3A), xylanase (XYNIV), and mannanase (Man5A)—in a cellulase cocktail obtained from Trichoderma reesei were individually analyzed through SDS-PAGE and zymogram assay. Lignin was isolated from woody (oak and pine lignin) and herbaceous (rice straw and kenaf lignin) plants. The relative adsorption of CBHs compared to the control was in the range of 14.15–18.61%. The carbohydrate binding motif (CBM) of the CBHs contributed to higher adsorption levels in oak and kenaf lignin, compared to those in pine and rice lignin. The adsorption of endoglucanase (Cel7B) by herbaceous plant lignin was two times higher than that of woody lignin, whereas XYNIV showed the opposite pattern. β-glucosidase (Cel3A) displayed the highest and lowest adsorption ratios on rice straw and kenaf lignin, respectively. Mannanase (Man5A) was found to have the lowest adsorption ratio on pine lignin. Our results showed that the hydrophobic properties of CBM and the enzyme structures are key factors in adsorption onto lignin, whereas the properties of specific lignin types indirectly affect adsorption.
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Affiliation(s)
- Dae-Seok Lee
- Bio-Energy Research Center, Chonnam National University, Gwangju 500-575, Korea; (D.-S.L.); (Y.S.)
| | - Younho Song
- Bio-Energy Research Center, Chonnam National University, Gwangju 500-575, Korea; (D.-S.L.); (Y.S.)
| | - Yoon-Gyo Lee
- Department of Wood Science and Landscape Architecture, Chonnam National University, Gwangju 500-757, Korea;
| | - Hyeun-Jong Bae
- Bio-Energy Research Center, Chonnam National University, Gwangju 500-575, Korea; (D.-S.L.); (Y.S.)
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757, Korea
- Correspondence: ; Tel.: +81-62-530-2097
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Industrially Important Genes from Trichoderma. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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Bhardwaj N, Kumar B, Agrawal K, Verma P. Current perspective on production and applications of microbial cellulases: a review. BIORESOUR BIOPROCESS 2021; 8:95. [PMID: 38650192 PMCID: PMC10992179 DOI: 10.1186/s40643-021-00447-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/21/2021] [Indexed: 12/27/2022] Open
Abstract
The potential of cellulolytic enzymes has been widely studied and explored for bioconversion processes and plays a key role in various industrial applications. Cellulase, a key enzyme for cellulose-rich waste feedstock-based biorefinery, has increasing demand in various industries, e.g., paper and pulp, juice clarification, etc. Also, there has been constant progress in developing new strategies to enhance its production, such as the application of waste feedstock as the substrate for the production of individual or enzyme cocktails, process parameters control, and genetic manipulations for enzyme production with enhanced yield, efficiency, and specificity. Further, an insight into immobilization techniques has also been presented for improved reusability of cellulase, a critical factor that controls the cost of the enzyme at an industrial scale. In addition, the review also gives an insight into the status of the significant application of cellulase in the industrial sector, with its techno-economic analysis for future applications. The present review gives a complete overview of current perspectives on the production of microbial cellulases as a promising tool to develop a sustainable and greener concept for industrial applications.
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Affiliation(s)
- Nisha Bhardwaj
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
- Department of Chemical Engineering, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai, Maharashtra, 400019, India
| | - Bikash Kumar
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Komal Agrawal
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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20
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Comparative Secretomics Analysis Reveals the Major Components of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30. Microorganisms 2021; 9:microorganisms9102042. [PMID: 34683363 PMCID: PMC8538001 DOI: 10.3390/microorganisms9102042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/16/2021] [Accepted: 09/24/2021] [Indexed: 11/23/2022] Open
Abstract
In this study, the major secretome components of Penicillium oxalicum 16 and Trichoderma reesei RUT-C30 under wheat bran (WB) and rice straw (RS) solid-state fermentation were systematically analyzed. The activities of the major components, e.g., cellulase, hemicellulase, and amylase, were consistent with their abundance in the secretomes. P. oxalicum 16 secreted more abundant glycoside hydrolases than T. reesei RUT-C30. The main up-regulated proteins from the induction of WB, compared with that from RS, were amylase, pectinase, and protease, whereas the main down-regulated enzymes were cellulase, hemicellulase, swollenin, and lytic polysaccharide monooxygenase (LPMO). Specifically, WB induced more β-1,4-glucosidases, namely, S8B0F3 (UniProt ID), and A0A024RWA5 than RS, but RS induced more β-1,4-exoglucanases and β-1,4-endoglucanases, namely, A0A024RXP8, A024SH76, S7B6D6, S7ZP52, A024SH20, A024S2H5, S8BGM3, S7ZX22, and S8AIJ2. The P. oxalicum 16 xylanases S8AH74 and S7ZA57 were the major components responsible for degrading soluble xylan, and S8BDN2 probably acted on solid-state hemicellulose instead of soluble xylan. The main hemicellulase component of T. reesei RUT-C30 in RS was the xyloglucanase A0A024S9Z6 with an abundance of 16%, but T. reesei RUT-C30 lacked the hemicellulase mannanase and had a small amount of the hemicellulase xylanase. P. oxalicum 16 produced more amylase than T. reesei RUT-C30, and the results suggest amylase S7Z6T2 may degrade soluble starch. The percentage of the glucoamylase S8B6D7 did not significantly change, and reached an average abundance of 5.5%. The major auxiliary degradation enzymes of P. oxalicum 16 were LPMOs S7Z716 and S7ZPW1, whereas those of T. reesei RUT-C30 were swollenin and LPMOs A0A024SM10, A0A024SFJ2, and A0A024RZP7.
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21
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Fang H, Li C, Zhao J, Zhao C. Biotechnological Advances and Trends in Engineering Trichoderma reesei towards Cellulase Hyperproducer. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0243-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Rangel Pedersen N, Tovborg M, Soleimani Farjam A, Della Pia EA. Multicomponent carbohydrase system from Trichoderma reesei: A toolbox to address complexity of cell walls of plant substrates in animal feed. PLoS One 2021; 16:e0251556. [PMID: 34086701 PMCID: PMC8177525 DOI: 10.1371/journal.pone.0251556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/27/2021] [Indexed: 11/19/2022] Open
Abstract
A diverse range of monocot and dicot grains and their by-products are commonly used in the animal feed industry. They all come with complex and variable cell wall structures which in turn contribute significant fiber to the complete feed. The cell wall is a highly interconnected matrix of various polysaccharides, proteins and lignin and, as such, requires a collaborative effort of different enzymes for its degradation. In this regard, we investigated the potential of a commercial multicomponent carbohydrase product from a wild type fermentation of Trichoderma reesei (T. reesei) (RONOZYME® MultiGrain) in degrading cell wall components of wheat, barley, rye, de-oiled rice bran, sunflower, rapeseed and cassava. A total of thirty-one different enzyme proteins were identified in the T. Reesei carbohydrase product using liquid chromatography with tandem mass spectrometry LC-MS/MS including glycosyl hydrolases and carbohydrate esterases. As measured by in vitro incubations and non-starch polysaccharide component analysis, and visualization by immunocytochemistry and confocal microscopy imaging of immuno-labeled samples with confocal microscopy, the carbohydrase product effectively solubilized cellulolytic and hemicellulolytic polysaccharides present in the cell walls of all the feed ingredients evaluated. The T. reesei fermentation also decreased viscosity of arabinoxylan, xyloglucan, galactomannan and β-glucan substrates. Combination of several debranching enzymes including arabinofuranosidase, xylosidase, α-galactosidase, acetyl xylan esterase, and 4-O-methyl-glucuronoyl methylesterase with both GH10 and GH11 xylanases in the carbohydrase product resulted in effective hydrolyzation of heavily branched glucuronoarabinoxylans. The different β-glucanases (both endo-β-1,3(4)-glucanase and endo-β-1,3-glucanase), cellulases and a β-glucosidase in the T. reesei fermentation effectively reduced polymerization of both β-glucans and cellulose polysaccharides of viscous cereals grains (wheat, barley, rye and oat). Interestingly, the secretome of T. reesei contained significant amounts of an exceptional direct chain-cutting enzyme from the GH74 family (Cel74A, xyloglucan-specific β-1,4-endoglucanase), that strictly cleaves the xyloglucan backbone at the substituted regions. Here, we demonstrated that the balance of enzymes present in the T. reesei secretome is capable of degrading various cell wall components in both monocot and dicot plant raw material used as animal feed.
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Lin MC, Kuo HW, Kao MR, Lin WD, Li CW, Hung KS, Yang SC, Yu SM, Ho THD. From simple and specific zymographic detections to the annotation of a fungus Daldinia caldariorum D263 that encodes a wide range of highly bioactive cellulolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:120. [PMID: 34020690 PMCID: PMC8140500 DOI: 10.1186/s13068-021-01959-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Lignocellulolytic enzymes are essential for agricultural waste disposal and production of renewable bioenergy. Many commercialized cellulase mixtures have been developed, mostly from saprophytic or endophytic fungal species. The cost of complete cellulose digestion is considerable because a wide range of cellulolytic enzymes is needed. However, most fungi can only produce limited range of highly bioactive cellulolytic enzymes. We aimed to investigate a simple yet specific method for discovering unique enzymes so that fungal species producing a diverse group of cellulolytic enzymes can be identified. RESULTS The culture medium of an endophytic fungus, Daldinia caldariorum D263, contained a complete set of cellulolytic enzymes capable of effectively digesting cellulose residues into glucose. By taking advantage of the unique product inhibition property of β-glucosidases, we have established an improved zymography method that can easily distinguish β-glucosidase and exoglucanase activity. Our zymography method revealed that D263 can secrete a wide range of highly bioactive cellulases. Analyzing the assembled genome of D263, we found over 100 potential genes for cellulolytic enzymes that are distinct from those of the commercially used fungal species Trichoderma reesei and Aspergillus niger. We further identified several of these cellulolytic enzymes by mass spectrometry. CONCLUSIONS The genome of Daldinia caldariorum D263 has been sequenced and annotated taking advantage of a simple yet specific zymography method followed by mass spectrometry analysis, and it appears to encode and secrete a wide range of bioactive cellulolytic enzymes. The genome and cellulolytic enzyme secretion of this unique endophytic fungus should be of value for identifying active cellulolytic enzymes that can facilitate conversion of agricultural wastes to fermentable sugars for the industrial production of biofuels.
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Affiliation(s)
- Meng-Chun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsion-Wen Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
| | - Mu-Rong Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Kuo-Sheng Hung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Sheng-Chih Yang
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC.
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC.
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Lee DS, Lee YG, Cho EJ, Song Y, Bae HJ. Hydrolysis pattern analysis of xylem tissues of woody plants pretreated with hydrogen peroxide and acetic acid: rapid saccharification of softwood for economical bioconversion. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:37. [PMID: 33549141 PMCID: PMC7866737 DOI: 10.1186/s13068-021-01889-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/25/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Woody plants with high glucose content are alternative bioresources for the production of biofuels and biochemicals. Various pretreatment methods may be used to reduce the effects of retardation factors such as lignin interference and cellulose structural recalcitrance on the degradation of the lignocellulose material of woody plants. RESULTS A hydrogen peroxide-acetic acid (HPAC) pretreatment was used to reduce the lignin content of several types of woody plants, and the effect of the cellulose structural recalcitrance on the enzymatic hydrolysis was analyzed. The cellulose structural recalcitrance and the degradation patterns of the wood fibers in the xylem tissues of Quercus acutissima (hardwood) resulted in greater retardation in the enzymatic saccharification than those in the tracheids of Pinus densiflora (softwood). In addition to the HPAC pretreatment, the application of supplementary enzymes (7.5 FPU cellulase for 24 h) further increased the hydrolysis rate of P. densiflora from 61.42 to 91.94% whereas the same effect was not observed for Q. acutissima. It was also observed that endoxylanase synergism significantly affected the hydrolysis of P. densiflora. However, this synergistic effect was lower for other supplementary enzymes. The maximum concentration of the reducing sugars produced from 10% softwood was 89.17 g L-1 after 36 h of hydrolysis with 15 FPU cellulase and other supplementary enzymes. Approximately 80 mg mL-1 of reducing sugars was produced with the addition of 7.5 FPU cellulase and other supplementary enzymes after 36 h, achieving rapid saccharification. CONCLUSION HPAC pretreatment removed the interference of lignin, reduced structural recalcitrance of cellulose in the P. densiflora, and enabled rapid saccharification of the woody plants including a high concentration of insoluble substrates with only low amounts of cellulase. HPAC pretreatment may be a viable alternative for the cost-efficient production of biofuels or biochemicals from softwood plant tissues.
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Affiliation(s)
- Dae-Seok Lee
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Yoon-Gyo Lee
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Eun Jin Cho
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Younho Song
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Hyeun-Jong Bae
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea.
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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26
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Li J, Solhi L, Goddard-Borger ED, Mathieu Y, Wakarchuk WW, Withers SG, Brumer H. Four cellulose-active lytic polysaccharide monooxygenases from Cellulomonas species. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:29. [PMID: 33485381 PMCID: PMC7828015 DOI: 10.1186/s13068-020-01860-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/13/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The discovery of lytic polysaccharide monooxygenases (LPMOs) has fundamentally changed our understanding of microbial lignocellulose degradation. Cellulomonas bacteria have a rich history of study due to their ability to degrade recalcitrant cellulose, yet little is known about the predicted LPMOs that they encode from Auxiliary Activity Family 10 (AA10). RESULTS Here, we present the comprehensive biochemical characterization of three AA10 LPMOs from Cellulomonas flavigena (CflaLPMO10A, CflaLPMO10B, and CflaLPMO10C) and one LPMO from Cellulomonas fimi (CfiLPMO10). We demonstrate that these four enzymes oxidize insoluble cellulose with C1 regioselectivity and show a preference for substrates with high surface area. In addition, CflaLPMO10B, CflaLPMO10C, and CfiLPMO10 exhibit limited capacity to perform mixed C1/C4 regioselective oxidative cleavage. Thermostability analysis indicates that these LPMOs can refold spontaneously following denaturation dependent on the presence of copper coordination. Scanning and transmission electron microscopy revealed substrate-specific surface and structural morphological changes following LPMO action on Avicel and phosphoric acid-swollen cellulose (PASC). Further, we demonstrate that the LPMOs encoded by Cellulomonas flavigena exhibit synergy in cellulose degradation, which is due in part to decreased autoinactivation. CONCLUSIONS Together, these results advance understanding of the cellulose utilization machinery of historically important Cellulomonas species beyond hydrolytic enzymes to include lytic cleavage. This work also contributes to the broader mapping of enzyme activity in Auxiliary Activity Family 10 and provides new biocatalysts for potential applications in biomass modification.
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Affiliation(s)
- James Li
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Laleh Solhi
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ethan D Goddard-Borger
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Yann Mathieu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Stephen G Withers
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
- BioProducts Institute, University of British Columbia, 2385 East Mall, Vancouver, BC, V6T 1Z4, Canada.
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Deciphering Trichoderma-Plant-Pathogen Interactions for Better Development of Biocontrol Applications. J Fungi (Basel) 2021; 7:jof7010061. [PMID: 33477406 PMCID: PMC7830842 DOI: 10.3390/jof7010061] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 12/31/2020] [Accepted: 01/02/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the fungal genus Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) are ubiquitous and commonly encountered as soil inhabitants, plant symbionts, saprotrophs, and mycoparasites. Certain species have been used to control diverse plant diseases and mitigate negative growth conditions. The versatility of Trichoderma’s interactions mainly relies on their ability to engage in inter- and cross-kingdom interactions. Although Trichoderma is by far the most extensively studied fungal biocontrol agent (BCA), with a few species already having been commercialized as bio-pesticides or bio-fertilizers, their wide application has been hampered by an unpredictable efficacy under field conditions. Deciphering the dialogues within and across Trichoderma ecological interactions by identification of involved effectors and their underlying effect is of great value in order to be able to eventually harness Trichoderma’s full potential for plant growth promotion and protection. In this review, we focus on the nature of Trichoderma interactions with plants and pathogens. Better understanding how Trichoderma interacts with plants, other microorganisms, and the environment is essential for developing and deploying Trichoderma-based strategies that increase crop production and protection.
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Sreeja-Raju A, Christopher M, Kooloth-Valappil P, Kuni-Parambil R, Gokhale DV, Sankar M, Abraham A, Pandey A, Sukumaran RK. Penicillium janthinellum NCIM1366 shows improved biomass hydrolysis and a larger number of CAZymes with higher induction levels over Trichoderma reesei RUT-C30. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:196. [PMID: 33292411 PMCID: PMC7706291 DOI: 10.1186/s13068-020-01830-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/16/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Major cost of bioethanol is attributed to enzymes employed in biomass hydrolysis. Biomass hydrolyzing enzymes are predominantly produced from the hyper-cellulolytic mutant filamentous fungus Trichoderma reesei RUT-C30. Several decades of research have failed to provide an industrial grade organism other than T. reesei, capable of producing higher titers of an effective synergistic biomass hydrolyzing enzyme cocktail. Penicillium janthinellum NCIM1366 was reported as a cellulase hyper producer and a potential alternative to T. reesei, but a comparison of their hydrolytic performance was seldom attempted. RESULTS Hydrolysis of acid or alkali-pretreated rice straw using cellulase enzyme preparations from P. janthinellum and T. reesei indicated 37 and 43% higher glucose release, respectively, with P. janthinellum enzymes. A comparison of these fungi with respect to their secreted enzymes indicated that the crude enzyme preparation from P. janthinellum showed 28% higher overall cellulase activity. It also had an exceptional tenfold higher beta-glucosidase activity compared to that of T. reesei, leading to a lower cellobiose accumulation and thus alleviating the feedback inhibition. P. janthinellum secreted more number of proteins to the extracellular medium whose total concentration was 1.8-fold higher than T. reesei. Secretome analyses of the two fungi revealed higher number of CAZymes and a higher relative abundance of cellulases upon cellulose induction in the fungus. CONCLUSIONS The results revealed the ability of P. janthinellum for efficient biomass degradation through hyper cellulase production, and it outperformed the established industrial cellulase producer T. reesei in the hydrolysis experiments. A higher level of induction, larger number of secreted CAZymes and a high relative proportion of BGL to cellulases indicate the possible reasons for its performance advantage in biomass hydrolysis.
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Affiliation(s)
- AthiraRaj Sreeja-Raju
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate, Pappanamcode, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Meera Christopher
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate, Pappanamcode, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prajeesh Kooloth-Valappil
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate, Pappanamcode, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rajasree Kuni-Parambil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Meena Sankar
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate, Pappanamcode, Thiruvananthapuram, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amith Abraham
- Department of Chemical Engineering, Hanyang University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Industrial Estate, Pappanamcode, Thiruvananthapuram, 695019, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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van der Zwan T, Sigg A, Hu J, Chandra RP, Saddler JN. Enzyme-Mediated Lignocellulose Liquefaction Is Highly Substrate-Specific and Influenced by the Substrate Concentration or Rheological Regime. Front Bioeng Biotechnol 2020; 8:917. [PMID: 32850753 PMCID: PMC7423843 DOI: 10.3389/fbioe.2020.00917] [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: 05/02/2020] [Accepted: 07/16/2020] [Indexed: 01/30/2023] Open
Abstract
The high viscosities/yield stresses of lignocellulose slurries makes their industrial processing a significant challenge. However, little is known regarding the degree to which liquefaction and its enzymatic requirements are specific to a substrate's physicochemical and rheological properties. In the work reported here, the substrate- and rheological regime-specificities of liquefaction of various substrates were assessed using real-time in-rheometer viscometry and offline oscillatory rheometry when hydrolyzed by combinations of cellobiohydrolase (Trichoderma reesei Cel7A), endoglucanase (Humicola insolens Cel45A), glycoside hydrolase (GH) family 10 xylanase, and GH family 11 xylanase. In contrast to previous work that has suggested that endoglucanase activity dominates enzymatic liquefaction, all of the enzymes were shown to have at least some liquefaction capacity depending on the substrate and reaction conditions. The contribution of individual enzymes was found to be influenced by the rheological regime; in the concentrated regime, the cellobiohydrolase outperformed the endoglucanase, achieving 2.4-fold higher yield stress reduction over the same timeframe, whereas the endoglucanase performed best in the semi-dilute regime. It was apparent that the significant differences in rheology and liquefaction mechanisms made it difficult to predict the liquefaction capacity of an enzyme or enzyme cocktail at different substrate concentrations.
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Affiliation(s)
- Timo van der Zwan
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Alexander Sigg
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, Technical University of Munich, Munich, Germany
| | - Jinguang Hu
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Richard P. Chandra
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Jack N. Saddler
- Forest Products Biotechnology and Bioenergy Group, Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
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Jiang X, Du J, He R, Zhang Z, Qi F, Huang J, Qin L. Improved Production of Majority Cellulases in Trichoderma reesei by Integration of cbh1 Gene From Chaetomium thermophilum. Front Microbiol 2020; 11:1633. [PMID: 32765463 PMCID: PMC7381231 DOI: 10.3389/fmicb.2020.01633] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/23/2020] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose is an abundant waste resource and has been considered as a promising material for production of biofuels or other valuable bio-products. Currently, one of the major bottlenecks in the economic utilization of lignocellulosic materials is the cost-efficiency of converting lignocellulose into soluble sugars for fermentation. One way to address this problem is to seek superior lignocellulose degradation enzymes or further improve current production yields of lignocellulases. In the present study, the lignocellulose degradation capacity of a thermophilic fungus Chaetomium thermophilum was firstly evaluated and compared to that of the biotechnological workhorse Trichoderma reesei. The data demonstrated that compared to T. reesei, C. thermophilum displayed substantially higher cellulose-utilizing efficiency with relatively lower production of cellulases, indicating that better cellulases might exist in C. thermophilum. Comparison of the protein secretome between C. thermophilum and T. reesei showed that the secreted protein categories were quite different in these two species. In addition, to prove that cellulases in C. thermophilum had better enzymatic properties, the major cellulase cellobiohydrolase I (CBH1) from C. thermophilum and T. reesei were firstly characterized, respectively. The data showed that the specific activity of C. thermophilum CBH1 was about 4.5-fold higher than T. reesei CBH1 in a wide range of temperatures and pH. To explore whether increasing CBH1 activity in T. reesei could contribute to improving the overall cellulose-utilizing efficiency of T. reesei, T. reesei cbh1 gene was replaced with C. thermophilum cbh1 gene by integration of C. thermophilum cbh1 gene into T. reesei cbh1 gene locus. The data surprisingly showed that this gene replacement not only increased the cellobiohydrolase activities by around 4.1-fold, but also resulted in stronger induction of other cellulases genes, which caused the filter paper activities, Azo-CMC activities and β-glucosidase activities increased by about 2.2, 1.9, and 2.3-fold, respectively. The study here not only provided new resources of superior cellulases genes and new strategy to improve the cellulase production in T. reesei, but also contribute to opening the path for fundamental research on C. thermophilum.
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Affiliation(s)
- Xianzhang Jiang
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jiawen Du
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Ruonan He
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhengying Zhang
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Feng Qi
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jianzhong Huang
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Lina Qin
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, China
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Salwan R, Sharma A, Sharma V. Recent Advances in Molecular Approaches for Mining Potential Candidate Genes of Trichoderma for Biofuel. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wang F, Zhang R, Han L, Guo W, Du Z, Niu K, Liu Y, Jia C, Fang X. Use of fusion transcription factors to reprogram cellulase transcription and enable efficient cellulase production in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:244. [PMID: 31636703 PMCID: PMC6792246 DOI: 10.1186/s13068-019-1589-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/09/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Trichoderma reesei is widely used for cellulase production and accepted as an example for cellulase research. Cre1-mediated carbon catabolite repression (CCR) can significantly inhibit the transcription of cellulase genes during cellulase fermentation in T. reesei. Early efforts have been undertaken to modify Cre1 for the release of CCR; however, this approach leads to arrested hyphal growth and decreased biomass accumulation, which negatively affects cellulase production. RESULTS In this study, novel fusion transcription factors (fTFs) were designed to release or attenuate CCR inhibition in cellulase transcription, while Cre1 was left intact to maintain normal hyphal growth. Four designed fTFs were introduced into the T. reesei genome, which generated several transformants, named Kuace3, Kuclr2, Kuace2, and Kuxyr1. No obvious differences in growth were observed between the parent and transformant strains. However, the transcription levels of cel7a, a major cellulase gene, were significantly elevated in all the transformants, particularly in Kuace2 and Kuxyr1, when grown on lactose as a carbon source. This suggested that CCR inhibition was released or attenuated in the transformant strains. The growth of Kuace2 and Kuxyr1 was approximately equivalent to that of the parent strain in fed-batch fermentation process. However, we observed a 3.2- and 2.1-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of the parent strain. Moreover, we observed a 6.1- and 3.9-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of Δcre1 strain. CONCLUSIONS A new strategy based on fTFs was successfully established in T. reesei to improve cellulase titers without impairing fungal growth. This study will be valuable for lignocellulosic biorefining and for guiding the development of engineering strategies for producing other important biochemical compounds in fungal species.
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Affiliation(s)
- Fangzhong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong China
| | - Ruiqin Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Lijuan Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Wei Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Zhiqiang Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Kangle Niu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Yucui Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Chunjiang Jia
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong China
| | - Xu Fang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
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Adsul M, Sandhu SK, Singhania RR, Gupta R, Puri SK, Mathur A. Designing a cellulolytic enzyme cocktail for the efficient and economical conversion of lignocellulosic biomass to biofuels. Enzyme Microb Technol 2019; 133:109442. [PMID: 31874688 DOI: 10.1016/j.enzmictec.2019.109442] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 11/19/2022]
Abstract
Concerns about dwindling fossil fuels and their unfavorable environmental impacts shifted the global focus towards the development of biofuels from lignocellulosic feedstocks. The structure of this biomass is very complex due to which variety of enzymes (cellulolytic, hemicellulolytic, auxiliary/AA9) and proteins (e.g. swollenin) required for efficient deconstruction. Major impediments in large-scale commercial production of cellulosic ethanol are the cost of cellulases and inability of any single microorganism to produce all cellulolytic components in sufficient titers. In the recent past, various methods for reducing the enzyme cost during cellulosic ethanol production have been attempted. These include designing optimal synergistic enzyme blends/cocktail, having certain ratios of enzymes from different microbial sources, for efficient hydrolysis of pretreated biomass. However, the mechanisms underlying the development, strategies for production and evaluation of optimal cellulolytic cocktails still remain unclear. This article aims to explore the technical and economic benefits of using cellulolytic enzyme cocktail, basic enzymatic and non-enzymatic components required for its development and various strategies employed for efficient cellulolytic cocktail preparation. Consideration was also given to the ways of evaluation of commercially available and in-house developed cocktails. Discussion about commercially available cellulolytic cocktails, current challenges and possible avenues in the development of cellulolytic cocktails included.
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Affiliation(s)
- Mukund Adsul
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India.
| | - Simranjeet Kaur Sandhu
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Reeta Rani Singhania
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Ravi Gupta
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Suresh K Puri
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
| | - Anshu Mathur
- DBT-IOC Centre for Advanced Bioenergy Research, R & D Centre, Indian Oil Corporation Ltd, Sector-13, Faridabad 121007, India
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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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He R, Ding R, Heyman JA, Zhang D, Tu R. Ultra-high-throughput picoliter-droplet microfluidics screening of the industrial cellulase-producing filamentous fungus Trichoderma reesei. J Ind Microbiol Biotechnol 2019; 46:1603-1610. [PMID: 31375945 DOI: 10.1007/s10295-019-02221-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/16/2019] [Indexed: 11/26/2022]
Abstract
The selection of improved producers among the huge number of variants in mutant libraries is a key issue in filamentous fungi of industrial biotechnology. Here, we developed a droplet-based microfluidic high-throughput screening platform for selection of high-cellulase producers from filamentous fungus Trichoderma reesei. The screening system used a fluorogenic assay to measure amount of cellulase and its activity. The key effectors such as cellulase-inducing medium, spore germination, droplet cultivation time, droplet fluorescence signal detection, and droplet cell sorting were studied. An artificial pre-mixed library of high- and low-cellulase-producing T. reesei strains was screened successfully to verify the feasibility of our method. Finally, two cellulase hyperproducers exhibiting improvements in cellulase activity of 27% and 46% were isolated from an atmospheric and room-temperature plasma (ARTP)-mutated library. This high-throughput screening system could be applied to the engineering of T. reesei strains and other industrially valuable protein-producing filamentous fungi.
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Affiliation(s)
- Ronglin He
- Tianjin Key Laboratory of Industrial Biology Systems and Processing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ruihua Ding
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - John A Heyman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Dongyuan Zhang
- Tianjin Key Laboratory of Industrial Biology Systems and Processing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Ran Tu
- Tianjin Key Laboratory of Industrial Biology Systems and Processing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Kostyleva EV, Sereda AS, Osipov DO, Velikoretskaya IA, Tsurikova NV. The Change in the Composition of Trichoderma reesei Carbohydrases Complex as a Result of Gamma Mutagenesis. Microbiol Insights 2019; 12:1178636119848368. [PMID: 31205417 PMCID: PMC6537285 DOI: 10.1177/1178636119848368] [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: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 11/17/2022] Open
Abstract
The filamentous fungus Trichoderma reesei is traditionally used as the main industrial producer of cellulases and hemicellulases. Recently, the relevance of carbohydrases hydrolyzing nonstarch polysaccharides of cereals has significantly increased in feed production. In processing of grain raw materials, endodepolymerases, mainly xylanases and endoglucanases, play a key role. Earlier, we carried out gamma mutagenesis of an industrial strain T. reesei BCM18.2/KK to increase the proportion of endodepolymerases in its enzyme complex. Endoglucanase activity of the strain was increased 5-fold, while xylanase activity increased more than 8-fold. It was interesting to determine the carbohydrases composition in enzyme preparations obtained from the original and mutant T. reesei strains. So, the strains were cultured in laboratory fermenters; concentrated preparations were obtained using freeze dryer. It was established that gamma mutagenesis resulted in significant changes in the carbohydrases complex of the strain. Cellobiohydrolase I being the major carbohydrase in the original strain was absent in the enzyme complex of the mutant. The share of xylanases and endoglucanases in the preparation from the mutant strain increased by 6% and 6.5%, respectively, compared with the preparation from the original strain. The obtained data show the ability of gamma irradiation to affect the component composition of T. reesei carbohydrase complex.
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Affiliation(s)
- Elena V Kostyleva
- All-Russian Research Institute of Food Biotechnology-A Branch of FRC of Food, Biotechnology, and Food Safety, Moscow, Russia
| | - Anna S Sereda
- All-Russian Research Institute of Food Biotechnology-A Branch of FRC of Food, Biotechnology, and Food Safety, Moscow, Russia
| | - Dmitrii O Osipov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russia
| | - Irina A Velikoretskaya
- All-Russian Research Institute of Food Biotechnology-A Branch of FRC of Food, Biotechnology, and Food Safety, Moscow, Russia
| | - Nina V Tsurikova
- All-Russian Research Institute of Food Biotechnology-A Branch of FRC of Food, Biotechnology, and Food Safety, Moscow, Russia
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Vita N, Borne R, Perret S, de Philip P, Fierobe HP. Turning a potent family-9 free cellulase into an operational cellulosomal component and vice versa. FEBS J 2019; 286:3359-3373. [PMID: 31004451 DOI: 10.1111/febs.14858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/18/2019] [Accepted: 04/16/2019] [Indexed: 11/29/2022]
Abstract
Ruminiclostridium cellulolyticum and Lachnoclostridium phytofermentans are cellulolytic clostridia either producing extracellular multienzymatic complexes termed cellulosomes or secreting free cellulases respectively. In the free state, the cellulase Cel9A secreted by L. phytofermentans is much more active on crystalline cellulose than any cellulosomal family-9 enzyme produced by R. cellulolyticum. Nevertheless, the incorporation of Cel9A in vitro in hybrid cellulosomes was formerly shown to generate artificial complexes with altered activity, whereas its incorporation in vivo in native R. cellulolyticum cellulosomes resulted in a strain displaying a weakened cellulolytic phenotype. In this study, we investigated why Cel9A is so potent in the free state but functions poorly as a cellulosomal component, in contrast to the most similar enzyme synthesized by R. cellulolyticum, Cel9G, weakly active in the free state but whose activity on crystalline cellulose is drastically increased in cellulosomes. We show that the removal of the C-terminal moiety of Cel9A encompassing the two X2 modules and the family-3b carbohydrate binding module (CBM3b), reduces its activity on crystalline cellulose. Grafting a dockerin module further diminishes the activity, but this truncated cellulosomal form of Cel9A displays important synergies in hybrid cellulosomes with the pivotal family-48 cellulosomal enzyme of R. cellulolyticum. The exact inverse approach was applied to the cellulosomal Cel9G. Grafting the two X2 modules and the CBM3b of Cel9A to Cel9G strongly increases its activity on crystalline cellulose, to reach Cel9A activity levels. Altogether these data emphasize the specific features required to generate an efficient free or cellulosomal family-9 cellulase.
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Filiatrault-Chastel C, Navarro D, Haon M, Grisel S, Herpoël-Gimbert I, Chevret D, Fanuel M, Henrissat B, Heiss-Blanquet S, Margeot A, Berrin JG. AA16, a new lytic polysaccharide monooxygenase family identified in fungal secretomes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:55. [PMID: 30923563 PMCID: PMC6420742 DOI: 10.1186/s13068-019-1394-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Lignocellulosic biomass is considered as a promising alternative to fossil resources for the production of fuels, materials and chemicals. Efficient enzymatic systems are needed to degrade the plant cell wall and overcome its recalcitrance. A widely used producer of cellulolytic cocktails is the ascomycete Trichoderma reesei, but this organism secretes a limited set of enzymes. To improve the saccharification yields, one strategy is to upgrade the T. reesei enzyme cocktail with enzymes produced by other biomass-degrading filamentous fungi isolated from biodiversity. RESULTS In this study, the enzymatic cocktails secreted by five strains from the genus Aspergillus (Aspergillus japonicus strains BRFM 405, 1487, 1489, 1490 and Aspergillus niger strain BRFM 430) were tested for their ability to boost a T. reesei reference cocktail for the saccharification of pretreated biomass. Proteomic analysis of fungal secretomes that significantly improved biomass degradation showed that the presence of proteins belonging to a putative LPMO family previously identified by genome analysis and awaiting experimental demonstration of activity. Members of this novel LPMO family, named AA16, are encountered in fungi and oomycetes with life styles oriented toward interactions with plant biomass. One AA16 protein from Aspergillus aculeatus (AaAA16) was produced to high level in Pichia pastoris. LPMO-type enzyme activity was demonstrated on cellulose with oxidative cleavage at the C1 position of the glucose unit. AaAA16 LPMO was found to significantly improve the activity of T. reesei CBHI on cellulosic substrates. CONCLUSIONS Although Aspergillus spp. has been investigated for decades for their CAZymes diversity, we identified members of a new fungal LPMO family using secretomics and functional assays. Properties of the founding member of the AA16 family characterized herein could be of interest for use in biorefineries.
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Affiliation(s)
- Camille Filiatrault-Chastel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - David Navarro
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Mireille Haon
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Sacha Grisel
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Isabelle Herpoël-Gimbert
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
| | - Didier Chevret
- Plateforme d’Analyse Protéomique de Paris Sud-Ouest, Institut Micalis, UMR1319, INRA, Agro-ParisTech, Jouy-En-Josas, France
| | - Mathieu Fanuel
- UR1268, INRA, Biopolymères Interactions Assemblages, Nantes, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257, CNRS, Aix Marseille Université, Marseille, France
- USC1408, INRA, Architecture et Fonction des Macromolécules Biologiques, Marseille, France
| | - Senta Heiss-Blanquet
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Antoine Margeot
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France
| | - Jean-Guy Berrin
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRA, Aix Marseille Université, Marseille, France
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Sharma S, Kour D, Rana KL, Dhiman A, Thakur S, Thakur P, Thakur S, Thakur N, Sudheer S, Yadav N, Yadav AN, Rastegari AA, Singh K. Trichoderma: Biodiversity, Ecological Significances, and Industrial Applications. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-10480-1_3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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40
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Schiano-di-Cola C, Røjel N, Jensen K, Kari J, Sørensen TH, Borch K, Westh P. Systematic deletions in the cellobiohydrolase (CBH) Cel7A from the fungus Trichoderma reesei reveal flexible loops critical for CBH activity. J Biol Chem 2018; 294:1807-1815. [PMID: 30538133 DOI: 10.1074/jbc.ra118.006699] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/08/2018] [Indexed: 11/06/2022] Open
Abstract
Glycoside hydrolase family 7 (GH7) cellulases are some of the most efficient degraders of cellulose, making them particularly relevant for industries seeking to produce renewable fuels from lignocellulosic biomass. The secretome of the cellulolytic model fungus Trichoderma reesei contains two GH7s, termed TrCel7A and TrCel7B. Despite having high structural and sequence similarities, the two enzymes are functionally quite different. TrCel7A is an exolytic, processive cellobiohydrolase (CBH), with high activity on crystalline cellulose, whereas TrCel7B is an endoglucanase (EG) with a preference for more amorphous cellulose. At the structural level, these functional differences are usually ascribed to the flexible loops that cover the substrate-binding areas. TrCel7A has an extensive tunnel created by eight peripheral loops, and the absence of four of these loops in TrCel7B makes its catalytic domain a more open cleft. To investigate the structure-function relationships of these loops, here we produced and kinetically characterized several variants in which four loops unique to TrCel7A were individually deleted to resemble the arrangement in the TrCel7B structure. Analysis of a range of kinetic parameters consistently indicated that the B2 loop, covering the substrate-binding subsites -3 and -4 in TrCel7A, was a key determinant for the difference in CBH- or EG-like behavior between TrCel7A and TrCel7B. Conversely, the B3 and B4 loops, located closer to the catalytic site in TrCel7A, were less important for these activities. We surmise that these results could be useful both in further mechanistic investigations and for guiding engineering efforts of this industrially important enzyme family.
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Affiliation(s)
- Corinna Schiano-di-Cola
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Nanna Røjel
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kenneth Jensen
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Jeppe Kari
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Trine Holst Sørensen
- From the Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, DK-4000 Roskilde, Denmark
| | - Kim Borch
- Novozymes A/S, Krogshøjvej 36, DK-2880 Bagsværd, Denmark, and
| | - Peter Westh
- the Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, DK-2800 Kgs. Lyngby, Denmark
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Cai C, Jin Y, Pang Y, Ke Q, Qiu W, Qiu X, Qin Y, Lou H. Tracing cellulase components in hydrolyzate during the enzymatic hydrolysis of corncob residue and its analysis. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.biteb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Du J, Zhang X, Li X, Zhao J, Liu G, Gao B, Qu Y. The cellulose binding region in Trichoderma reesei cellobiohydrolase I has a higher capacity in improving crystalline cellulose degradation than that of Penicillium oxalicum. BIORESOURCE TECHNOLOGY 2018; 266:19-25. [PMID: 29940438 DOI: 10.1016/j.biortech.2018.06.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/16/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Commercial cellulase preparations for lignocellulose bioconversion are mainly produced by the fungus Trichoderma reesei. The maximum cellulose conversion of T. reesei cellulase mixture was 15%-20% higher than that of Penicillium oxalicum in the hydrolysis of corncob residue and Avicel. Nevertheless, both preparations hydrolyzed more than 92% of cellulose in NaOH-mercerized Avicel. When added to Avicel hydrolysis residue that was less reactive to P. oxalicum cellulases, cellobiohydrolase I (CBH I) from T. reesei resulted in a higher cellulose conversion than its homologous proteins from P. oxalicum and Aspergillus niger at the same protein loadings. Further domain exchange experiment attributed the high hydrolytic efficiency of T. reesei CBH I to its inter-domain linker and cellulose-binding domain. The results in part explained the superior performance of T. reesei cellulases on the degradation of native crystalline cellulose, and highlighted the important role of cellulose-binding region in determining the degree of hydrolysis by cellulases.
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Affiliation(s)
- Jian Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China
| | - Xiu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China; Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, Shandong, PR China.
| | - Baoyu Gao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, Shandong, PR China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, PR China; National Glycoengineering Research Center, Shandong University, Qingdao 266237, Shandong, PR China
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Kostyleva EV, Tsurikova NV, Sereda A, Velikoretskaya IA, Veselkina TN, Lobanov NS, Shashkov IA, Sinitsyn A. Enhancement of Activity of Carbohydrases with Endo-depolymerase Action in Trichoderma reesei Using Mutagenesis. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Identification of Key Components for the Optimization of Cellulase Mixtures Using a Proteomic Strategy. Methods Mol Biol 2018. [PMID: 29856050 DOI: 10.1007/978-1-4939-7877-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Efficient degradation of complex lignocellulosic materials requires the synergistic action of different types of enzymes. Characterizing the compositions of lignocellulolytic enzyme mixtures could provide comprehensive understandings about the enzymatic degradation of lignocelluloses. In this chapter, we present a proteomic strategy for the analysis of enzyme mixtures produced by lignocellulolytic fungi. The described method is easy to carry out and is suitable to determine the composition of lignocellulolytic enzyme mixtures in a semiquantitative manner. Comparison of the compositions of enzyme mixtures with different degrading efficiencies allows for the identification of candidate targets for the optimization of lignocellulolytic enzyme mixtures.
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de Gouvêa PF, Bernardi AV, Gerolamo LE, de Souza Santos E, Riaño-Pachón DM, Uyemura SA, Dinamarco TM. Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse. BMC Genomics 2018; 19:232. [PMID: 29614953 PMCID: PMC5883313 DOI: 10.1186/s12864-018-4627-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sugarcane bagasse has been proposed as a lignocellulosic residue for second-generation ethanol (2G) produced by breaking down biomass into fermentable sugars. The enzymatic cocktails for biomass degradation are mostly produced by fungi, but low cost and high efficiency can consolidate 2G technologies. A. fumigatus plays an important role in plant biomass degradation capabilities and recycling. To gain more insight into the divergence in gene expression during steam-exploded bagasse (SEB) breakdown, this study profiled the transcriptome of A. fumigatus by RNA sequencing to compare transcriptional profiles of A. fumigatus grown on media containing SEB or fructose as the sole carbon source. Secretome analysis was also performed using SDS-PAGE and LC-MS/MS. RESULTS The maximum activities of cellulases (0.032 U mL-1), endo-1,4-β--xylanase (10.82 U mL-1) and endo-1,3-β glucanases (0.77 U mL-1) showed that functional CAZymes (carbohydrate-active enzymes) were secreted in the SEB culture conditions. Correlations between transcriptome and secretome data identified several CAZymes in A. fumigatus. Particular attention was given to CAZymes related to lignocellulose degradation and sugar transporters. Genes encoding glycoside hydrolase classes commonly expressed during the breakdown of cellulose, such as GH-5, 6, 7, 43, 45, and hemicellulose, such as GH-2, 10, 11, 30, 43, were found to be highly expressed in SEB conditions. Lytic polysaccharide monooxygenases (LPMO) classified as auxiliary activity families AA9 (GH61), CE (1, 4, 8, 15, 16), PL (1, 3, 4, 20) and GT (1, 2, 4, 8, 20, 35, 48) were also differentially expressed in this condition. Similarly, the most important enzymes related to biomass degradation, including endoxylanases, xyloglucanases, β-xylosidases, LPMOs, α-arabinofuranosidases, cellobiohydrolases, endoglucanases and β-glucosidases, were also identified in the secretome. CONCLUSIONS This is the first report of a transcriptome and secretome experiment of Aspergillus fumigatus in the degradation of pretreated sugarcane bagasse. The results suggest that this strain employs important strategies for this complex degradation process. It was possible to identify a set of genes and proteins that might be applied in several biotechnology fields. This knowledge can be exploited for the improvement of 2G ethanol production by the rational design of enzymatic cocktails.
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Affiliation(s)
- Paula Fagundes de Gouvêa
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Aline Vianna Bernardi
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luis Eduardo Gerolamo
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Emerson de Souza Santos
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Mauricio Riaño-Pachón
- Brazilian Bioethanol Science and Technology Laboratory, Campinas, São Paulo, Brazil
- Current address: Laboratory of Regulatory Systems Biology, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Sergio Akira Uyemura
- Faculty of Pharmaceutical Science, Department of Clinical, Toxicological and Bromatological Analysis, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Taisa Magnani Dinamarco
- Faculty of Philosophy, Sciences and Literature of Ribeirão Preto, Chemistry Department, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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Souza MFD, Silva ASD, Bon EP. A novel Trichoderma harzianum strain from the Amazon Forest with high cellulolytic capacity. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Cologna NDMD, Gómez-Mendoza DP, Zanoelo FF, Giannesi GC, Guimarães NCDA, Moreira LRDS, Filho EXF, Ricart CAO. Exploring Trichoderma and Aspergillus secretomes: Proteomics approaches for the identification of enzymes of biotechnological interest. Enzyme Microb Technol 2018; 109:1-10. [DOI: 10.1016/j.enzmictec.2017.08.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022]
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Spertino S, Boatti L, Icardi S, Manfredi M, Cattaneo C, Marengo E, Cavaletto M. Cellulomonas fimi secretomes: In vivo and in silico approaches for the lignocellulose bioconversion. J Biotechnol 2018; 270:21-29. [PMID: 29409863 DOI: 10.1016/j.jbiotec.2018.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/30/2017] [Accepted: 01/26/2018] [Indexed: 12/17/2022]
Abstract
Lignocellulose degradation is a challenging step for value added products and biofuels production. Cellulomonas fimi secretes complex mixtures of carbohydrate active enzymes (CAZymes) which synergistically degrade cellulose and hemicelluloses. Their characterization may provide new insights for enzymatic cocktails implementation. Bioinformatic analysis highlighted 1127 secreted proteins, constituting the in silico secretome, graphically represented in a 2DE map. According to Blast2GO functional annotation, many of these are involved in carbohydrates metabolism. In vivo secretomes were obtained, growing C. fimi on glucose, CMC or wheat straw for 24 h. Zymography revealed degradative activity on carbohydrates and proteomic analysis identified some CAZymes, only in secretomes obtained with CMC and wheat straw. An interaction between cellobiohydrolases is proposed as a strategy adopted by soluble multimodular cellulases. Such approach can be crucial for a better characterization and industrial exploitation of the synergism among C. fimi enzymes.
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Affiliation(s)
- Stefano Spertino
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy.
| | - Lara Boatti
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Sara Icardi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Marcello Manfredi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy; ISALIT S.r.l., Novara, Italy
| | - Chiara Cattaneo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Maria Cavaletto
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
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Lytic xylan oxidases from wood-decay fungi unlock biomass degradation. Nat Chem Biol 2018; 14:306-310. [DOI: 10.1038/nchembio.2558] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022]
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