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He J, Zeng G, Liu Z, Guo Z, Zhang W, Li Y, Zhou Y, Xu H. Replacing traditional nursery soil with spent mushroom substrate improves rice seedling quality and soil substrate properties. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:39625-39636. [PMID: 38824472 DOI: 10.1007/s11356-024-33723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/15/2024] [Indexed: 06/03/2024]
Abstract
Currently, large quantities of spent mushroom substrate (SMS) are produced annually. Because SMS has high water retention and nutrients, it has great potential to replace traditional topsoil for raising seedlings in agricultural production. However, few studies have examined the effects of substituting SMS for paddy soil on rice seedling growth and soil nutrients. SMS was mixed with rice soil in different proportions (20%, 50%, and 80%), and chemical fertilizer, organic fertilizer, and peat substrate were added in addition to equivalent nitrogen as a traditional seedling nursery method for comparison. Compared to traditional paddy soil (CK), the seedling qualities of the three SMS ratio treatments were all higher. Adding SMS at different ratios promoted rice seedling root growth, elevated the soluble protein concentration, and amplified the superoxide dismutase (SOD) enzymatic action in rice seedlings. Total porosity and aeration porosity of the soil increased by 17.40% and 32.90%, respectively. Soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) increased by 21.26-118.48%, 50.44-71.68%, and 23.08-80.17%, respectively. Besides, the relative abundance of Bacillus, Bacteroidetes, and other bacteria as well as the abundance of Ascomycota were all significantly increased. Adding 50% SMS increased the abundance of Pseudomonas by 8.42 times. The seedling quality of the 50% SMS treatment was even higher than chemical fertilizer and organic fertilizer treatments, only second to the peat substrate treatment. In summary, partial substitution of paddy soil with SMS can ameliorate substrate properties, improve seedling quality, and increase microbial diversity, indicating the suitability of SMS as a replacement for rice soil in seedling substrates. The 50% SMS ratio is the best. This study provides a basis for SMS to replace traditional rice soil in seedling cultivation.
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Affiliation(s)
- Jinfeng He
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Guiyang Zeng
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Zhihui Liu
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Zhangliang Guo
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Wenzhuo Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, People's Republic of China
| | - Yici Li
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Yaoyu Zhou
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China
| | - Huaqin Xu
- College of Environment and Ecology, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, People's Republic of China.
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Askari H, Soleimanian-Zad S, Kadivar M, Shahbazi S. Creating a novel genetic diversity of Trichoderma afroharzianum by γ-radiation for xylanase-cellulase production. Heliyon 2024; 10:e28349. [PMID: 38590889 PMCID: PMC10999882 DOI: 10.1016/j.heliyon.2024.e28349] [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: 07/24/2023] [Revised: 02/19/2024] [Accepted: 03/17/2024] [Indexed: 04/10/2024] Open
Abstract
Creating novel sources of a microbial strain using induced mutation can increase enzyme production for industrial use. According to this, we have developed a mutant strain of Trichoderma afroharzianum by Co60 gamma irradiation. Trichoderma mutants were isolated from an optimum dose of 250 Gy. The qualitative and quantitative screening were used for evaluating their enzyme production and the DNA barcoding method was used to identify the best Trichoderma mutant isolates. The highest cellulase (exo-glucanase, endoglucanase, β-glucosidase, and total cellulase) and xylanase activities were observed in superior mutant isolates of Trichoderma afroharzianum NAS107-M44 and Trichoderma afroharzianum NAS107-M82, which is approximately 1.6-2.5 times higher than its parent strain, respectively. The electrophoretic pattern of proteins showed that the exo-glucanase I, endo-glucanase III, and the xylanase I enzymes hydrolyzed the corn bran, synergistically. Overall, gamma irradiation-induced mutation could be an expedient technique to access such superior mutants for the bioconversion of corn bran wastes.
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Affiliation(s)
- Hamed Askari
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Sabihe Soleimanian-Zad
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mahdi Kadivar
- Department of Food Science and Technology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Samira Shahbazi
- Nuclear Agriculture School, Nuclear Science and Technology Research Institute (NSTRI), Atomic Energy Organization of Iran (AEOI), Karaj, Iran
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Nousi A, Molina GA, Schiano-di-Cola C, Sørensen TH, Borch K, Pedersen JN, Westh P, Marie R. Impact of Synergy Partner Cel7B on Cel7A Binding Rates: Insights from Single-Molecule Data. J Phys Chem B 2024; 128:635-647. [PMID: 38227769 PMCID: PMC10824242 DOI: 10.1021/acs.jpcb.3c05697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Enzymatic degradation of cellulosic biomass is a well-established route for the sustainable production of biofuels, chemicals, and materials. A strategy employed by nature and industry to achieve an efficient degradation of cellulose is that cellobiohydrolases (or exocellulases), such as Cel7A, work synergistically with endoglucanases, such as Cel7B, to achieve the complete degradation of cellulose. However, a complete mechanistic understanding of this exo-endo synergy is still lacking. Here, we used single-molecule fluorescence microscopy to quantify the binding kinetics of Cel7A on cellulose when it is acting alone on the cellulose fibrils and in the presence of its synergy partner, the endoglucanase Cel7B. To this end, we used a fluorescently tagged Cel7A and studied its binding in the presence of the unlabeled Cel7B. This provided the single-molecule data necessary for the estimation of the rate constants of association kON and dissociation kOFF of Cel7A for the substrate. We show that the presence of Cel7B does not impact the dissociation rate constant, kOFF. But, the association rate of Cel7A decreases by a factor of 2 when Cel7B is present at a molar proportion of 10:1. This ratio has previously been shown to lead to synergy. This decrease in association rate is observed in a wide range of total enzyme concentrations, from sub nM to μM concentrations. This decrease in kON is consistent with the formation of cellulase clusters recently observed by others using atomic force microscopy.
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Affiliation(s)
- Aimilia Nousi
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gustavo Avelar Molina
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | - Kim Borch
- Novozymes
A/S, Krogshøjvej
36, 2880 Bagsværd, Denmark
| | - Jonas N. Pedersen
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
| | - Peter Westh
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Rodolphe Marie
- Department
of Health Technology, Technical University
of Denmark, 2800 Kongens Lyngby, Denmark
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Arai T, Wada M, Nishiguchi H, Takimura Y, Ishii J. Inducer-free recombinant protein production in Trichoderma reesei: secretory production of endogenous enzymes and heterologous nanobodies using glucose as the sole carbon source. Microb Cell Fact 2023; 22:103. [PMID: 37208691 DOI: 10.1186/s12934-023-02109-y] [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: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei has been used as a host organism for the production of lignocellulosic biomass-degrading enzymes. Although this microorganism has high potential for protein production, it has not yet been widely used for heterologous recombinant protein production. Transcriptional induction of the cellulase genes is essential for high-level protein production in T. reesei; however, glucose represses this transcriptional induction. Therefore, cellulose is commonly used as a carbon source for providing its degraded sugars such as cellobiose, which act as inducers to activate the strong promoters of the major cellulase (cellobiohydrolase 1 and 2 (cbh1 and cbh2) genes. However, replacement of cbh1 and/or cbh2 with a gene encoding the protein of interest (POI) for high productivity and occupancy of recombinant proteins remarkably impairs the ability to release soluble inducers from cellulose, consequently reducing the production of POI. To overcome this challenge, we first used an inducer-free biomass-degrading enzyme expression system, previously developed to produce cellulases and hemicellulases using glucose as the sole carbon source, for recombinant protein production using T. reesei. RESULTS We chose endogenous secretory enzymes and heterologous camelid small antibodies (nanobody) as model proteins. By using the inducer-free strain as a parent, replacement of cbh1 with genes encoding two intrinsic enzymes (aspartic protease and glucoamylase) and three different nanobodies (1ZVH, caplacizumab, and ozoralizumab) resulted in their high secretory productions using glucose medium without inducers such as cellulose. Based on signal sequences (carrier polypeptides) and protease inhibitors, additional replacement of cbh2 with the nanobody gene increased the percentage of POI to about 20% of total secreted proteins in T. reesei. This allowed the production of caplacizumab, a bivalent nanobody, to be increased to 9.49-fold (508 mg/L) compared to the initial inducer-free strain. CONCLUSIONS In general, whereas the replacement of major cellulase genes leads to extreme decrease in the degradation capacity of cellulose, our inducer-free system enabled it and achieved high secretory production of POI with increased occupancy in glucose medium. This system would be a novel platform for heterologous recombinant protein production in T. reesei.
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Affiliation(s)
- Toshiharu Arai
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Mayumi Wada
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan
| | - Hiroki Nishiguchi
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan
| | - Yasushi Takimura
- Biological Science Research, Kao Corporation, 1334 Minato, Wakayama, 640‑8580, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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Liu B, Xia H, Jiang C, Riaz M, Yang L, Chen Y, Fan X, Xia X. 14 year applications of chemical fertilizers and crop straw effects on soil labile organic carbon fractions, enzyme activities and microbial community in rice-wheat rotation of middle China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156608. [PMID: 35700778 DOI: 10.1016/j.scitotenv.2022.156608] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Traditional fertilization management can damage soil structure and lead to severe soil erosion. The practice of crop straw returning to the field reduces the negative impact of straw burning and improves soil quality. We investigated the effects of these agricultural practices on soil organic carbon components, enzyme activities, and soil microorganisms over 14 years of field experiments. Specifically, we studied four management strategies: no fertilizer or crop straw returning (CK), traditional chemical fertilization (NPK), crop straw returning (S), and crop straw returning with chemical fertilizer (NPKS). We found NPKS treatments significantly (P < 0.05) increased the dissolved organic carbon (DOC), microbial biomass carbon (MBC), particulate organic carbon (POC) and readily oxidized organic carbon (ROC) concentrations by 79.32 %, 82.16 %, 92.46 %, and 104.32 % relative to CK. Furthermore, under NPKS, the activities of soil enzymes related C, N, and P (α-glucosidase (αG), β-glucosidase (βG), cellulase (CBH), xylanase (βX), acetyl β-glucosaminidase (NAG), leucine aminopeptidase (LAP), and acid phosphate (AP)) were increased by 54.66 %, 113.26 %, 76.73 %, 52.41 %, 45.74 %, 56.69 %, and 68.92 % relative to CK, respectively. Redundancy analysis and structural equation modelling showed that straw returning had positive effects on soil microbial community diversity and richness, and also improved microbial activity which is favorable in the degradation of soil carbon. Furthermore, we found that soil fungi were more sensitive than bacteria to changes in soil carbon composition and enzyme activities following straw returning. These results suggest that straw returning combined with chemical fertilizer can be an effective strategy to improve soil labile organic carbon components, enzyme activities, and ecological function of microorganisms.
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Affiliation(s)
- Bo Liu
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, PR China
| | - Hao Xia
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China; The Key Laboratory of Oasis Ecoagriculture, Xinjiang Production and Construction Corps, Shihezi University, Shihezi, Xinjiang 832000, PR China
| | - Muhammad Riaz
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, PR China
| | - Li Yang
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, PR China
| | - Yunfeng Chen
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, PR China
| | - Xianpeng Fan
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, PR China
| | - Xiange Xia
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, PR China.
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Abstract
The depletion of fossil fuel resources and the negative impact of their use on the climate have resulted in the need for alternative sources of clean, sustainable energy. One available alternative, bioethanol, is a potential substitute for, or additive to, petroleum-derived gasoline. In the lignocellulose-to-bioethanol process, the cellulose hydrolysis step represents a major hurdle that hinders commercialization. To achieve economical production of bioethanol from lignocellulosic materials, the rate and yield of the enzymatic hydrolysis of cellulose, which is preferred over other chemically catalyzed processes, must be enhanced. To achieve this, product inhibition and enzyme loss, which are two major challenges, must be overcome. The implementation of membranes, which can permeate molecules selectively based on their size, offers a solution to this problem. Membrane bioreactors (MBRs) can enhance enzymatic hydrolysis yields and lower costs by retaining enzymes for repeated usage while permeating the products. This paper presents a critical discussion of the use of MBRs as a promising approach to the enhanced enzymatic hydrolysis of cellulosic materials. Various MBR configurations and factors that affect their performance are presented.
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7
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Zajki-Zechmeister K, Eibinger M, Nidetzky B. Enzyme Synergy in Transient Clusters of Endo- and Exocellulase Enables a Multilayer Mode of Processive Depolymerization of Cellulose. ACS Catal 2022; 12:10984-10994. [PMID: 36082050 PMCID: PMC9442579 DOI: 10.1021/acscatal.2c02377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Biological degradation of cellulosic materials relies on the molecular-mechanistic principle that internally chain-cleaving endocellulases work synergistically with chain end-cleaving exocellulases in polysaccharide chain depolymerization. How endo-exo synergy becomes effective in the deconstruction of a solid substrate that presents cellulose chains assembled into crystalline material is an open question of the mechanism, with immediate implications on the bioconversion efficiency of cellulases. Here, based on single-molecule evidence from real-time atomic force microscopy, we discover that endo- and exocellulases engage in the formation of transient clusters of typically three to four enzymes at the cellulose surface. The clusters form specifically at regular domains of crystalline cellulose microfibrils that feature molecular defects in the polysaccharide chain organization. The dynamics of cluster formation correlates with substrate degradation through a multilayer-processive mode of chain depolymerization, overall leading to the directed ablation of single microfibrils from the cellulose surface. Each multilayer-processive step involves the spatiotemporally coordinated and mechanistically concerted activity of the endo- and exocellulases in close proximity. Mechanistically, the cooperativity with the endocellulase enables the exocellulase to pass through its processive cycles ∼100-fold faster than when acting alone. Our results suggest an advanced paradigm of efficient multienzymatic degradation of structurally organized polymer materials by endo-exo synergetic chain depolymerization.
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Affiliation(s)
- Krisztina Zajki-Zechmeister
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Manuel Eibinger
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute
of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 10-12/1, 8010 Graz, Austria
- Austrian
Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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Anuganti M, Fu H, Ekatan S, Kumar CV, Lin Y. Kinetic Study on Enzymatic Hydrolysis of Cellulose in an Open, Inhibition-Free System. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5180-5192. [PMID: 33872034 DOI: 10.1021/acs.langmuir.1c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Due to the complexity of cellulases and the requirement of enzyme adsorption on cellulose prior to reactions, it is difficult to evaluate their reaction with a general mechanistic scheme. Nevertheless, it is of great interest to come up with an approximate analytic description of a valid model for the purpose of developing an intuitive understanding of these complex enzyme systems. Herein, we used the surface plasmonic resonance method to monitor the action of a cellobiohydrolase by itself, as well as its mixture with a synergetic endoglucanase, on the surface of a regenerated model cellulose film, under continuous flow conditions. We found a phenomenological approach by taking advantage of the long steady state of cellulose hydrolysis in the open, inhibition-free system. This provided a direct and reliable way to analyze the adsorption and reaction processes with a minimum number of fitting parameters. We investigated a generalized Langmuir-Michaelis-Menten model to describe a full set of kinetic results across a range of enzyme concentrations, compositions, and temperatures. The overall form of the equations describing the pseudo-steady-state kinetics of the flow-system shares some interesting similarities with the Michaelis-Menten equation. The use of familiar Michaelis-Menten parameters in the analysis provides a unifying framework to study cellulase kinetics. The strategy may provide a shortcut for approaching a quantitative while intuitive understanding of enzymatic degradation of cellulose from top to bottom. The open system approach and the kinetic analysis should be applicable to a variety of cellulases and reaction systems to accelerate the progress in the field.
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Affiliation(s)
- Murali Anuganti
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Hailin Fu
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Stephen Ekatan
- Polymer Program, Institute of Material Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Challa V Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Yao Lin
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
- Polymer Program, Institute of Material Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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Meng QS, Zhang F, Liu CG, Bai FW, Zhao XQ. Measurement of Cellulase and Xylanase Activities in Trichoderma reesei. Methods Mol Biol 2021; 2234:135-146. [PMID: 33165786 DOI: 10.1007/978-1-0716-1048-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The microbial cellulase system is responsible for the generation of glucose from cellulose. Cellulases are comprised of at least three major groups of enzymes, namely endoglucanases, exoglucanases, and β-glucosidases. On the other hand, xylanases function in the degradation of hemicellulose and work synergistically with cellulases for the degradation of lignocellulosic biomass. Here, we describe the most commonly used methods for the activity measurement of cellulases and xylanases.
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Affiliation(s)
- Qing-Shan Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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10
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Ren M, Wang Y, Liu G, Zuo B, Zhang Y, Wang Y, Liu W, Liu X, Zhong Y. The effects of deletion of cellobiohydrolase genes on carbon source-dependent growth and enzymatic lignocellulose hydrolysis in Trichoderma reesei. J Microbiol 2020; 58:687-695. [PMID: 32524344 DOI: 10.1007/s12275-020-9630-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
The saprophytic fungus Trichoderma reesei has long been used as a model to study microbial degradation of lignocellulosic biomass. The major cellulolytic enzymes of T. reesei are the cellobiohydrolases CBH1 and CBH2, which constitute more than 70% of total proteins secreted by the fungus. However, their physiological functions and effects on enzymatic hydrolysis of cellulose substrates are not sufficiently elucidated. Here, the cellobiohydrolase-encoding genes cbh1 and cbh2 were deleted, individually or combinatively, by using an auxotrophic marker-recycling technique in T. reesei. When cultured on media with different soluble carbon sources, all three deletion strains (Δcbh1, Δcbh2, and Δcbh1Δcbh2) exhibited no dramatic variation in morphological phenotypes, but their growth rates increased apparently when cultured on soluble cellulase-inducing carbon sources. In addition, Δcbh1 showed dramatically reduced growth and Δcbh1Δcbh2 could hardly grew on microcrystalline cellulose (MCC), whereas all strains grew equally on sodium carboxymethyl cellulose (CMC-Na), suggesting that the influence of the CBHs on growth was carbon source-dependent. Moreover, five representative cellulose substrates were used to analyse the influence of the absence of CBHs on saccharification efficiency. CBH1 deficiency significantly affected the enzymatic hydrolysis rates of various cellulose substrates, where acid pre-treated corn stover (PCS) was influenced the least. CBH2 deficiency reduced the hydrolysis of MCC, PCS, and acid pre-treated and delignified corncob but improved the hydrolysis ability of filter paper. These results demonstrate the specific contributions of CBHs to the hydrolysis of different types of biomass, which could facilitate the development of tailor-made strains with highly efficient hydrolysis enzymes for certain biomass types in the biofuel industry.
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Affiliation(s)
- Meibin Ren
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Yifan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Guoxin Liu
- Zibo Center Hospital, Zi Bo, 255036, P. R. China
| | - Bin Zuo
- Leling Shengli New Energy Co., Ltd., Leling, 253600, P. R. China
| | - Yuancheng Zhang
- Leling Shengli New Energy Co., Ltd., Leling, 253600, P. R. China
| | - Yunhe Wang
- Leling Shengli New Energy Co., Ltd., Leling, 253600, P. R. China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Xiangmei Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China.
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China.
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11
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Enzymatic Hydrolysis of Softwood Derived Paper Sludge by an In Vitro Recombinant Cellulase Cocktail for the Production of Fermentable Sugars. Catalysts 2020. [DOI: 10.3390/catal10070775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Paper sludge is an attractive biomass feedstock for bioconversion to ethanol due to its low cost and the lack of pretreatment required for its bioprocessing. This study assessed the use of a recombinant cellulase cocktail (mono-components: S. cerevisiae-derived PcBGL1B (BGL), TeCel7A (CBHI), ClCel6A (CBHII) and TrCel5A (EGII) mono-component cellulase enzymes) for the efficient saccharification of softwood-derived paper sludge to produce fermentable sugars. The paper sludge mainly contained 74.3% moisture and 89.7% (per dry mass (DM)) glucan with a crystallinity index of 91.5%. The optimal protein ratio for paper sludge hydrolysis was observed at 9.4: 30.2: 30.2: 30.2% for BGL: CBHI: CBHII: EGII. At a protein loading of 7.5 mg/g DW paper sludge, the yield from hydrolysis was approximately 80%, based on glucan, with scanning electron microscopy micrographs indicating a significant alteration in the microfibril size (length reduced from ≥ 2 mm to 93 µm) of the paper sludge. The paper sludge hydrolysis potential of the Opt CelMix (formulated cellulase cocktail) was similar to the commercial Cellic CTec2® and Celluclast® 1.5 L cellulase preparations and better than Viscozyme® L. Low enzyme loadings (15 mg/g paper sludge) of the Opt CelMix and solid loadings ranging between 1 to 10% (w/v) rendered over 80% glucan conversion. The high glucose yields attained on the paper sludge by the low enzyme loading of the Opt CelMix demonstrated the value of enzyme cocktail optimisation on specific substrates for efficient cellulose conversion to fermentable sugars.
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Fernandes ÉS, Bueno D, Pagnocca FC, Brienzo M. Minor Biomass Particle Size for an Efficient Cellulose Accessibility and Enzymatic Hydrolysis. ChemistrySelect 2020. [DOI: 10.1002/slct.202001008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Érika S. Fernandes
- São Paulo State University (UNESP) Institute for Research in Bioenergy (IPBEN) Rio Claro-SP 13500-230 Brazil
| | - Danilo Bueno
- São Paulo State University (UNESP) Institute for Research in Bioenergy (IPBEN) Rio Claro-SP 13500-230 Brazil
| | - Fernando C. Pagnocca
- São Paulo State University (UNESP) Center for the Study of Social Insects (CEIS) Rio Claro, SP 13500-230 Brazil
| | - Michel Brienzo
- São Paulo State University (UNESP) Institute for Research in Bioenergy (IPBEN) Rio Claro-SP 13500-230 Brazil
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13
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Mohamad Sobri MF, Abd-Aziz S, Abu Bakar FD, Ramli N. In-Silico Characterization of Glycosyl Hydrolase Family 1 β-Glucosidase from Trichoderma asperellum UPM1. Int J Mol Sci 2020; 21:ijms21114035. [PMID: 32512945 PMCID: PMC7311958 DOI: 10.3390/ijms21114035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
β-glucosidases (Bgl) are widely utilized for releasing non-reducing terminal glucosyl residues. Nevertheless, feedback inhibition by glucose end product has limited its application. A noticeable exception has been found for β-glucosidases of the glycoside hydrolase (GH) family 1, which exhibit tolerance and even stimulation by glucose. In this study, using local isolate Trichoderma asperellum UPM1, the gene encoding β-glucosidase from GH family 1, hereafter designated as TaBgl2, was isolated and characterized via in-silico analyses. A comparison of enzyme activity was subsequently made by heterologous expression in Escherichia coli BL21(DE3). The presence of N-terminal signature, cis-peptide bonds, conserved active site motifs, non-proline cis peptide bonds, substrate binding, and a lone conserved stabilizing tryptophan (W) residue confirms the identity of Trichoderma sp. GH family 1 β-glucosidase isolated. Glucose tolerance was suggested by the presence of 14 of 22 known consensus residues, along with corresponding residues L167 and P172, crucial in the retention of the active site's narrow cavity. Retention of 40% of relative hydrolytic activity on ρ-nitrophenyl-β-D-glucopyranoside (ρNPG) in a concentration of 0.2 M glucose was comparable to that of GH family 1 β-glucosidase (Cel1A) from Trichoderma reesei. This research thus underlines the potential in the prediction of enzymatic function, and of industrial importance, glucose tolerance of family 1 β-glucosidases following relevant in-silico analyses.
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Affiliation(s)
- Mohamad Farhan Mohamad Sobri
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.F.M.S.); (S.A.-A.)
- School of Bioprocess Engineering, Universiti Malaysia Perlis, Kompleks Pusat Pengajian Jejawi 3, Arau 02600, Perlis, Malaysia
| | - Suraini Abd-Aziz
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.F.M.S.); (S.A.-A.)
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600 UKM, Selangor, Malaysia;
| | - Norhayati Ramli
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400 UPM, Selangor, Malaysia; (M.F.M.S.); (S.A.-A.)
- Correspondence: ; Tel.: +60-3-9769-1948
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Li H, Yi S, Bell EW, Huang Q, Zhao X. Recombinant Penicillium oxalicum 16 β-Glucosidase 1 Displays Comprehensive Inhibitory Resistance to Several Lignocellulose Pretreatment Products, Ethanol, and Salt. Appl Biochem Biotechnol 2020; 191:772-784. [PMID: 31858406 PMCID: PMC7427447 DOI: 10.1007/s12010-019-03183-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/11/2019] [Indexed: 11/29/2022]
Abstract
β-Glucosidase (BGL) is a rate-limiting enzyme of lignocellulose hydrolysis for second-generation bioethanol production, but its inhibition by lignocellulose pretreatment products, ethanol, and salt is apparent. Here, the recombinant Penicillium oxalicum 16 BGL 1 (rPO16BGL1) from Pichia pastoris GS115 kept complete activity at 0.2-1.4 mg/mL furan derivatives and phenolic compounds, 50 mg/mL sodium chloride (potassium chloride), or 100 mg/mL ethanol at 40 °C. rPO16BGL1 retained above 50% residual activity at 30 mg/mL organic acid sodium, and 60% residual activity at 40 °C with 300 mg/mL ethanol. Sodium chloride and potassium chloride had a complicated effect on rPO16BGL1, which resulted in activation or inhibition. The inhibition kinetics of the enzyme reaction demonstrated that organic acids and organic acid sodium were non-competitive inhibitors and that ethanol was a competitive inhibitor at < 1.5 mg/mL salicin. Moreover, substrate inhibition of the enzyme was found at > 2 mg/mL salicin, and the Km/KI and Km/KSI average values revealed that the inhibitory strength was ranked as salicin-organic acids > organic acids > salicin-organic acid sodium salt > organic acid sodium salt > salicin > salicin-KCl > salicin-NaCl > salicin-ethanol > ethanol.
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Affiliation(s)
- Hanxin Li
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Shi Yi
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Eric W Bell
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Qiuxia Huang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China.
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15
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Composition of Synthesized Cellulolytic Enzymes Varied with the Usage of Agricultural Substrates and Microorganisms. Appl Biochem Biotechnol 2020; 191:1695-1710. [PMID: 32206967 DOI: 10.1007/s12010-020-03297-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/12/2020] [Indexed: 10/25/2022]
Abstract
We evaluated various agricultural lignocellulosic biomass and variety of fungi to produce cellulolytic enzymes cocktail to yield high amount of reducing sugars. Solid-state fermentation was performed using water hyacinth, paddy straw, corn straw, soybean husk/tops, wheat straw, and sugarcane bagasse using fungi like Nocardiopsis sp. KNU, Trichoderma reesei, Trichoderma viride, Aspergillus flavus, and Phanerochaete chrysosporium alone and in combination to produce cellulolytic enzymes. Water hyacinth produced (U ml-1) endoglucanase (51.13) and filter paperase (0.55), and corn straw produced (U ml-1) β-glucosidase (4.65), xylanase (113.32), and glucoamylase (41.27) after 7-day incubation using Nocardiopsis sp. KNU. Production of cellulolytic enzymes was altered due to addition of various nitrogen sources, metal ions, vitamins, and amino acids. The maximum cellulolytic enzymes were produced by P. chrysosporium (endoglucanase; 166.32 U ml-1 and exoglucanase; 12.20 U ml-1), and by T. viride (filter paperase; 1.57 U ml-1). Among all, co-culture of T. reesei, T. viride, A. flavus, and P. chrysosporium showed highest β-glucosidase (17.05 U ml-1). The highest xylanase (1129 U ml-1) was observed in T. viride + P. chrysosporium co-culture. This study revealed the dependency on substrate and microorganism to produce good quality enzyme cocktail to obtain maximum reducing sugars.
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16
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Galiwango E, Abdel Rahman NS, Al-Marzouqi AH, Abu-Omar MM, Khaleel AA. Isolation and characterization of cellulose and α-cellulose from date palm biomass waste. Heliyon 2019; 5:e02937. [PMID: 32382665 PMCID: PMC7201136 DOI: 10.1016/j.heliyon.2019.e02937] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/11/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
Towards the utilization of different parts of date palm biomass waste, low-concentration acid-alkali treatment was used to isolate the contained cellulose and α-cellulose. The cellulose yields achieved from the rachis, leaflet, and fiber parts of the biomass were 74.70%, 71.50%, and 73.82%, respectively, while the corresponding α-cellulose yields were 78.63%, 75.64%, and 70.40%, respectively. The cellulose samples were bleached and characterized by thermogravimetric analysis (TGA), Fourier-transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), and X-ray diffraction (XRD). The XRD results revealed high crystallinity of both the cellulose and α-cellulose samples, while the TGA thermograms indicated that the alkali treatment completely removed lignin and hemicelluloses from the rachis. The results of this study demonstrate the promise of using date palm biomass waste as raw material to produce cellulose and α-cellulose.
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Affiliation(s)
- Emmanuel Galiwango
- Department of Chemical and Petroleum Engineering, United Arab Emirates University, P. O. Box 15551, Al Ain, United Arab Emirates
| | - Nour S. Abdel Rahman
- Department of Chemical and Petroleum Engineering, United Arab Emirates University, P. O. Box 15551, Al Ain, United Arab Emirates
| | - Ali H. Al-Marzouqi
- Department of Chemical and Petroleum Engineering, United Arab Emirates University, P. O. Box 15551, Al Ain, United Arab Emirates
- Corresponding author.
| | - Mahdi M. Abu-Omar
- Department of Chemistry and Biochemistry and Biochemistry, UC Santa Barbara, Santa Barbara, CA, 93106-9510, USA
| | - Abbas A. Khaleel
- Department of Chemistry, United Arab Emirates University, P. O. Box 15551, Al Ain, United Arab Emirates
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Nguyen KA, Kumla J, Suwannarach N, Penkhrue W, Lumyong S. Optimization of high endoglucanase yields production from polypore fungus, Microporus xanthopus strain KA038 under solid-state fermentation using green tea waste. Biol Open 2019; 8:bio.047183. [PMID: 31784423 PMCID: PMC6899011 DOI: 10.1242/bio.047183] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Polypores are diverse macrofungi that have been extensively studied for their lignocellulolytic enzyme production capabilities. Currently, these enzymes are being used for many industrial purposes. However, the high cost associated with their production is the main barrier to their broader application. This work aimed to study the optimal medium and conditions for endoglucanase production using solid state fermentation. Seven polypore strains were used for endoglucanase activity screening. The fermentation experiments were carried out in 250 ml Erlenmeyer flasks with green tea waste as a substrate. Notably, Microporus xanthopus strain KA038 showed the best level of activity (38.62 IU/gds). Various parameters such as moisture content, nitrogen source, initial pH value, inoculum size and incubation time were considered to determine the optimal conditions for endoglucanase production. The optimal medium consisted of green tea leaves as a carbon source, beef extract as an organic nitrogen source, NH4H2PO4 as an inorganic nitrogen source, pH 7.0 and an incubation temperature at 30°C for 4 days resulted in a high enzyme yield with M. xanthopus strain KA038 (81.8 IU/gds).This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Kim Anh Nguyen
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Master's Degree Program in Applied Microbiology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand .,Center of Excellence in Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Academy of Science, The Royal Society of Thailand, Dusit, Bangkok 10300, Thailand
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18
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Release of sugars and fatty acids from heavy oil biodegradation by common hydrolytic enzymes. Sci Rep 2019; 9:15584. [PMID: 31666548 PMCID: PMC6821806 DOI: 10.1038/s41598-019-51796-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/06/2019] [Indexed: 11/25/2022] Open
Abstract
In response to recent advances in understanding relating to the remarkable persistence of soil organic matter during burial and diagenesis, we examine the extent to which bitumen compositionally reflects the soil organic matter from which it was derived. Through a simple set of experiments, exposure of bitumen to lipase and cellulase, two enzymes effective in the biodegradation of soil organic matter, resulted in the release of glycerin, palmitic and oleic fatty acids from lipase digestion in addition to the release of glucose, alkylphenols and acyclic polyols from fermentation with cellulase, consistent with the products expected these enzymes. These results are significant in that they suggest that heavy oils are more similar to their soil precursor than previously thought, that biodegradation of bitumen can be accelerated using common over the counter enzymes in aerobic conditions and that heavy oils, which are 1000 times more abundant than coal, can release similar biomolecules as those generated in bioreactor culture or biomass harvest, using two of the most abundantly produced enzymes presently available.
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19
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Yoav S, Stern J, Salama-Alber O, Frolow F, Anbar M, Karpol A, Hadar Y, Morag E, Bayer EA. Directed Evolution of Clostridium thermocellum β-Glucosidase A Towards Enhanced Thermostability. Int J Mol Sci 2019; 20:E4701. [PMID: 31547488 PMCID: PMC6801902 DOI: 10.3390/ijms20194701] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 12/27/2022] Open
Abstract
β-Glucosidases are key enzymes in the process of cellulose utilization. It is the last enzyme in the cellulose hydrolysis chain, which converts cellobiose to glucose. Since cellobiose is known to have a feedback inhibitory effect on a variety of cellulases, β-glucosidase can prevent this inhibition by hydrolyzing cellobiose to non-inhibitory glucose. While the optimal temperature of the Clostridium thermocellum cellulosome is 70 °C, C. thermocellum β-glucosidase A is almost inactive at such high temperatures. Thus, in the current study, a random mutagenesis directed evolutionary approach was conducted to produce a thermostable mutant with Kcat and Km, similar to those of the wild-type enzyme. The resultant mutant contained two mutations, A17S and K268N, but only the former was found to affect thermostability, whereby the inflection temperature (Ti) was increased by 6.4 °C. A17 is located near the central cavity of the native enzyme. Interestingly, multiple alignments revealed that position 17 is relatively conserved, whereby alanine is replaced only by serine. Upon the addition of the thermostable mutant to the C. thermocellum secretome for subsequent hydrolysis of microcrystalline cellulose at 70 °C, a higher soluble glucose yield (243%) was obtained compared to the activity of the secretome supplemented with the wild-type enzyme.
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Affiliation(s)
- Shahar Yoav
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Orly Salama-Alber
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Michael Anbar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Alon Karpol
- CelDezyner, 2 Bergman St, Tamar Science Park, Rehovot 7670504, Israel.
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, the Advanced School for Environmental Studies, The Hebrew University of Jerusalem, Rehovot 76100, Israel.
| | - Ely Morag
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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Gatt E, Khatri V, Bley J, Barnabé S, Vandenbossche V, Beauregard M. Enzymatic hydrolysis of corn crop residues with high solid loadings: New insights into the impact of bioextrusion on biomass deconstruction using carbohydrate-binding modules. BIORESOURCE TECHNOLOGY 2019; 282:398-406. [PMID: 30884460 DOI: 10.1016/j.biortech.2019.03.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Lignocellulosic biomass is a sustainable source of renewable substrate to produce low carbon footprint energy and materials. Biomass conversion is usually performed in two steps: a biomass pretreatment for improving cellulose accessibility followed by enzymatic hydrolysis of cellulose. In this study we investigated the efficiency of a bioextrusion pretreatment (extrusion in the presence of cellulase enzyme) for production of reducing sugars from corn crop agricultural residues. Our results demonstrate that bioextrusion increased the reducing sugar conversion yield by at least 94% at high solid/liquid ratio (14%-40%). Monitoring biomass surface with carbohydrate-binding modules (FTCM-depletion assay) revealed that well known negative impact of high solid/liquid ratio on conversion yield is not due to the lack of exposed cellulose which was abundant under such conditions. Bioextrusion was found to be less efficient on alkaline pretreated biomass but being a mild and solvent limiting pretreatment, it might help to minimize the waste stream.
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Affiliation(s)
- Etienne Gatt
- Laboratoire de Chimie Agro-industrielle, LCA, Université de Toulouse, INRA, Toulouse, France.
| | - Vinay Khatri
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; PROTEO, Université Laval, Québec G1V 4G2, Canada.
| | - Julien Bley
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, Canada; Innofibre, 3351 Boulevard des Forges, Québec G9A 5E6, Canada
| | - Simon Barnabé
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, Canada
| | - Virginie Vandenbossche
- Laboratoire de Chimie Agro-industrielle, LCA, Université de Toulouse, INRA, Toulouse, France.
| | - Marc Beauregard
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, Canada; PROTEO, Université Laval, Québec G1V 4G2, Canada
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Valenzuela SV, Valls C, Schink V, Sánchez D, Roncero MB, Diaz P, Martínez J, Pastor FJ. Differential activity of lytic polysaccharide monooxygenases on celluloses of different crystallinity. Effectiveness in the sustainable production of cellulose nanofibrils. Carbohydr Polym 2019; 207:59-67. [DOI: 10.1016/j.carbpol.2018.11.076] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/20/2018] [Accepted: 11/23/2018] [Indexed: 01/14/2023]
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Li P, Zhang C, Xu D. Molecular dynamics investigations of cello-oligosaccharide recognition by Cel9G-CBM3c from Clostridium cellulovorans. Phys Chem Chem Phys 2018; 20:5235-5245. [PMID: 29399685 DOI: 10.1039/c7cp07175b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The processive mechanism of cellulases against cellulose represents one of the key mechanisms in the conversion of biomass. A reliable model of substrate binding in a multidomain cellulase is a prerequisite for fully understanding this mechanism. In this study, the specificity of the recognition of the polysaccharide by the multidomain endoglucanase Cel9G from Clostridium cellulovorans was investigated by molecular dynamics simulations. Aromatic ring-containing residues were found to be critical for stabilizing the substrate. The calculated subtotal contributions of polar residues close to the active site, e.g., D58, E244, R315 and D420, also have some critical functions in substrate binding. Unlike other members of the carbohydrate-binding module family, CBM3c alone is shown not to bind cellulose very well, which is also consistent with experimental conclusions.
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Affiliation(s)
- Penghui Li
- MOE Key Laboratory of Green Chemistry, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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23
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Kucharska K, Rybarczyk P, Hołowacz I, Łukajtis R, Glinka M, Kamiński M. Pretreatment of Lignocellulosic Materials as Substrates for Fermentation Processes. Molecules 2018; 23:E2937. [PMID: 30423814 PMCID: PMC6278514 DOI: 10.3390/molecules23112937] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022] Open
Abstract
Lignocellulosic biomass is an abundant and renewable resource that potentially contains large amounts of energy. It is an interesting alternative for fossil fuels, allowing the production of biofuels and other organic compounds. In this paper, a review devoted to the processing of lignocellulosic materials as substrates for fermentation processes is presented. The review focuses on physical, chemical, physicochemical, enzymatic, and microbiologic methods of biomass pretreatment. In addition to the evaluation of the mentioned methods, the aim of the paper is to understand the possibilities of the biomass pretreatment and their influence on the efficiency of biofuels and organic compounds production. The effects of different pretreatment methods on the lignocellulosic biomass structure are described along with a discussion of the benefits and drawbacks of each method, including the potential generation of inhibitory compounds for enzymatic hydrolysis, the effect on cellulose digestibility, the generation of compounds that are toxic for the environment, and energy and economic demand. The results of the investigations imply that only the stepwise pretreatment procedure may ensure effective fermentation of the lignocellulosic biomass. Pretreatment step is still a challenge for obtaining cost-effective and competitive technology for large-scale conversion of lignocellulosic biomass into fermentable sugars with low inhibitory concentration.
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Affiliation(s)
- Karolina Kucharska
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Piotr Rybarczyk
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Iwona Hołowacz
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Rafał Łukajtis
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Marta Glinka
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
- Department of Analytical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
| | - Marian Kamiński
- Department of Process Engineering and Chemical Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland.
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Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B. Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. Chem Rev 2018; 118:2593-2635. [PMID: 29155571 PMCID: PMC5982588 DOI: 10.1021/acs.chemrev.7b00421] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M. Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Bradley Kelemen
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
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Ramakrishnan S, Brodeur G, Telotte JC. Analysis of the Long Time Behavior of Enzymatic Cellulose Hydrolysis Kinetics. INTERNATIONAL JOURNAL OF CHEMICAL REACTOR ENGINEERING 2018. [DOI: 10.1515/ijcre-2017-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractEnzymatic hydrolysis of biomass to produce sugars that can be converted to fuels and other valuable chemicals, is viewed as the prime technology for utilization of this renewable resource. To accelerate technology development, models are needed that are able to accurately predict the hydrolysis rate so that reactors can be tailored to the multitude of processing conditions and substrates that can be used. Of particular interest is the ability to predict the long time conversion in the hydrolysis reaction which dictates the maximum possible sugar concentration. It is our aim in this article to develop a simple model which is able to predict the long-term conversion of cellulose to soluble sugars. Drawing on the analogy from the theory of reactions in continuous mixtures, it is shown that analysis of the long time kinetics of hydrolysis by examining the behavior of the “lump” of the reacting material results in a simple expression which is capable of predicting the kinetics. Many features of actual enzyme systems can be included in the development of the hydrolysis model, such as the large size of the enzyme molecules, adsorption onto substrate, inhibition by different factors (solvent, glucose etc.), but, when the analysis is carried out to calculate the total sugar concentration, it is shown that the equations reduce to a simple expression. Analysis of this model is given with comparison to other models and experimental data available in the literature. In addition to predicting the long-term kinetics, it is shown that the model does a surprising job of predicting the initial hydrolysis rates as well.
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Khatri V, Meddeb-Mouelhi F, Adjallé K, Barnabé S, Beauregard M. Determination of optimal biomass pretreatment strategies for biofuel production: investigation of relationships between surface-exposed polysaccharides and their enzymatic conversion using carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:144. [PMID: 29796085 PMCID: PMC5960114 DOI: 10.1186/s13068-018-1145-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/09/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Pretreatment of lignocellulosic biomass (LCB) is a key step for its efficient bioconversion into ethanol. Determining the best pretreatment and its parameters requires monitoring its impacts on the biomass material. Here, we used fluorescent protein-tagged carbohydrate-binding modules method (FTCM)-depletion assay to study the relationship between surface-exposed polysaccharides and enzymatic hydrolysis of LCB. RESULTS Our results indicated that alkali extrusion pretreatment led to the highest hydrolysis rates for alfalfa stover, cattail stems and flax shives, despite its lower lignin removal efficiency compared to alkali pretreatment. Corn crop residues were more sensitive to alkali pretreatments, leading to higher hydrolysis rates. A clear relationship was consistently observed between total surface-exposed cellulose detected by the FTCM-depletion assay and biomass enzymatic hydrolysis. Comparison of bioconversion yield and total composition analysis (by NREL/TP-510-42618) of LCB prior to or after pretreatments did not show any close relationship. Lignin removal efficiency and total cellulose content (by NREL/TP-510-42618) led to an unreliable prediction of enzymatic polysaccharide hydrolysis. CONCLUSIONS Fluorescent protein-tagged carbohydrate-binding modules method (FTCM)-depletion assay provided direct evidence that cellulose exposure is the key determinant of hydrolysis yield. The clear and robust relationships that were observed between the cellulose accessibility by FTCM probes and enzymatic hydrolysis rates change could be evolved into a powerful prediction tool that might help develop optimal biomass pretreatment strategies for biofuel production.
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Affiliation(s)
- Vinay Khatri
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- PROTEO, Université Laval, Québec, QC G1V 4G2 Canada
| | - Fatma Meddeb-Mouelhi
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- PROTEO, Université Laval, Québec, QC G1V 4G2 Canada
| | - Kokou Adjallé
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
| | - Simon Barnabé
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
| | - Marc Beauregard
- Centre de recherche sur les matériaux lignocellulosiques, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7 Canada
- PROTEO, Université Laval, Québec, QC G1V 4G2 Canada
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Abstract
Cellulosic biomass, the most common organic compound of primary energy source on earth, is a network of interwoven biopolymers of plant cell walls. Degradation of cellulose is important for global carbon recycling. Moreover, biofuel, a renewable fuel whose energy can be derived from cellulosic biomass by enzymatic hydrolysis of cellulases. Among cellulases are endoglucases that act synergistically for subsequent hydrolytic reactions to break down the polymeric cellulose. However, in cellulolytic enzyme activity endoglucanase plays a prominent role in initiating and sustaining the hydrolytic process. Endoglucanase randomly cleaves the cellulose polymer into smaller sugar and oligomeric polysaccharides. Characterization and quantification of endoglucanase activity is important for industry and in the overall study of cellulose degradation. All assays including those for endoglucanase fall into two broad categories either qualitative or quantitative. Quantitative assays can tell if the enzyme is present, how much and its activity. Measurement can be done indirectly using a secondary colorimetric product like (1) molybdenum blue, (2) 3-amino-5-nitrosalicylic acid, (3) bicinchoninic acid (BCA), and (4) 2-cyanoacetamide or directly using an antibody in an ELISA. In this chapter, we discuss several common protocols for the measurement of endoglucanase activity.
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Affiliation(s)
- M Shafiqur Rahman
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Sheran Fernando
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Brian Ross
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
- Northern Ontario School of Medicine, Thunder Bay, ON, Canada
| | - Jiangning Wu
- Department of Chemical Engineering, Ryerson University, Toronto, ON, Canada
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
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Kumar D, Murthy GS. Development and validation of a stochastic molecular model of cellulose hydrolysis by action of multiple cellulase enzymes. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0184-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Gaikwad A. Interactions of mixing and reaction kinetics of depolymerization of cellulose to renewable fuels. CHEM ENG COMMUN 2017. [DOI: 10.1080/00986445.2017.1371015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ashwin Gaikwad
- Department of Chemical Engineering, Visvesvaraya National Institute of Technology, Nagpur, India
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30
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Kansou K, Rémond C, Paës G, Bonnin E, Tayeb J, Bredeweg B. Testing scientific models using Qualitative Reasoning: Application to cellulose hydrolysis. Sci Rep 2017; 7:14122. [PMID: 29074872 PMCID: PMC5658447 DOI: 10.1038/s41598-017-14281-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
With the accumulation of scientific information in natural science, even experts can find difficult to keep integrating new piece of information. It is critical to explore modelling solutions able to capture information scattered in publications as a computable representation form. Traditional modelling techniques are important in that regard, but relying on numerical information comes with limitations for integrating results from distinct studies, high-level representations can be more suited. We present an approach to stepwise construct mechanistic explanation from selected scientific papers using the Qualitative Reasoning framework. As a proof of concept, we apply the approach to modelling papers about cellulose hydrolysis mechanism, focusing on the causal explanations for the decreasing of hydrolytic rate. Two explanatory QR models are built to capture classical explanations for the phenomenon. Our results show that none of them provides sufficient explanation for a set of basic experimental observations described in the literature. Combining the two explanations into a third one allowed to get a new and sufficient explanation for the experimental results. In domains where numerical data are scarce and strongly related to the experimental conditions, this approach can aid assessing the conceptual validity of an explanation and support integration of knowledge from different sources.
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Affiliation(s)
- Kamal Kansou
- INRA, Biopolymères Interactions Assemblages, BP 71267, 44316, Nantes, France.
| | - Caroline Rémond
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Gabriel Paës
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Estelle Bonnin
- INRA, Biopolymères Interactions Assemblages, BP 71267, 44316, Nantes, France
| | - Jean Tayeb
- FARE laboratory, INRA, University of Reims Champagne-Ardenne, 51100, Reims, France
| | - Bert Bredeweg
- Informatics Institute, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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Lee CR, Sung BH, Lim KM, Kim MJ, Sohn MJ, Bae JH, Sohn JH. Co-fermentation using Recombinant Saccharomyces cerevisiae Yeast Strains Hyper-secreting Different Cellulases for the Production of Cellulosic Bioethanol. Sci Rep 2017; 7:4428. [PMID: 28667330 PMCID: PMC5493647 DOI: 10.1038/s41598-017-04815-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/19/2017] [Indexed: 01/02/2023] Open
Abstract
To realize the economical production of ethanol and other bio-based chemicals from lignocellulosic biomass by consolidated bioprocessing (CBP), various cellulases from different sources were tested to improve the level of cellulase secretion in the yeast Saccharomyces cerevisiae by screening an optimal translational fusion partner (TFP) as both a secretion signal and fusion partner. Among them, four indispensable cellulases for cellulose hydrolysis, including Chaetomium thermophilum cellobiohydrolase (CtCBH1), Chrysosporium lucknowense cellobiohydrolase (ClCBH2), Trichoderma reesei endoglucanase (TrEGL2), and Saccharomycopsis fibuligera β-glucosidase (SfBGL1), were identified to be highly secreted in active form in yeast. Despite variability in the enzyme levels produced, each recombinant yeast could secrete approximately 0.6–2.0 g/L of cellulases into the fermentation broth. The synergistic effect of the mixed culture of the four strains expressing the essential cellulases with the insoluble substrate Avicel and several types of cellulosic biomass was demonstrated to be effective. Co-fermentation of these yeast strains produced approximately 14 g/L ethanol from the pre-treated rice straw containing 35 g/L glucan with 3-fold higher productivity than that of wild type yeast using a reduced amount of commercial cellulases. This process will contribute to the cost-effective production of bioenergy such as bioethanol and biochemicals from cellulosic biomass.
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Affiliation(s)
- Cho-Ryong Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Kwang-Mook Lim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Mi-Jin Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Min Jeong Sohn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Bae
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Hoon Sohn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea. .,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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32
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Tsai TT, Huang TH, Chang CJ, Yi-Ju Ho N, Tseng YT, Chen CF. Antibacterial cellulose paper made with silver-coated gold nanoparticles. Sci Rep 2017; 7:3155. [PMID: 28600506 PMCID: PMC5466604 DOI: 10.1038/s41598-017-03357-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/26/2017] [Indexed: 12/17/2022] Open
Abstract
In this study, we investigated the antibacterial activity of silver-coated gold nanoparticles (Au-Ag NPs) immobilized on cellulose paper. Ag NPs are known to have strong antibacterial properties, while Au NPs are biocompatible and relatively simple to prepare. We made the Au-Ag NPs using a facile process called Ag enhancement, in which Au NPs serve as the nuclei for precipitation of a Ag coating, the thickness of which can be easily controlled by varying the ratio of the reactants. After synthesis, electron microscopy showed that the Au-Ag NPs displayed a core-shell structure, and that they could be successfully immobilized onto a cellulose membrane by heat treatment. We then investigated the antibacterial properties of this NP-coated cellulose paper against E. coli JM109. The inhibition rate, growth curve, and AATCC 100 activity test showed that cellulose paper coated with 15 nm Au-Ag NPs possessed excellent antibacterial activity against E. coli JM109. These results suggest that Au-Ag NPs immobilized on cellulose paper could be a valuable antibacterial technology for applications such as food packaging, clothing, wound dressings, and other personal care products.
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Affiliation(s)
- Tsung-Ting Tsai
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 333, Taiwan
| | - Tse-Hao Huang
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 333, Taiwan.,Institute of Applied Mechanics, National Taiwan University, Taipei, 106, Taiwan
| | - Chih-Jung Chang
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 333, Taiwan
| | - Natalie Yi-Ju Ho
- Department of Orthopaedic Surgery, Bone and Joint Research Center, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 333, Taiwan
| | - Yu-Ting Tseng
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Chien-Fu Chen
- Institute of Applied Mechanics, National Taiwan University, Taipei, 106, Taiwan.
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Aich S, Singh RK, Kundu P, Pandey SP, Datta S. Genome-wide characterization of cellulases from the hemi-biotrophic plant pathogen, Bipolaris sorokiniana, reveals the presence of a highly stable GH7 endoglucanase. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:135. [PMID: 28559926 PMCID: PMC5445349 DOI: 10.1186/s13068-017-0822-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Bipolaris sorokiniana is a filamentous fungus that causes spot blotch disease in cereals like wheat and has severe economic consequences. However, information on the identities and role of the cell wall-degrading enzymes (CWDE) in B. sorokiniana is very limited. Several fungi produce CWDE like glycosyl hydrolases (GHs) that help in host cell invasion. To understand the role of these CWDE in B. sorokiniana, the first step is to identify and annotate all possible genes of the GH families like GH3, GH6, GH7, GH45 and AA9 and then characterize them biochemically. RESULTS We confirmed and annotated the homologs of GH3, GH6, GH7, GH45 and AA9 enzymes in the B. sorokiniana genome using the sequence and domain features of these families. Quantitative real-time PCR analyses of these homologs revealed that the transcripts of the BsGH7-3 (3rd homolog of the GH 7 family in B. sorokiniana) were most abundant. BsGH7-3, the gene of BsGH7-3, was thus cloned into pPICZαC Pichia pastoris vector and expressed in X33 P. pastoris host to be characterized. BsGH7-3 enzyme showed a temperature optimum of 60 °C and a pHopt of 8.1. BsGH7-3 was identified to be an endoglucanase based on its broad substrate specificity and structural comparisons with other such endoglucanases. BsGH7-3 has a very long half-life and retains 100% activity even in the presence of 4 M NaCl, 4 M KCl and 20% (v/v) ionic liquids. The enzyme activity is stimulated up to fivefold in the presence of Mn+2 and Fe+2 without any deleterious effects on enzyme thermostability. CONCLUSIONS Here we reanalysed the B. sorokiniana genome and selected one GH7 enzyme for further characterization. The present work demonstrates that BsGH7-3 is an endoglucanase with a long half-life and no loss in activity in the presence of denaturants like salt and ionic liquids, and lays the foundation towards exploring the Bipolaris genome for other cell wall-degrading enzymes.
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Affiliation(s)
- Shritama Aich
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, India
| | - Ravi K. Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 India
| | - Pritha Kundu
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 India
| | - Shree P. Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 India
| | - Supratim Datta
- Protein Engineering Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur, India
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Ogunmolu FE, Jagadeesha NBK, Kumar R, Kumar P, Gupta D, Yazdani SS. Comparative insights into the saccharification potentials of a relatively unexplored but robust Penicillium funiculosum glycoside hydrolase 7 cellobiohydrolase. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:71. [PMID: 28344646 PMCID: PMC5360062 DOI: 10.1186/s13068-017-0752-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/09/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND GH7 cellobiohydrolases (CBH1) are vital for the breakdown of cellulose. We had previously observed the enzyme as the most dominant protein in the active cellulose-hydrolyzing secretome of the hypercellulolytic ascomycete-Penicillium funiculosum (NCIM1228). To understand its contributions to cellulosic biomass saccharification in comparison with GH7 cellobiohydrolase from the industrial workhorse-Trichoderma reesei, we natively purified and functionally characterized the only GH7 cellobiohydrolase identified and present in the genome of the fungus. RESULTS There were marginal differences observed in the stability of both enzymes, with P. funiculosum (PfCBH1) showing an optimal thermal midpoint (Tm) of 68 °C at pH 4.4 as against an optimal Tm of 65 °C at pH 4.7 for T. reesei (TrCBH1). Nevertheless, PfCBH1 had an approximate threefold lower binding affinity (Km), an 18-fold higher turnover rate (kcat), a sixfold higher catalytic efficiency as well as a 26-fold higher enzyme-inhibitor complex equilibrium dissociation constant (Ki) than TrCBH1 on p-nitrophenyl-β-d-lactopyranoside (pNPL). Although both enzymes hydrolyzed cellooligomers (G2-G6) and microcrystalline cellulose, releasing cellobiose and glucose as the major products, the propensity was more with PfCBH1. We equally observed this trend during the hydrolysis of pretreated wheat straws in tandem with other core cellulases under the same conditions. Molecular dynamic simulations conducted on a homology model built using the TrCBH1 structure (PDB ID: 8CEL) as a template enabled us to directly examine the effects of substrate and products on the protein dynamics. While the catalytic triads-EXDXXE motifs-were conserved between the two enzymes, subtle variations in regions enclosing the catalytic path were observed, and relations to functionality highlighted. CONCLUSION To the best of our knowledge, this is the first report about a comprehensive and comparative description of CBH1 from hypercellulolytic ascomycete-P. funiculosum NCIM1228, against the backdrop of the same enzyme from the industrial workhorse-T. reesei. Our study reveals PfCBH1 as a viable alternative for CBH1 from T. reesei in industrial cellulase cocktails.
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Affiliation(s)
- Funso Emmanuel Ogunmolu
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Navya Bhatt Kammachi Jagadeesha
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Rakesh Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Pawan Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067 India
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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35
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Díaz AB, Marzo C, Caro I, de Ory I, Blandino A. Valorization of exhausted sugar beet cossettes by successive hydrolysis and two fermentations for the production of bio-products. BIORESOURCE TECHNOLOGY 2017; 225:225-233. [PMID: 27894041 DOI: 10.1016/j.biortech.2016.11.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Exhausted sugar beet cossettes (ESBC) show an enormous potential as a source of sugars for the production of bio-products. Enzyme hydrolysis with the combined effect of mainly cellulases, xylanases and pectinases, turned out to be very efficient, obtaining almost double the concentration of sugars measured with the sole action of Celluclast® and β-glucosidase, and increasing 5 times the hydrolysis rate. As the sole pretreatment, ESBC soaked in the hydrolysis buffer were autoclaved, avoiding the application of severe conventional biomass pretreatments. Moreover, a promising alternative for the complete utilization of glucose, xylose, arabinose, mannose and maltose contained in ESBC is proposed in this paper. It consists of sequential fermentation of sugars released in the hydrolysis step to produce bioethanol and lactic acid as main bio-products. Compared to separate fermentations, with this strategy glucose and hemicellulose derived sugars were completely consumed and the 44% of pectin derived sugars.
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Affiliation(s)
- A B Díaz
- Laboratory of Microbiology, Faculty of Marine and Environmental Sciences, University of Cádiz, Pol. Río San Pedro s/n, Puerto Real, Spain.
| | - C Marzo
- Department of Chemical Engineering and Food Technology, Faculty of Sciences, International Agro-Food Campus of Excellence (CeiA3), University of Cádiz, Pol. Río San Pedro s/n, Puerto Real, Spain
| | - I Caro
- Department of Chemical Engineering and Food Technology, Faculty of Sciences, International Agro-Food Campus of Excellence (CeiA3), University of Cádiz, Pol. Río San Pedro s/n, Puerto Real, Spain
| | - I de Ory
- Department of Chemical Engineering and Food Technology, Faculty of Sciences, International Agro-Food Campus of Excellence (CeiA3), University of Cádiz, Pol. Río San Pedro s/n, Puerto Real, Spain
| | - A Blandino
- Department of Chemical Engineering and Food Technology, Faculty of Sciences, International Agro-Food Campus of Excellence (CeiA3), University of Cádiz, Pol. Río San Pedro s/n, Puerto Real, Spain
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36
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Fonseca-Maldonado R, Meleiro LP, Mendes LFS, Alves LF, Carli S, Morero LD, Basso LGM, Costa-Filho AJ, Ward RJ. Lignocellulose binding of a Cel5A-RtCBM11 chimera with enhanced β-glucanase activity monitored by electron paramagnetic resonance. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:269. [PMID: 29163671 PMCID: PMC5686792 DOI: 10.1186/s13068-017-0964-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/07/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The Bacillus subtilis endo-β-1,4-glucanase (BsCel5A) hydrolyzes β-1,3-1,4-linked glucan, and the enzyme includes a family 3 carbohydrate-binding module (CBM3) that binds β-1,4-linked glucan. METHODS Here we investigate the BsCel5A β-1,3-1,4 glucanase activity after exchanging the CBM3 domain for the family 11 CBM from Ruminiclostridium thermocellum celH (RtCBM11) having β-1,3-1,4 glucan affinity. RESULTS The BsCel5A-RtCBM11 presents a 50.4% increase in Vmax, a 10% reduction in K0.5, and a 2.1-fold increase in catalytic efficiency. Enzyme mobility and binding to barley β-1,3-1,4 glucan and pre-treated sugarcane bagasse were investigated using Electron Paramagnetic Resonance (EPR) with Site-Directed Spin Labeling (SDSL) of the binding site regions of the CBM3 and RtCBM11 domains in the BsCel5A-CBM3 and BsCel5A-RtCBM11, respectively. Although higher mobility than the RtCBM11 was shown, no interaction of the spin-labeled CBM3 with β-1,3-1,4 glucan was observed. In contrast, a Ka value of 0.22 mg/mL was estimated from titration of the BsCel5A-RtCBM11 with β-1,3-1,4 glucan. Enzyme binding as inferred from altered EPR spectra of the BsCel5A-RtCBM11 was observed only after xylan or lignin extraction from sugarcane bagasse. Binding to xylan- or lignin-free lignocellulose was correlated with a 4.5- to 5-fold increase in total reducing sugar release as compared to the milled intact sugarcane bagasse, suggesting that xylan impedes enzyme access to the β-1,3-1,4 glucan. CONCLUSIONS These results show that the non-specific binding of the BsCel5A-RtCBM11 to the lignin component of the cell wall is minimal, and represent the first reported use of EPR to directly study the interaction of glycoside hydrolyse enzymes with natural insoluble substrates.
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Affiliation(s)
- Raquel Fonseca-Maldonado
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
- Departamento de Gestão, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo/IFSP Campus Jacareí, Jacareí, São Paulo Brazil
| | - Luana P. Meleiro
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
| | - Luís F. S. Mendes
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Luana F. Alves
- Departamento de Bioquímica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Sibeli Carli
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
| | - Lucas D. Morero
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Luis G. M. Basso
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Antonio J. Costa-Filho
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Richard J. Ward
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
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Xue D, Lin D, Gong C, Peng C, Yao S. Expression of a bifunctional cellulase with exoglucanase and endoglucanase activities to enhance the hydrolysis ability of cellulase from a marine Aspergillus niger. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.09.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Xue DS, Liang LY, Zheng G, Lin DQ, Zhang QL, Yao SJ. Expression of Piromyces rhizinflata cellulase in marine Aspergillus niger to enhance halostable cellulase activity by adjusting enzyme-composition. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Baramee S, Teeravivattanakit T, Phitsuwan P, Waeonukul R, Pason P, Tachaapaikoon C, Kosugi A, Sakka K, Ratanakhanokchai K. A novel GH6 cellobiohydrolase from Paenibacillus curdlanolyticus B-6 and its synergistic action on cellulose degradation. Appl Microbiol Biotechnol 2016; 101:1175-1188. [PMID: 27743043 DOI: 10.1007/s00253-016-7895-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/12/2016] [Accepted: 09/25/2016] [Indexed: 11/30/2022]
Abstract
We recently discovered a novel glycoside hydrolase family 6 (GH6) cellobiohydrolase from Paenibacillus curdlanolyticus B-6 (PcCel6A), which is rarely found in bacteria. This enzyme is a true exo-type cellobiohydrolase which exhibits high substrate specificity on amorphous cellulose and low substrate specificity on crystalline cellulose, while this showed no activity on substitution substrates, carboxymethyl cellulose and xylan, distinct from all other known GH6 cellobiohydrolases. Product profiles, HPLC analysis of the hydrolysis products and a schematic drawing of the substrate-binding subsites catalysing cellooligosaccharides can explain the new mode of action of this enzyme which prefers to hydrolyse cellopentaose. PcCel6A was not inhibited by glucose or cellobiose at concentrations up to 300 and 100 mM, respectively. A good synergistic effect for glucose production was found when PcCel6A acted together with processive endoglucanase Cel9R from Clostridium thermocellum and β-glucosidase CglT from Thermoanaerobacter brockii. These properties of PcCel6A make it a suitable candidate for industrial application in the cellulose degradation process.
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Affiliation(s)
- Sirilak Baramee
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Thitiporn Teeravivattanakit
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paripok Phitsuwan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuo Sakka
- Graduated School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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Eibinger M, Sigl K, Sattelkow J, Ganner T, Ramoni J, Seiboth B, Plank H, Nidetzky B. Functional characterization of the native swollenin from Trichoderma reesei: study of its possible role as C1 factor of enzymatic lignocellulose conversion. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:178. [PMID: 27570542 PMCID: PMC5000517 DOI: 10.1186/s13068-016-0590-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/15/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Through binding to cellulose, expansin-like proteins are thought to loosen the structural order of crystalline surface material, thus making it more accessible for degradation by hydrolytic enzymes. Swollenin SWO1 is the major expansin-like protein from the fungus Trichoderma reesei. Here, we have performed a detailed characterization of a recombinant native form of SWO1 with respect to its possible auxiliary role in the enzymatic saccharification of lignocellulosic substrates. RESULTS The swo1 gene was overexpressed in T. reesei QM9414 Δxyr1 mutant, featuring downregulated cellulase production, and the protein was purified from culture supernatant. SWO1 was N-glycosylated and its circular dichroism spectrum suggested a folded protein. Adsorption isotherms (25 °C, pH 5.0, 1.0 mg substrate/mL) revealed SWO1 to be 120- and 20-fold more specific for binding to birchwood xylan and kraft lignin, respectively, than for binding to Avicel PH-101. The SWO1 binding capacity on lignin (25 µmol/g) exceeded 12-fold that on Avicel PH-101 (2.1 µmol/g). On xylan, not only the binding capacity (22 µmol/g) but also the affinity of SWO1 (K d = 0.08 µM) was enhanced compared to Avicel PH-101 (K d = 0.89 µM). SWO1 caused rapid release of a tiny amount of reducing sugars (<1 % of total) from different substrates (Avicel PH-101, nanocrystalline cellulose, steam-pretreated wheat straw, barley β-glucan, cellotetraose) but did not promote continued saccharification. Atomic force microscopy revealed that amorphous cellulose films were not affected by SWO1. Also with AFM, binding of SWO1 to cellulose nanocrystallites was demonstrated at the single-molecule level, but adsorption did not affect this cellulose. SWO1 exhibited no synergy with T. reesei cellulases in the hydrolysis of the different celluloses. However, SWO1 boosted slightly (1.5-fold) the reducing sugar release from a native grass substrate. CONCLUSIONS SWO1 is a strongly glycosylated protein, which has implications for producing it in heterologous hosts. Although SWO1 binds to crystalline cellulose, its adsorption to xylan is much stronger. SWO1 is not an auxiliary factor of the enzymatic degradation of a variety of cellulosic substrates. Effect of SWO1 on sugar release from intact plant cell walls might be exploitable with certain (e.g., mildly pretreated) lignocellulosic feedstocks.
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Affiliation(s)
- Manuel Eibinger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Karin Sigl
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
| | - Jürgen Sattelkow
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Thomas Ganner
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Jonas Ramoni
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstrasse 1A/166, 1060 Vienna, Austria
| | - Harald Plank
- Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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Loman AA, Ju LK. Towards complete hydrolysis of soy flour carbohydrates by enzyme mixtures for protein enrichment: A modeling approach. Enzyme Microb Technol 2016; 86:25-33. [DOI: 10.1016/j.enzmictec.2016.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/27/2015] [Accepted: 01/19/2016] [Indexed: 01/15/2023]
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Eibinger M, Zahel T, Ganner T, Plank H, Nidetzky B. Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:56. [PMID: 26962329 PMCID: PMC4784381 DOI: 10.1186/s13068-016-0463-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of cellulose involves the spatiotemporally correlated action of distinct polysaccharide chain cleaving activities confined to the surface of an insoluble substrate. Because cellulases differ in preference for attacking crystalline compared to amorphous cellulose, the spatial distribution of structural order across the cellulose surface imposes additional constraints on the dynamic interplay between the enzymes. Reconstruction of total system behavior from single-molecule activity parameters is a longstanding key goal in the field. RESULTS We have developed a stochastic, cellular automata-based modeling approach to describe degradation of cellulosic material by a cellulase system at single-molecule resolution. Substrate morphology was modeled to represent the amorphous and crystalline phases as well as the different spatial orientations of the polysaccharide chains. The enzyme system model consisted of an internally chain-cleaving endoglucanase (EG) as well as two processively acting, reducing and non-reducing chain end-cleaving cellobiohydrolases (CBHs). Substrate preference (amorphous: EG, CBH II; crystalline: CBH I) and characteristic frequencies for chain cleavage, processive movement, and dissociation were assigned from biochemical data. Once adsorbed, enzymes were allowed to reach surface-exposed substrate sites through "random-walk" lateral diffusion or processive motion. Simulations revealed that slow dissociation of processive enzymes at obstacles obstructing further movement resulted in local jamming of the cellulases, with consequent delay in the degradation of the surface area affected. Exploiting validation against evidence from atomic force microscopy imaging as a unique opportunity opened up by the modeling approach, we show that spatiotemporal characteristics of cellulose surface degradation by the system of synergizing cellulases were reproduced quantitatively at the nanometer resolution of the experimental data. This in turn gave useful prediction of the soluble sugar release rate. CONCLUSIONS Salient dynamic features of cellulose surface degradation by different cellulases acting in synergy were reproduced in simulations in good agreement with evidence from high-resolution visualization experiments. Due to the single-molecule resolution of the modeling approach, the utility of the presented model lies not only in predicting system behavior but also in elucidating inherently complex (e.g., stochastic) phenomena involved in enzymatic cellulose degradation. Thus, it creates synergy with experiment to advance the mechanistic understanding for improved application.
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Affiliation(s)
- Manuel Eibinger
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Zahel
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
| | - Thomas Ganner
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
| | - Harald Plank
- />Institute for Electron Microscopy and Nanoanalysis, Graz University of Technology, Steyrergasse 17, 8010 Graz, Austria
- />Graz Centre for Electron Microscopy, Steyrergasse 17, 8010 Graz, Austria
| | - Bernd Nidetzky
- />Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010 Graz, Austria
- />Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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Niu H, Shah N, Kontoravdi C. Modelling of amorphous cellulose depolymerisation by cellulases, parametric studies and optimisation. Biochem Eng J 2016; 105:455-472. [PMID: 26865832 PMCID: PMC4705870 DOI: 10.1016/j.bej.2015.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A mechanistic model for heterogeneous cellulose hydrolysis by cellulases. A modeling framework for uncertainty analysis, model reduction and refinement. The parameters were estimated. Composition of cellulases cocktail was optimized using the model.
Improved understanding of heterogeneous cellulose hydrolysis by cellulases is the basis for optimising enzymatic catalysis-based cellulosic biorefineries. A detailed mechanistic model is developed to describe the dynamic adsorption/desorption and synergistic chain-end scissions of cellulases (endoglucanase, exoglucanase, and β-glucosidase) upon amorphous cellulose. The model can predict evolutions of the chain lengths of insoluble cellulose polymers and production of soluble sugars during hydrolysis. Simultaneously, a modelling framework for uncertainty analysis is built based on a quasi-Monte-Carlo method and global sensitivity analysis, which can systematically identify key parameters, help refine the model and improve its identifiability. The model, initially comprising 27 parameters, is found to be over-parameterized with structural and practical identification problems under usual operating conditions (low enzyme loadings). The parameter estimation problem is therefore mathematically ill posed. The framework allows us, on the one hand, to identify a subset of 13 crucial parameters, of which more accurate confidence intervals are estimated using a given experimental dataset, and, on the other hand, to overcome the identification problems. The model’s predictive capability is checked against an independent set of experimental data. Finally, the optimal composition of cellulases cocktail is obtained by model-based optimisation both for enzymatic hydrolysis and for the process of simultaneous saccharification and fermentation.
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Affiliation(s)
- Hongxing Niu
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, England, UK
| | - Nilay Shah
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, England, UK
| | - Cleo Kontoravdi
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, England, UK
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Laothanachareon T, Bunterngsook B, Suwannarangsee S, Eurwilaichitr L, Champreda V. Synergistic action of recombinant accessory hemicellulolytic and pectinolytic enzymes to Trichoderma reesei cellulase on rice straw degradation. BIORESOURCE TECHNOLOGY 2015; 198:682-690. [PMID: 26433794 DOI: 10.1016/j.biortech.2015.09.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/12/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
Synergism between core cellulases and accessory hydrolytic/non-hydrolytic enzymes is the basis of efficient hydrolysis of lignocelluloses. In this study, the synergistic action of three recombinant accessory enzymes, namely GH62 α-l-arabinofuranosidase (ARA), CE8 pectin esterase (PET), and GH10 endo-1,4-beta-xylanase (XYL) from Aspergillus aculeatus expressed in Pichia pastoris to a commercial Trichoderma reesei cellulase (Accellerase® 1500; ACR) on hydrolysis of alkaline pretreated rice straw was studied using a mixture design approach. Applying the full cubic model, the optimal ratio of quaternary enzyme mixture was predicted to be ACR:ARA:PET:XYL of 0.171:0.079:0.100:0.150, which showed a glucose releasing efficiency of 0.173 gglc/FPU, higher than the binary ACR:XYL mixture (0.122 gglc/FPU) and ACR alone (0.081 gglc/FPU) leading to a 47.3% increase in glucose yield compared with that from ACR at the same cellulase dosage. The result demonstrates the varying degree of synergism of accessory enzymes to cellulases useful for developing tailor-made enzyme systems for bio-industry.
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Affiliation(s)
- Thanaporn Laothanachareon
- Enzyme Technology Laboratory and Integrative Biorefinery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, 113 Pahonyothin Road, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- Enzyme Technology Laboratory and Integrative Biorefinery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, 113 Pahonyothin Road, Pathumthani 12120, Thailand
| | - Surisa Suwannarangsee
- Enzyme Technology Laboratory and Integrative Biorefinery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, 113 Pahonyothin Road, Pathumthani 12120, Thailand
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory and Integrative Biorefinery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, 113 Pahonyothin Road, Pathumthani 12120, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory and Integrative Biorefinery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, 113 Pahonyothin Road, Pathumthani 12120, Thailand.
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Huron M, Hudebine D, Lopes Ferreira N, Lachenal D. Mechanistic modeling of enzymatic hydrolysis of cellulose integrating substrate morphology and cocktail composition. Biotechnol Bioeng 2015; 113:1011-23. [PMID: 26524470 DOI: 10.1002/bit.25873] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/20/2015] [Accepted: 10/26/2015] [Indexed: 11/12/2022]
Abstract
A mechanistic model of enzymatic hydrolysis taking into account the morphology of the cellulosic particles and its evolution with time was developed. The individual behavior of the main enzymes involved in the reaction (cellobiohydrolases, endoglucanases, and β-glucosidases), as well as synergy effects, were also included. A large panel of experimental tests was done to fit and validate the model. This database included different enzymes mixtures and operating conditions and allowed to determine and compare with accuracy the adsorption and kinetic parameters of the different enzymes. Model predictions on short hydrolysis times were very satisfactory. On longer times, a deactivation constant was added to represent the hydrolysis slowdown. The model also allowed to predict the impact of enzymes ratios and initial substrate parameters (chain length distribution, polymerization degree) on hydrolysis, and to follow the evolution of these parameters with time. This model revealed general trends on the impact of cellulose morphology on hydrolysis. It is a useful tool to better understand the mechanisms involved in enzymatic hydrolysis of cellulose and to determine optimal cellulolytic cocktails for process design.
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Affiliation(s)
- Maïté Huron
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize - BP 3, 69360 Solaize, France
| | - Damien Hudebine
- IFP Energies Nouvelles, Rond-point de l'échangeur de Solaize - BP 3, 69360 Solaize, France.
| | | | - Dominique Lachenal
- Grenoble INP-Pagora, 461 rue de la Papeterie BP65, Saint Martin d'Hères Cedex, France
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Payne CM, Knott BC, Mayes HB, Hansson H, Himmel ME, Sandgren M, Ståhlberg J, Beckham GT. Fungal Cellulases. Chem Rev 2015; 115:1308-448. [DOI: 10.1021/cr500351c] [Citation(s) in RCA: 533] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christina M. Payne
- Department
of Chemical and Materials Engineering and Center for Computational
Sciences, University of Kentucky, 177 F. Paul Anderson Tower, Lexington, Kentucky 40506, United States
| | - Brandon C. Knott
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
| | - Heather B. Mayes
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Henrik Hansson
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Michael E. Himmel
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Mats Sandgren
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Jerry Ståhlberg
- Department
of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Almas allé 5, SE-75651 Uppsala, Sweden
| | - Gregg T. Beckham
- National
Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver
West Parkway, Golden, Colorado 80401, United States
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49
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Bali G, Meng X, Deneff JI, Sun Q, Ragauskas AJ. The effect of alkaline pretreatment methods on cellulose structure and accessibility. CHEMSUSCHEM 2015; 8:275-9. [PMID: 25421020 DOI: 10.1002/cssc.201402752] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/30/2014] [Indexed: 05/04/2023]
Abstract
The effects of different alkaline pretreatments on cellulose structural features and accessibility are compared and correlated with the enzymatic hydrolysis of Populus. The pretreatments are shown to modify polysaccharides and lignin content to enhance the accessibility for cellulase enzymes. The highest increase in the cellulose accessibility was observed in dilute sodium hydroxide, followed by methods using ammonia soaking and lime (Ca(OH)2 ). The biggest increase of cellulose accessibility occurs during the first 10 min of pretreatment, with further increases at a slower rate as severity increases. Low temperature ammonia soaking at longer residence times dissolved a major portion of hemicellulose and exhibited higher cellulose accessibility than high temperature soaking. Moreover, the most significant reduction of degree of polymerization (DP) occurred for dilute sodium hydroxide (NaOH) and ammonia pretreated Populus samples. The study thus identifies important cellulose structural features and relevant parameters related to biomass recalcitrance.
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Affiliation(s)
- Garima Bali
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, 500, 10th St. NW, Atlanta, GA-30332-0620 (USA)
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50
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Lebaz N, Cockx A, Spérandio M, Morchain J. Population balance approach for the modelling of enzymatic hydrolysis of cellulose. CAN J CHEM ENG 2014. [DOI: 10.1002/cjce.22088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Noureddine Lebaz
- Toulouse White Biotechnology; 3 rue des satellites 31400 Toulouse France
- Université de Toulouse; INSA; UPS; INP; LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
- CNRS; UMR5504; F-31400 Toulouse France
| | - Arnaud Cockx
- Université de Toulouse; INSA; UPS; INP; LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
- CNRS; UMR5504; F-31400 Toulouse France
| | - Mathieu Spérandio
- Université de Toulouse; INSA; UPS; INP; LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
- CNRS; UMR5504; F-31400 Toulouse France
| | - Jérôme Morchain
- Université de Toulouse; INSA; UPS; INP; LISBP; 135 Avenue de Rangueil F-31077 Toulouse France
- INRA; UMR792 Ingénierie des Systèmes Biologiques et des Procédés; F-31400 Toulouse France
- CNRS; UMR5504; F-31400 Toulouse France
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