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Gado JE, Harrison BE, Sandgren M, Ståhlberg J, Beckham GT, Payne CM. Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases. J Biol Chem 2021; 297:100931. [PMID: 34216620 PMCID: PMC8329511 DOI: 10.1016/j.jbc.2021.100931] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/18/2021] [Accepted: 06/29/2021] [Indexed: 11/28/2022] Open
Abstract
Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.
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Affiliation(s)
- Japheth E Gado
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, USA; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Brent E Harrison
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Christina M Payne
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, USA.
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2
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Novy V, Nielsen F, Cullen D, Sabat G, Houtman CJ, Hunt CG. The characteristics of insoluble softwood substrates affect fungal morphology, secretome composition, and hydrolytic efficiency of enzymes produced by Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:105. [PMID: 33902680 PMCID: PMC8074412 DOI: 10.1186/s13068-021-01955-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/11/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND On-site enzyme production using Trichoderma reesei can improve yields and lower the overall cost of lignocellulose saccharification by exploiting the fungal gene regulatory mechanism that enables it to continuously adapt enzyme secretion to the substrate used for cultivation. To harness this, the interrelation between substrate characteristics and fungal response must be understood. However, fungal morphology or gene expression studies often lack structural and chemical substrate characterization. Here, T. reesei QM6a was cultivated on three softwood substrates: northern bleached softwood Kraft pulp (NBSK) and lodgepole pine pretreated either by dilute-acid-catalyzed steam pretreatment (LP-STEX) or mild alkaline oxidation (LP-ALKOX). With different pretreatments of similar starting materials, we presented the fungus with systematically modified substrates. This allowed the elucidation of substrate-induced changes in the fungal response and the testing of the secreted enzymes' hydrolytic strength towards the same substrates. RESULTS Enzyme activity time courses correlated with hemicellulose content and cellulose accessibility. Specifically, increased amounts of side-chain-cleaving hemicellulolytic enzymes in the protein produced on the complex substrates (LP-STEX; LP-ALKOX) was observed by secretome analysis. Confocal laser scanning micrographs showed that fungal micromorphology responded to changes in cellulose accessibility and initial culture viscosity. The latter was caused by surface charge and fiber dimensions, and likely restricted mass transfer, resulting in morphologies of fungi in stress. Supplementing a basic cellulolytic enzyme mixture with concentrated T. reesei supernatant improved saccharification efficiencies of the three substrates, where cellulose, xylan, and mannan conversion was increased by up to 27, 45, and 2800%, respectively. The improvement was most pronounced for proteins produced on LP-STEX and LP-ALKOX on those same substrates, and in the best case, efficiencies reached those of a state-of-the-art commercial enzyme preparation. CONCLUSION Cultivation of T. reesei on LP-STEX and LP-ALKOX produced a protein mixture that increased the hydrolytic strength of a basic cellulase mixture to state-of-the-art performance on softwood substrates. This suggests that the fungal adaptation mechanism can be exploited to achieve enhanced performance in enzymatic hydrolysis without a priori knowledge of specific substrate requirements.
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Affiliation(s)
- Vera Novy
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA.
- Department of Biology and Bioengineering, Division of Industrial Biotechnology, Chalmers University of Technology, Kemivägen 10, 412 96, Göteborg, Sweden.
| | - Fredrik Nielsen
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Daniel Cullen
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Grzegorz Sabat
- University of Wisconsin Biotechnology Center, Madison, WI, 53706, USA
| | - Carl J Houtman
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
| | - Christopher G Hunt
- US Department of Agriculture, Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI, 53726, USA
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3
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Abdel-Azeem AM, Hasan GA, Mohesien MT. Biodegradation of Agricultural Wastes by Chaetomium Species. Fungal Biol 2020. [DOI: 10.1007/978-3-030-31612-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Effect of Enzyme Interaction with Lignin Isolated from Pretreated Miscanthus x gigantues on Cellulolytic Efficiency. Processes (Basel) 2019. [DOI: 10.3390/pr7100755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The effect of binding between the lignin isolates from an alkali (NaOH)– and an acid (H2SO4)– pretreated Miscanthus and cellulolytic enzymes in Cellic® CTec2 was investigated. Additonally, cellobiose and Avicel were enzymatically hydrolyzed with and without lignin isolates to study how enzyme binding onto lignin affects its conversion to glucose. Three carbohydrate–lignin loadings (0.5:0.25, 0.5:0.5, and 0.5:1.0% (w/v)) were employed. The results indicated that β-glucosidase (BG) had a strong tendency to bind to all lignin isolates. The overall tendency of enzyme binding onto lignin isolate was similar regardless of pretreatment chemical concentration. Though enzyme binding onto lignin isolates was observed, hydrolysis in the presence of these isolates did not have a significant (p > 0.05) impact on glucose production from cellobiose and Avicel. Cellobiose to glucose conversion of 99% was achieved via hydrolysis at both 5 and 10 FPU/g carbohydrate. Hydrolysis of Avicel with 5 and 10 FPU/g CTec2 resulted in 29.3 and 47.7% conversion to glucose, respectively.
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5
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Novy V, Nielsen F, Seiboth B, Nidetzky B. The influence of feedstock characteristics on enzyme production in Trichoderma reesei: a review on productivity, gene regulation and secretion profiles. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:238. [PMID: 31624500 PMCID: PMC6781402 DOI: 10.1186/s13068-019-1571-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/21/2023]
Abstract
Biorefineries, designed for the production of lignocellulose-based chemicals and fuels, are receiving increasing attention from the public, governments, and industries. A major obstacle for biorefineries to advance to commercial scale is the high cost of the enzymes required to derive the fermentable sugars from the feedstock used. As summarized in this review, techno-economic studies suggest co-localization and integration of enzyme manufacturing with the cellulosic biorefinery as the most promising alternative to alleviate this problem. Thus, cultivation of Trichoderma reesei, the principal producer of lignocellulolytic enzymes, on the lignocellulosic biomass processed on-site can reduce the cost of enzyme manufacturing. Further, due to a complex gene regulation machinery, the fungus can adjust the gene expression of the lignocellulolytic enzymes towards the characteristics of the feedstock, increasing the hydrolytic efficiency of the produced enzyme cocktail. Despite extensive research over decades, the underlying regulatory mechanisms are not fully elucidated. One aspect that has received relatively little attention in literature is the influence the characteristics of a lignocellulosic substrate, i.e., its chemical and physical composition, has on the produced enzyme mixture. Considering that the fungus is dependent on efficient enzymatic degradation of the lignocellulose for continuous supply of carbon and energy, a relationship between feedstock characteristics and secretome composition can be expected. The aim of this review was to systematically collect, appraise, and aggregate data and integrate results from studies analyzing enzyme production by T. reesei on insoluble cellulosic model substrates and lignocellulosic biomass. The results show that there is a direct effect of the substrate's complexity (rated by structure, composition of the lignin-carbohydrate complex, and recalcitrance in enzymatic saccharification) on enzyme titers and the composition of specific activities in the secretome. It further shows that process-related factors, such as substrate loading and cultivation set-up, are direct targets for increasing enzyme yields. The literature on transcriptome and secretome composition further supports the proposed influence of substrate-related factors on the expression of lignocellulolytic enzymes. This review provides insights into the interrelation between the characteristics of the substrate and the enzyme production by T. reesei, which may help to advance integrated enzyme manufacturing of substrate-specific enzymes cocktails at scale.
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Affiliation(s)
- Vera Novy
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Fredrik Nielsen
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Present Address: Department of Wood Science, Faculty of Forestry, The University of British Columbia, Vancouver, Canada
| | - Bernhard Seiboth
- Institute of Chemical, Environmental and Bioscience Engineering, Vienna University of Technology, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib) GmbH, Graz, Austria
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6
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Effective and reusable T. reesei immobilized on SBA-15 for monomeric sugar production from cellulose hydrolysis. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2019.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Binod P, Gnansounou E, Sindhu R, Pandey A. Enzymes for second generation biofuels: Recent developments and future perspectives. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2018.06.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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8
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Geronimo I, Ntarima P, Piens K, Gudmundsson M, Hansson H, Sandgren M, Payne CM. Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases. J Biol Chem 2019; 294:3169-3180. [PMID: 30602567 DOI: 10.1074/jbc.ra118.007027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
β-Glucosidases enhance enzymatic biomass conversion by relieving cellobiose inhibition of endoglucanases and cellobiohydrolases. However, the susceptibility of these enzymes to inhibition and transglycosylation at high glucose or cellobiose concentrations severely limits their activity and, consequently, the overall efficiency of enzyme mixtures. We determined the impact of these two processes on the hydrolytic activity of the industrially relevant family 3 β-glucosidases from Hypocrea jecorina, HjCel3A and HjCel3B, and investigated the underlying molecular mechanisms through kinetic studies, binding free energy calculations, and molecular dynamics (MD) simulations. HjCel3B had a 7-fold higher specificity for cellobiose than HjCel3A but greater tendency for glucose inhibition. Energy decomposition analysis indicated that cellobiose has relatively weak electrostatic interactions with binding site residues, allowing it to be easily displaced by glucose and free to inhibit other hydrolytic enzymes. HjCel3A is, thus, preferable as an industrial β-glucosidase despite its lower activity caused by transglycosylation. This competing pathway to hydrolysis arises from binding of glucose or cellobiose at the product site after formation of the glycosyl-enzyme intermediate. MD simulations revealed that binding is facilitated by hydrophobic interactions with Trp-37, Phe-260, and Tyr-443. Targeting these aromatic residues for mutation to reduce substrate affinity at the product site would therefore potentially mitigate transglycosidic activity. Engineering improved variants of HjCel3A and other structurally similar β-glucosidases would have a significant economic effect on enzymatic biomass conversion in terms of yield and production cost as the process can be consequently conducted at higher substrate loadings.
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Affiliation(s)
- Inacrist Geronimo
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046
| | - Patricia Ntarima
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Kathleen Piens
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Mikael Gudmundsson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Christina M Payne
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, .,the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
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9
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Cai C, Jin Y, Pang Y, Ke Q, Qiu W, Qiu X, Qin Y, Lou H. Tracing cellulase components in hydrolyzate during the enzymatic hydrolysis of corncob residue and its analysis. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.biteb.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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10
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Tsuji A, Yuasa K, Asada C. Cellulose-binding activity of a 21-kDa endo-ß-1,4-glucanase lacking cellulose-binding domain and its synergy with other cellulases in the digestive fluid of Aplysia kurodai. PLoS One 2018; 13:e0205915. [PMID: 30412581 PMCID: PMC6226162 DOI: 10.1371/journal.pone.0205915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/03/2018] [Indexed: 12/05/2022] Open
Abstract
Endo-ß-1,4-glucanase AkEG21 belonging to glycosyl hydrolase family 45 (GHF45) is the most abundant cellulase in the digestive fluid of sea hare (Aplysia kurodai). The specific activity of this 21-kDa enzyme is considerably lower than those of other endo ß-1,4-glucanases in the digestive fluid of A. kurodai, therefore its role in whole cellulose hydrolysis by sea hare is still uncertain. Although AkEG21 has a catalytic domain without a cellulose binding domain, it demonstrated stable binding to cellulose fibers, similar to that of fungal cellobiohydrolase (CBH) 1 and CBH 2, which is strongly inhibited by cellohexaose, suggesting the involvement of the catalytic site in cellulose binding. Cellulose-bound AkEG21 hydrolyzed cellulose to cellobiose, cellotriose and cellotetraose, but could not digest an external substrate, azo-carboxymethyl cellulose. Cellulose hydrolysis was considerably stimulated by the synergistic action of cellulose-bound AkEG21 and AkEG45, another ß-1,4-endoglucanase present in the digestive fluid of sea hare; however no synergy in carboxymethylcellulose hydrolysis was observed. When AkEG21 was removed from the digestive fluid by immunoprecipitation, the cellulose hydrolyzing activity of the fluid was significantly reduced, indicating a critical role of AkEG21 in cellulose hydrolysis by A. kurodai. These findings suggest that AkEG21 is a processive endoglucanase functionally equivalent to the CBH, which provides a CBH-independent mechanism for the mollusk to digest seaweed cellulose to glucose.
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Affiliation(s)
- Akihiko Tsuji
- Department of Biomolecular Function and Technology, Graduate School of Bioscience & Bioindustry, Tokushima University, Minamijosanjima, Tokushima, Japan
- * E-mail:
| | - Keizo Yuasa
- Department of Biomolecular Function and Technology, Graduate School of Bioscience & Bioindustry, Tokushima University, Minamijosanjima, Tokushima, Japan
| | - Chikako Asada
- Department of Bioresource Chemistry and Technology, Graduate School of Bioscience & Bioindustry, Tokushima University, Minamijosanjima, Tokushima, Japan
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11
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Sun J, Lu J, Xie G. Secretome analysis of Trichoderma reesei
CICC41495 for degradation of arabinoxylan in malted barley. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Junyong Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
| | - Guangfa Xie
- School of Biotechnology; Jiangnan University; 1800 Lihu Road Wuxi 214122 People's Republic of China
- National Engineering Research Center for Chinese Rice Wine; China Shaoxing Rice Wine Group Co. Ltd; Shaoxing 312000 People's Republic of China
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12
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Characterization of a Thermophilic Monosaccharide Stimulated β-Glucosidase from Acidothermus cellulolyticus. Chem Res Chin Univ 2018. [DOI: 10.1007/s40242-018-7408-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Spertino S, Boatti L, Icardi S, Manfredi M, Cattaneo C, Marengo E, Cavaletto M. Cellulomonas fimi secretomes: In vivo and in silico approaches for the lignocellulose bioconversion. J Biotechnol 2018; 270:21-29. [PMID: 29409863 DOI: 10.1016/j.jbiotec.2018.01.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/30/2017] [Accepted: 01/26/2018] [Indexed: 12/17/2022]
Abstract
Lignocellulose degradation is a challenging step for value added products and biofuels production. Cellulomonas fimi secretes complex mixtures of carbohydrate active enzymes (CAZymes) which synergistically degrade cellulose and hemicelluloses. Their characterization may provide new insights for enzymatic cocktails implementation. Bioinformatic analysis highlighted 1127 secreted proteins, constituting the in silico secretome, graphically represented in a 2DE map. According to Blast2GO functional annotation, many of these are involved in carbohydrates metabolism. In vivo secretomes were obtained, growing C. fimi on glucose, CMC or wheat straw for 24 h. Zymography revealed degradative activity on carbohydrates and proteomic analysis identified some CAZymes, only in secretomes obtained with CMC and wheat straw. An interaction between cellobiohydrolases is proposed as a strategy adopted by soluble multimodular cellulases. Such approach can be crucial for a better characterization and industrial exploitation of the synergism among C. fimi enzymes.
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Affiliation(s)
- Stefano Spertino
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy.
| | - Lara Boatti
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Sara Icardi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Marcello Manfredi
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy; ISALIT S.r.l., Novara, Italy
| | - Chiara Cattaneo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Emilio Marengo
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
| | - Maria Cavaletto
- Department of Scienze e Innovazione Tecnologica, University of Piemonte Orientale, Alessandria, Italy
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14
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Xu S, Wang Y, Tang Y, Ji Y. A protein-based mixed selector chiral monolithic stationary phase in capillary electrochromatography. NEW J CHEM 2018. [DOI: 10.1039/c8nj02309c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mixed selector CSP combines the enantioselectivities of both individual proteins, thus expanding their application range practically.
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Affiliation(s)
- Shujuan Xu
- Department of Analytical Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
| | - Yuying Wang
- Department of Analytical Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
| | - Yixia Tang
- Department of Analytical Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
| | - Yibing Ji
- Department of Analytical Chemistry
- China Pharmaceutical University
- Nanjing 210009
- China
- Key Laboratory of Drug Quality Control and Pharmacovigilance
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15
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Qian Y, Zhong L, Gao J, Sun N, Wang Y, Sun G, Qu Y, Zhong Y. Production of highly efficient cellulase mixtures by genetically exploiting the potentials of Trichoderma reesei endogenous cellulases for hydrolysis of corncob residues. Microb Cell Fact 2017; 16:207. [PMID: 29162107 PMCID: PMC5696804 DOI: 10.1186/s12934-017-0825-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 11/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trichoderma reesei is one of the most important fungi utilized for cellulase production. However, its cellulase system has been proven to be present in suboptimal ratio for deconstruction of lignocellulosic substrates. Although previous enzymatic optimization studies have acquired different types of in vitro synthetic mixtures for efficient lignocellulose hydrolysis, production of in vivo optimized cellulase mixtures by industrial strains remains one of the obstacles to reduce enzyme cost in the biofuels production from lignocellulosic biomass. RESULTS In this study, we used a systematic genetic strategy based on the pyrG marker to overexpress the major cellulase components in a hypercellulolytic T. reesei strain and produce the highly efficient cellulase mixture for saccharification of corncob residues. We found that overexpression of CBH2 exhibited a 32-fold increase in the transcription level and a comparable protein level to CBH1, the most abundant secreted protein in T. reesei, but did not contribute much to the cellulolytic ability. However, when EG2 was overexpressed with a 46-fold increase in the transcription level and a comparable protein level to CBH2, the engineered strain QPE36 showed a 1.5-fold enhancement in the total cellulase activity (up to 5.8 U/mL FPA) and a significant promotion of saccharification efficiency towards differently pretreated corncob residues. To assist the following genetic manipulations, the marker pyrG was successfully excised by homologous recombination based on resistance to 5-FOA. Furthermore, BGL1 was overexpressed in the EG2 overexpression strain QE51 (pyrG-excised) and a 11.6-fold increase in BGL activity was obtained. The EG2-BGL1 double overexpression strain QEB4 displayed a remarkable enhancement of cellulolytic ability on pretreated corncob residues. Especially, a nearly complete cellulose conversion (94.2%) was found for the delignified corncob residues after 48 h enzymatic saccharification. CONCLUSIONS These results demonstrate that genetically exploiting the potentials of T. reesei endogenous cellulases to produce highly efficient cellulase mixtures is a powerful strategy to promote the saccharification efficiency, which will eventually facilitate cost reduction for lignocellulose-based biofuels.
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Affiliation(s)
- Yuanchao Qian
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Lixia Zhong
- Shandong Institute for Food and Drug Control, Jinan, 250101, People's Republic of China
| | - Jia Gao
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Ningning Sun
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Yifan Wang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Guoyong Sun
- Anaesthesiology Department of the Second Hospital of Shandong University, Jinan, 250100, People's Republic of China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, 250100, People's Republic of China.
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Reyes-Sosa FM, López Morales M, Platero Gómez AI, Valbuena Crespo N, Sánchez Zamorano L, Rocha-Martín J, Molina-Heredia FP, Díez García B. Management of enzyme diversity in high-performance cellulolytic cocktails. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:156. [PMID: 28649275 PMCID: PMC5477296 DOI: 10.1186/s13068-017-0845-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/12/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Modern biorefineries require enzymatic cocktails of improved efficiency to generate fermentable sugars from lignocellulosic biomass. Cellulolytic fungi, among other microorganisms, have demonstrated the highest potential in terms of enzymatic productivity, complexity and efficiency. On the other hand, under cellulolytic-inducing conditions, they often produce a considerable diversity of carbohydrate-active enzymes which allow them to adapt to changing environmental conditions. However, industrial conditions are fixed and adjusted to the optimum of the whole cocktail, resulting in underperformance of individual enzymes. RESULTS One of these cellulolytic cocktails from Myceliophthora thermophila has been analyzed here by means of LC-MS/MS. Pure GH6 family members detected have been characterized, confirming previous studies, and added to whole cocktails to compare their contribution in the hydrolysis of industrial substrates. Finally, independent deletions of two GH6 family members, as an example of the enzymatic diversity management, led to the development of a strain producing a more efficient cellulolytic cocktail. CONCLUSIONS These data indicate that the deletion of noncontributive cellulases (here EG VI) can increase the cellulolytic efficiency of the cocktail, validating the management of cellulase diversity as a strategy to obtain improved fungal cellulolytic cocktails.
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Affiliation(s)
| | - Macarena López Morales
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Ana Isabel Platero Gómez
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Noelia Valbuena Crespo
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Laura Sánchez Zamorano
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Javier Rocha-Martín
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Fernando P. Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y CSIC, Américo Vespucio 49, 41092 Seville, Spain
| | - Bruno Díez García
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
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17
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Matsunaga H, Haginaka J. Separation of enantiomers on chiral stationary phase based on cellulase: Effect of preparation method and silica particle diameters on chiral recognition ability. J Chromatogr A 2016; 1467:155-162. [PMID: 27266335 DOI: 10.1016/j.chroma.2016.05.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
Cellulase (Cel) was immobilized onto aminopropyl-silica gels via its amino and carboxy groups, respectively, using N,N'-disuccinimidyl carbonate, and 1-ethyl-3-(3'-dimethylaminopropyl)carbodimide and N-hydroxysulfosuccinimide. They were termed N-Cel and C-Cel, respectively. Despite their smaller retention factors on a C-Cel column, the enantioseparation factors and resolution of β-blockers, propranolol, alprenolol, oxprenolol and pindolol, were similar with N- and C-Cel columns. In addition, C-Cel was prepared using aminopropyl-silica gels, whose nominal particle diameters were 5 and 3, and 2.1μm, respectively. A C-Cel column prepared with 2.1-μm aminopropyl-silica gels gave the highest enantioselectivity and column efficiency among three C-Cel columns. Furthermore, the influence of N,N-dimethyl-n-octylamine (DMOA) or cellobiose concentrations on the retentivity and enantioselectivity for β-blockers on a C-Cel column was investigated. The results indicate that single-site competition of β-blockers with DMOA or cellobiose on the catalytic binding site of Cel and the further bindings at the secondary site in a non-competitive fashion could occur. Furthermore, the enantioselective bindings of β-blockers could occur at the catalytic biding cite of Cel and at the secondary binding site.
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Affiliation(s)
- Hisami Matsunaga
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, 11-68, Koshien Kyuban-cho, Nishinomiya 663-8179, Japan
| | - Jun Haginaka
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, 11-68, Koshien Kyuban-cho, Nishinomiya 663-8179, Japan.
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18
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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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19
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Pretreatment Processes for Cellulosic Ethanol Production: Processes Integration and Modeling for the Utilization of Lignocellulosics Such as Sugarcane Straw. GREEN FUELS TECHNOLOGY 2016. [DOI: 10.1007/978-3-319-30205-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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20
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de Amorim Araújo J, Ferreira TC, Rubini MR, Duran AGG, De Marco JL, de Moraes LMP, Torres FAG. Coexpression of cellulases in Pichia pastoris as a self-processing protein fusion. AMB Express 2015; 5:84. [PMID: 26698316 PMCID: PMC4689727 DOI: 10.1186/s13568-015-0170-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/11/2015] [Indexed: 02/06/2023] Open
Abstract
The term cellulase refers to any component of the enzymatic complex produced by some fungi, bacteria and protozoans which act serially or synergistically to catalyze the cleavage of cellulosic materials. Cellulases have been widely used in many industrial applications ranging from food industry to the production of second generation ethanol. In an effort to develop new strategies to minimize the costs of enzyme production we describe the development of a Pichia pastoris strain able to coproduce two different cellulases. For that purpose the eglII (endoglucanase II) and cbhII (cellobiohydrolase II) genes from Trichoderma reesei were fused in-frame separated by the self-processing 2A peptide sequence from the foot-and-mouth disease virus. The protein fusion construct was placed under the control of the strong inducible AOX1 promoter. Analysis of culture supernatants from methanol-induced yeast transformants showed that the protein fusion was effectively processed. Enzymatic assay showed that the processed enzymes were fully functional with the same catalytic properties of the individual enzymes produced separately. Furthermore, when combined both enzymes acted synergistically on filter paper to produce cellobiose as the main end-product. Based on these results we propose that P. pastoris should be considered as an alternative platform for the production of cellulases at competitive costs.
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21
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Lehmann L, Rønnest NP, Jørgensen CI, Olsson L, Stocks SM, Jørgensen HS, Hobley T. Linking hydrolysis performance to Trichoderma reesei cellulolytic enzyme profile. Biotechnol Bioeng 2015; 113:1001-10. [PMID: 26524197 DOI: 10.1002/bit.25871] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 11/07/2022]
Abstract
Trichoderma reesei expresses a large number of enzymes involved in lignocellulose hydrolysis and the mechanism of how these enzymes work together is too complex to study by traditional methods, for example, by spiking with single enzymes and monitoring hydrolysis performance. In this study, a multivariate approach, partial least squares regression, was used to see whether it could help explain the correlation between enzyme profile and hydrolysis performance. Diverse enzyme mixtures were produced by T. reesei Rut-C30 by exploiting various fermentation conditions and used for hydrolysis of washed pretreated corn stover as a measure of enzyme performance. In addition, the enzyme mixtures were analyzed by liquid chromatography-tandem mass spectrometry to identify and quantify the different proteins. A multivariate model was applied for the prediction of enzyme performance based on the combination of different proteins present in an enzyme mixture. The multivariate model was used for identification of candidate proteins that are correlated to enzyme performance on pretreated corn stover. A very large variation in hydrolysis performance was observed and this was clearly caused by the difference in fermentation conditions. Besides β-glucosidase, the multivariate model identified several xylanases, Cip1 and Cip2, as relevant proteins to study further.
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Affiliation(s)
- Linda Lehmann
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Nanna P Rønnest
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Lisbeth Olsson
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | | | | | - Timothy Hobley
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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22
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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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23
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Tsai CT, Meyer AS. Enzymatic cellulose hydrolysis: enzyme reusability and visualization of β-glucosidase immobilized in calcium alginate. Molecules 2014; 19:19390-406. [PMID: 25429563 PMCID: PMC6271082 DOI: 10.3390/molecules191219390] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 11/16/2022] Open
Abstract
The high cellulase enzyme dosages required for hydrolysis of cellulose is a major cost challenge in lignocellulosic ethanol production. One method to decrease the enzyme dosage and increase biocatalytic productivity is to re-use β-glucosidase (BG) via immobilization. In the present research, glutaraldehyde cross-linked BG was entrapped in calcium alginate gel particles. More than 60% of the enzyme activity could be recovered under optimized conditions, and glutaraldehyde cross-linking decreased leakage of BG from the calcium alginate particles. The immobilized BG aggregates were visualized by confocal laser scanning microscopy (CLSM). The CLSM images, which we believe are the first to be published, corroborate that more BG aggregates were entrapped in the matrix when the enzymes were cross-linked by glutaraldehyde as opposed to when they are not cross-linked. The particles with the immobilized BG were recycled for cellulase catalyzed hydrolysis of Avicel. No significant loss in BG activity was observed for up to 20 rounds of reaction recycle steps of the BG particles of 48 h each, verifying a significant stabilization of the BG by immobilization. Similar high glucose yields were obtained by one round of enzymatic hydrolysis of hydrothermally pretreated barley straw during a 72 h reaction with immobilized BG and free BG.
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Affiliation(s)
- Chien-Tai Tsai
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Anne S Meyer
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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24
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Ko JK, Ximenes E, Kim Y, Ladisch MR. Adsorption of enzyme onto lignins of liquid hot water pretreated hardwoods. Biotechnol Bioeng 2014; 112:447-56. [PMID: 25116138 DOI: 10.1002/bit.25359] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/02/2014] [Accepted: 07/28/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Ja Kyong Ko
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette Indiana 47907-2022
- Department of Agricultural and Biological Engineering; Purdue University; West Lafayette Indiana 47907-2022
| | - Eduardo Ximenes
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette Indiana 47907-2022
- Department of Agricultural and Biological Engineering; Purdue University; West Lafayette Indiana 47907-2022
| | - Youngmi Kim
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette Indiana 47907-2022
- Department of Agricultural and Biological Engineering; Purdue University; West Lafayette Indiana 47907-2022
| | - Michael R. Ladisch
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette Indiana 47907-2022
- Department of Agricultural and Biological Engineering; Purdue University; West Lafayette Indiana 47907-2022
- Weldon School of Biomedical Engineering; Purdue University; West Lafayette Indiana 47907-2022
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25
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Cui YX, Liu JJ, Liu Y, Cheng QY, Yu Q, Chen X, Ren XD. Protoplast fusion enhances lignocellulolytic enzyme activities in Trichoderma reesei. Biotechnol Lett 2014; 36:2495-9. [DOI: 10.1007/s10529-014-1627-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/06/2014] [Indexed: 11/29/2022]
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26
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Lozano P, Bernal B, Jara AG, Belleville MP. Enzymatic membrane reactor for full saccharification of ionic liquid-pretreated microcrystalline cellulose. BIORESOURCE TECHNOLOGY 2014; 151:159-165. [PMID: 24220543 DOI: 10.1016/j.biortech.2013.10.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/16/2013] [Accepted: 10/18/2013] [Indexed: 06/02/2023]
Abstract
Ultrafiltration reactors based on polymeric or ceramic membranes were shown to be suitable catalytic systems for fast enzymatic saccharification of cellulose, allowing the full recovery and reuse of enzymes. By pre-treating cellulose with the IL 1-butyl-3-methylimidazolium chloride, the suitability of this substrate for enzymatic saccharification in a reactor based on polymeric ultrafiltration membranes was demonstrated, leading to 95% cellulose hydrolysis in 4h at 50°C. The filtration process gave a clear glucose solution (up to 113 mM) at constant permeate flow (24.7 L h(-1) m(-2)), allowing the enzyme to be reused for 9 operation cycles under semi-continuous operation, without any loss of enzyme activity. Under continuous operation mode and using ceramic ultrafiltration membranes at different residence times, the enzymatic reactor showed constant profiles in both the permeate flow rate and the glucose concentration, demonstrating the excellent suitability of the proposed approach for the saccharification of cellulose.
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Affiliation(s)
- Pedro Lozano
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, P.O. Box 4021, E-30100 Murcia, Spain.
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27
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Silveira MHL, Aguiar RS, Siika-aho M, Ramos LP. Assessment of the enzymatic hydrolysis profile of cellulosic substrates based on reducing sugar release. BIORESOURCE TECHNOLOGY 2014; 151:392-396. [PMID: 24157315 DOI: 10.1016/j.biortech.2013.09.135] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/26/2013] [Accepted: 09/28/2013] [Indexed: 06/02/2023]
Abstract
The activity profile of a 1:0.30 mixture of Celluclast 1.5L FG and Novozym 188 (Novozymes) was investigated using Whatman #1 filter paper (W1FP) as a single substrate for hydrolysis. The procedure was based on the ability of the enzymes to release total (RS(Tot)), insoluble (RS(Insol)) and soluble (RS(Sol)) reducing sugars from W1FP. RS(Insol) was used to estimate endoglucanase (EnG) activity whereas exoglucanases (ExG) were assessed by measuring RSSol in the presence of δ-gluconolactone. Finally, the β-glucosidase (βG) activity was derived from the difference between RS(Sol) measurements in the presence and absence of δ-gluconolactone. When this analytical procedure was applied to W1FP using 9.64 mg mL(-1) of the enzyme mixture, the relative contributions of EnG, ExG and βG to the total cellulase activity were 63.28%, 12.02% and 24.70%, respectively. Also, this ratio changed with changes in the enzyme loading, giving a new insight into the synergy that exists among the enzymes.
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Affiliation(s)
- Marcos Henrique Luciano Silveira
- Research Center in Applied Chemistry (CEPESQ), Department of Chemistry, Federal University of Paraná, P.O. Box 19081, Curitiba, Paraná 81531-970, Brazil; VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT Espoo, Finland
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28
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Inoue H, Decker SR, Taylor LE, Yano S, Sawayama S. Identification and characterization of core cellulolytic enzymes from Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) critical for hydrolysis of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:151. [PMID: 25342974 PMCID: PMC4196096 DOI: 10.1186/s13068-014-0151-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/25/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of pretreated lignocellulosic biomass is an essential process for the production of fermentable sugars for industrial use. A better understanding of fungal cellulase systems will provide clues for maximizing the hydrolysis of target biomass. Talaromyces cellulolyticus is a promising fungus for cellulase production and efficient biomass hydrolysis. Several cellulolytic enzymes purified from T. cellulolyticus were characterized in earlier studies, but the core enzymes critical for hydrolysis of lignocellulosic biomass remain unknown. RESULTS Six cellulolytic enzymes critical for the hydrolysis of crystalline cellulose were purified from T. cellulolyticus culture supernatant using an enzyme assay based on synergistic hydrolysis of Avicel. The purified enzymes were identified by their substrate specificities and analyses of trypsin-digested peptide fragments and were classified into the following glycosyl hydrolase (GH) families: GH3 (β-glucosidase, Bgl3A), GH5 (endoglucanase, Cel5A), GH6 (cellobiohydrolase II, Cel6A), GH7 (cellobiohydrolase I and endoglucanase, Cel7A and Cel7B, respectively), and GH10 (xylanase, Xyl10A). Hydrolysis of dilute acid-pretreated corn stover (PCS) with mixtures of the purified enzymes showed that Cel5A, Cel7B, and Xyl10A each had synergistic effects with a mixture of Cel6A and Cel7A. Cel5A seemed to be more effective in the synergistic hydrolysis of the PCS than Cel7B. The ratio of Cel5A, Cel6A, Cel7A, and Xyl10A was statistically optimized for the hydrolysis of PCS glucan in the presence of Bgl3A. The resultant mixture achieved higher PCS glucan hydrolysis at lower enzyme loading than a culture filtrate from T. cellulolyticus or a commercial enzyme preparation, demonstrating that the five enzymes play a role as core enzymes in the hydrolysis of PCS glucan. CONCLUSIONS Core cellulolytic enzymes in the T. cellulolyticus cellulase system were identified to Cel5A, Cel6A, Cel7A, Xyl10A, and Bgl3A and characterized. The optimized mixture of these five enzymes was highly effective for the hydrolysis of PCS glucan, providing a foundation for future improvement of the T. cellulolyticus cellulase system.
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Affiliation(s)
- Hiroyuki Inoue
- />Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Stephen R Decker
- />Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401 USA
| | - Larry E Taylor
- />Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401 USA
| | - Shinichi Yano
- />Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Shigeki Sawayama
- />Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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29
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Anderson LN, Culley DE, Hofstad BA, Chauvigné-Hines LM, Zink EM, Purvine SO, Smith RD, Callister SJ, Magnuson JM, Wright AT. Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30. MOLECULAR BIOSYSTEMS 2013; 9:2992-3000. [PMID: 24121482 DOI: 10.1039/c3mb70333a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignocellulosic biomass has great promise as a highly abundant and renewable source for the production of biofuels. However, the recalcitrant nature of lignocellulose toward hydrolysis into soluble sugars remains a significant challenge to harnessing the potential of this source of bioenergy. A primary method for deconstructing lignocellulose is via chemical treatments, high temperatures, and hydrolytic enzyme cocktails, many of which are derived from the fungus Trichoderma reesei. Herein, we use an activity-based probe for glycoside hydrolases to rapidly identify optimal conditions for maximum enzymatic lignocellulose deconstruction. We also demonstrate that subtle changes to enzyme composition and activity in various strains of T. reesei can be readily characterized by our probe approach. The approach also permits multimodal measurements, including fluorescent gel-based analysis of activity in response to varied conditions and treatments, and mass spectrometry-based quantitative identification of labelled proteins. We demonstrate the promise this probe approach holds to facilitate rapid production of enzyme cocktails for high-efficiency lignocellulose deconstruction to accommodate high-yield biofuel production.
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Affiliation(s)
- Lindsey N Anderson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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30
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Ng IS, Chi X, Wu X, Bao Z, Lu Y, Chang JS, Ling X. Cloning and expression of Cel8A from Klebsiella pneumoniae in Escherichia coli and comparison to cel gene of Cellulomonas uda. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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Li X, Jackson P, Rubtsov DV, Faria-Blanc N, Mortimer JC, Turner SR, Krogh KB, Johansen KS, Dupree P. Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active enzymes. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:94. [PMID: 23819705 PMCID: PMC3717103 DOI: 10.1186/1754-6834-6-94] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/28/2013] [Indexed: 05/17/2023]
Abstract
BACKGROUND Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. RESULTS A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 samples simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of samples is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify enzymes with unusual oligosaccharide products. CONCLUSIONS The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active enzymes.
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Affiliation(s)
- Xiaofei Li
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Peter Jackson
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Denis V Rubtsov
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Nuno Faria-Blanc
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Jenny C Mortimer
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Simon R Turner
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | | | | | - Paul Dupree
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
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Rodriguez-Gomez D, Hobley TJ. Is an organic nitrogen source needed for cellulase production by Trichoderma reesei Rut-C30? World J Microbiol Biotechnol 2013; 29:2157-65. [PMID: 23712479 DOI: 10.1007/s11274-013-1381-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/15/2013] [Indexed: 12/29/2022]
Abstract
The effect of organic and inorganic nitrogen sources on Trichoderma reesei Rut-C30 cellulase production was investigated in submerged cultivations. Stirred tank bioreactors and shake flasks, with and without pH control, respectively, were employed. The experimental design involved the addition of individual organic nitrogen sources (soy peptone, glutamate, glycine and alanine) within a basal medium containing Avicel (i.e. micro crystalline cellulose) and ammonium sulphate. It was found that in the shake flask experiments, the highest cellulase activities (~0.1 ± 0.02 FPU ml(-1)) were obtained with media containing soy peptone (3-6 g l(-1)) and glutamate (3.6 g l(-1)). However, these improvements in the cellulase titers in the presence of the organic nitrogen sources appeared to be related to smaller changes in the pH of the medium. This was confirmed using stirred tank bioreactors with pH control. No significant differences were observed in the highest cellulase titers and the protein pattern (according to the SDS-PAGE) of supernatants from pH controlled stirred tank bioreactor cultivations, when different nitrogen sources were used in the medium. Here the cellulase activities (~1.0 ± 0.2 FPU ml(-1)) were also much greater (8-150 times) than in shake flask cultivation. Consequently, the addition of ammonium sulphate as sole nitrogen source to Avicel basal medium is recommended when performing cultivations in stirred tank bioreactors with strict pH controlled conditions.
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Lou H, Zhu JY, Lan TQ, Lai H, Qiu X. pH-Induced lignin surface modification to reduce nonspecific cellulase binding and enhance enzymatic saccharification of lignocelluloses. CHEMSUSCHEM 2013; 6:919-27. [PMID: 23554287 DOI: 10.1002/cssc.201200859] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Indexed: 05/02/2023]
Abstract
We studied the mechanism of the significant enhancement in the enzymatic saccharification of lignocelluloses at an elevated pH of 5.5-6.0. Four lignin residues with different sulfonic acid contents were isolated from enzymatic hydrolysis of lodgepole pine pretreated by either dilute acid (DA) or sulfite pretreatment to overcome recalcitrance of lignocelluloses (SPORL). The adsorption isotherms of a commercial Trichoderma reesi cellulase cocktail (CTec2) produced by these lignin residues at 50 °C were measured in the pH range of 4.5-6.0. The zeta potentials of these lignin samples were also measured. We discovered that an elevated pH significantly increased the lignin surface charge (negative), which causes lignin to become more hydrophilic and reduces its coordination affinity to cellulase and, consequently, the nonspecific binding of cellulase. The decreased nonspecific cellulase binding to lignin is also attributed to enhanced electrostatic interactions at elevated pH through the increased negative charges of cellulase enzymes with low pI. The results validate the hypothesis that the increases in enzymatic saccharification efficiencies at elevated pH for different pretreated lignocelluloses are solely the result of decreased nonspecific cellulase binding to lignin. This study contradicts the well-established concept that the optimal pH is 4.8-5.0 for enzymatic hydrolysis using Trichoderma reesi cellulose, which is widely accepted and exclusively practiced in numerous laboratories throughout the world. Because an elevated pH can be easily implemented commercially without capital cost and with minimal operating cost, this study has both scientific importance and practical significance.
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Affiliation(s)
- Hongming Lou
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, PR China
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Lan TQ, Wei D, Yang ST, Liu X. Enhanced cellulase production by Trichoderma viride in a rotating fibrous bed bioreactor. BIORESOURCE TECHNOLOGY 2013; 133:175-182. [PMID: 23428816 DOI: 10.1016/j.biortech.2013.01.088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/17/2013] [Accepted: 01/19/2013] [Indexed: 06/01/2023]
Abstract
Filamentous fungi are widely used to produce cellulase, but how the fermentation conditions affect their production is not well known. In this study, cellulase production by Trichoderma viride in submerged fermentations with free cells in a stirred-tank reactor (STR) and immobilized cells in a rotating fibrous-bed bioreactor (RFBB) were investigated. Compared to free-cell fermentation, immobilized-cell fermentation gave 35.5% higher FPase activity and 69.7% higher saccharification yield of sugarcane bagasse (SCB). The secretory proteins in the fermentation broths were analyzed with two-dimensional gel electrophoresis (2-DE) and MALDI-TOF-TOF mass spectrometry, which identified 24 protein spots with differential expression levels. Among them, cellobiohydrolase CBH II and endoglucanase EG II were highly expressed and secreted in the immobilized-cell fermentation, while the free-cell fermentation produced more CBH І and EG ІV. These results showed that immobilized-cell fermentation with T. viride in the RFBB was advantageous for cellulase production.
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Affiliation(s)
- Tian-Qing Lan
- State Key Laboratory of Pulp and Paper Engineering, School of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, PR China
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A simple and fast method for the determination of endo- and exo-cellulase activity in cellulase preparations using filter paper. Enzyme Microb Technol 2012; 51:280-5. [DOI: 10.1016/j.enzmictec.2012.07.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 06/22/2012] [Accepted: 07/23/2012] [Indexed: 11/17/2022]
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Chylenski P, Felby C, Østergaard Haven M, Gama M, Selig MJ. Precipitation of Trichoderma reesei commercial cellulase preparations under standard enzymatic hydrolysis conditions for lignocelluloses. Biotechnol Lett 2012; 34:1475-82. [PMID: 22476551 DOI: 10.1007/s10529-012-0916-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 03/21/2012] [Indexed: 11/24/2022]
Affiliation(s)
- Piotr Chylenski
- Faculty of Science, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
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37
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Langston JA, Brown K, Xu F, Borch K, Garner A, Sweeney MD. Cloning, expression, and characterization of a cellobiose dehydrogenase from Thielavia terrestris induced under cellulose growth conditions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:802-12. [PMID: 22484439 DOI: 10.1016/j.bbapap.2012.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 11/19/2022]
Abstract
The enzyme cellobiose dehydrogenase (CDH) is of considerable interest, not only for its biotechnological applications, but also its potential biological role in lignocellulosic biomass breakdown. The enzyme catalyzes the oxidation of cellobiose and other cellodextrins, utilizing a variety of one- and two-electron acceptors, although the electron acceptor employed in nature is still unknown. In this study we show that a CDH is present in the secretome of the thermophilic ascomycete Thielavia terrestris when grown with cellulose, along with a mixture of cellulases and hemicellulases capable of breaking down lignocellulosic biomass. We report the cloning of this T. terrestris CDH gene (cbdA), its recombinant expression in Aspergillus oryzae, and purification and characterization of the T. terrestris CDH protein (TtCDH). The TtCDH shows spectral properties and enzyme activity similar to other characterized CDH enzymes. Substrate specificity was determined for a number of carbohydrate electron donors in the presence of the two-electron acceptor 2,6-dichlorophenol-indophenol. The TtCDH also shows dramatic synergy with Thermoascus aurantiacus glycoside hydrolase family 61A protein in the presence of a β-glucosidase for the cleavage of cellulose.
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Santhanam N, Badri DV, Decker SR, Manter DK, Reardon KF, Vivanco JM. Lignocellulose Decomposition by Microbial Secretions. SIGNALING AND COMMUNICATION IN PLANTS 2012. [DOI: 10.1007/978-3-642-23047-9_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Cellulolytic Enzyme Production and Enzymatic Hydrolysis for Second-Generation Bioethanol Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 128:1-24. [DOI: 10.1007/10_2011_131] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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40
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Saloheimo M, Pakula TM. The cargo and the transport system: secreted proteins and protein secretion in Trichoderma reesei (Hypocrea jecorina). Microbiology (Reading) 2012; 158:46-57. [DOI: 10.1099/mic.0.053132-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Markku Saloheimo
- VTT Technical Research Centre of Finland, PO Box 1000, FIN-02044 VTT, Finland
| | - Tiina M. Pakula
- VTT Technical Research Centre of Finland, PO Box 1000, FIN-02044 VTT, Finland
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41
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Salinas A, Vega M, Lienqueo ME, Garcia A, Carmona R, Salazar O. Cloning of novel cellulases from cellulolytic fungi: Heterologous expression of a family 5 glycoside hydrolase from Trametes versicolor in Pichia pastoris. Enzyme Microb Technol 2011; 49:485-91. [DOI: 10.1016/j.enzmictec.2011.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 09/15/2011] [Accepted: 10/11/2011] [Indexed: 10/16/2022]
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42
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Hasunuma T, Kondo A. Development of yeast cell factories for consolidated bioprocessing of lignocellulose to bioethanol through cell surface engineering. Biotechnol Adv 2011; 30:1207-18. [PMID: 22085593 DOI: 10.1016/j.biotechadv.2011.10.011] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/12/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
Abstract
To build an energy and material secure future, a next generation of renewable fuels produced from lignocellulosic biomass is required. Although lignocellulosic biomass, which represents an abundant, inexpensive and renewable source for bioethanol production, is of great interest as a feedstock, the complicated ethanol production processes involved make the cost of producing bioethanol from it higher compared to corn starch and cane juice. Therefore, consolidated bioprocessing (CBP), which combines enzyme production, saccharification and fermentation in a single step, has gained increased recognition as a potential bioethanol production system. CBP requires a highly engineered microorganism developed for several different process-specific characteristics. The dominant strategy for engineering a CBP biocatalyst is to express multiple components of a cellulolytic system from either fungi or bacteria in the yeast Saccharomyces cerevisiae. The development of recombinant yeast strains displaying cellulases and hemicellulases on the cell surface represents significant progress toward realization of CBP. Regardless of the process used for biomass hydrolysis, CBP-enabling microorganisms encounter a variety of toxic compounds produced during biomass pretreatment that inhibit microbial growth and ethanol yield. Systems biology approaches including disruptome screening, transcriptomics, and metabolomics have been recently exploited to gain insight into the molecular and genetic traits involved in tolerance and adaptation to the fermentation inhibitors. In this review, we focus on recent advances in development of yeast strains with both the ability to directly convert lignocellulosic material to ethanol and tolerance in the harsh environments containing toxic compounds in the presence of ethanol.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Xu J, Wang Z, Cheng JJ. Bermuda grass as feedstock for biofuel production: a review. BIORESOURCE TECHNOLOGY 2011; 102:7613-20. [PMID: 21683586 DOI: 10.1016/j.biortech.2011.05.070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/24/2011] [Accepted: 05/25/2011] [Indexed: 05/20/2023]
Abstract
Bermuda grass is a promising feedstock for the production of fuel ethanol in the Southern United States. This paper presents a review of the significant amount of research on the conversion of Bermuda grass to ethanol and a brief discussion on the factors affecting the biomass production in the field. The biggest challenge of biomass conversion comes from the recalcitrance of lignocellulose. A variety of chemical, physico-chemical, and biological pretreatment methods have been investigated to improve the digestibility of Bermuda grass with encouraging results reported. The subsequent enzymatic hydrolysis and fermentation steps have also been extensively studied and effectively optimized. It is expected that the development of genetic engineering technologies for the grass and fermenting organisms has the potential to greatly improve the economic viability of Bermuda grass-based fuel ethanol production systems. Other energy applications of Bermuda grass include anaerobic digestion for biogas generation and pyrolysis for syngas production.
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Affiliation(s)
- Jiele Xu
- Department of Biological and Agricultural Engineering, Campus Box 7625, North Carolina State University, Raleigh, NC 27695, USA
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Chundawat SPS, Lipton MS, Purvine SO, Uppugundla N, Gao D, Balan V, Dale BE. Proteomics-based compositional analysis of complex cellulase-hemicellulase mixtures. J Proteome Res 2011; 10:4365-72. [PMID: 21678892 DOI: 10.1021/pr101234z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Efficient deconstruction of cellulosic biomass to fermentable sugars for fuel and chemical production is accomplished by a complex mixture of cellulases, hemicellulases, and accessory enzymes (e.g., >50 extracellular proteins). Cellulolytic enzyme mixtures, produced industrially mostly using fungi like Trichoderma reesei, are poorly characterized in terms of their protein composition and its correlation to hydrolytic activity on cellulosic biomass. The secretomes of commercial glycosyl hydrolase-producing microbes was explored using a proteomics approach with high-throughput quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we show that proteomics-based spectral counting approach is a reasonably accurate and rapid analytical technique that can be used to determine protein composition of complex glycosyl hydrolase mixtures that also correlates with the specific activity of individual enzymes present within the mixture. For example, a strong linear correlation was seen between Avicelase activity and total cellobiohydrolase content. Reliable, quantitative and cheaper analytical methods that provide insight into the cellulosic biomass degrading fungal and bacterial secretomes would lead to further improvements toward commercialization of plant biomass-derived fuels and chemicals.
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Affiliation(s)
- Shishir P S Chundawat
- Biomass Conversion Research Laboratory, Chemical Engineering and Materials Science, Michigan State University , 3815 Technology Boulevard, Suite 1045, Lansing, Michigan 48910, United States.
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Ng IS, Tsai SW, Ju YM, Yu SM, Ho THD. Dynamic synergistic effect on Trichoderma reesei cellulases by novel β-glucosidases from Taiwanese fungi. BIORESOURCE TECHNOLOGY 2011; 102:6073-81. [PMID: 21377353 DOI: 10.1016/j.biortech.2010.12.110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/28/2010] [Accepted: 12/30/2010] [Indexed: 05/02/2023]
Abstract
Dynamic synergistic effects in cellulosic bioconversion have been revealed between Trichoderma reesei cellulases and β-glucosidases (BGLs) from six Taiwanese fungi. A high level of synergy (8.9-fold) was observed with the addition of Chaetomella raphigera BGL to T. reesei cellulases. In addition, the C. raphigera BGL possessed the highest activity (V(max)/K(m)=46.6 U/mg mM) and lowest glucose inhibition (Ki=4.6mM) with the substrate 4-nitrophenyl β-d-glucopyranoside. For the natural cellobiose substrate, however, the previously isolated Aspergillus niger BGL Novo-188 had the highest V(max)/K(m) (0.72 U/mg mM) and lowest Ki (59.5mM). The demonstrated dynamic synergistic effects between some BGLs and the T. reesei cellulase system suggest that BGLs not only prevent the inhibition by cellobiose, but also enhance activities of endo- and exo-cellulases in cellulosic bioconversion. Comparisons of kinetic parameters and synergism analyses between BGLs and T. reesei cellulases can be used for further optimization of the cellulosic bioconversion process.
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Affiliation(s)
- I-Son Ng
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Use of label-free quantitative proteomics to distinguish the secreted cellulolytic systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Appl Environ Microbiol 2011; 77:4042-54. [PMID: 21498747 DOI: 10.1128/aem.02811-10] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extremely thermophilic, Gram-positive bacteria Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis efficiently degrade both cellulose and hemicellulose, which makes them relevant models for lignocellulosic biomass deconstruction to produce sustainable biofuels. To identify the shared and unique features of secreted cellulolytic apparatuses from C. bescii and C. obsidiansis, label-free quantitative proteomics was used to analyze protein abundance over the course of fermentative growth on crystalline cellulose. Both organisms' secretomes consisted of more than 400 proteins, of which the most abundant were multidomain glycosidases, extracellular solute-binding proteins, flagellin, putative pectate lyases, and uncharacterized proteins with predicted secretion signals. Among the identified proteins, 53 to 57 significantly changed in abundance during cellulose fermentation in favor of glycosidases and extracellular binding proteins. Mass spectrometric characterizations, together with cellulase activity measurements, revealed a substantial abundance increase of a few bifunctional multidomain glycosidases composed of glycosidase (GH) domain family 5, 9, 10, 44, or 48 and family 3 carbohydrate binding (CBM3) modules. In addition to their orthologous cellulases, the organisms expressed unique glycosidases with different domain organizations: C. obsidiansis expressed the COB47_1671 protein with GH10/5 domains, while C. bescii expressed the Athe_1857 (GH10/48) and Athe_1859 (GH5/44) proteins. Glycosidases containing CBM3 domains were selectively enriched via binding to amorphous cellulose. Preparations from both bacteria contained highly thermostable enzymes with optimal cellulase activities at 85°C and pH 5. The C. obsidiansis preparation, however, had higher cellulase specific activity and greater thermostability. The C. bescii culture produced more extracellular protein and additional SDS-PAGE bands that demonstrated glycosidase activity.
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Secretome of the Coprophilous Fungus Doratomyces stemonitis C8, Isolated from Koala Feces. Appl Environ Microbiol 2011; 77:3793-801. [PMID: 21498763 DOI: 10.1128/aem.00252-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coprophilous fungi inhabit herbivore feces, secreting enzymes to degrade the most recalcitrant parts of plant biomass that have resisted the digestive process. Consequently, the secretomes of coprophilous fungi have high potential to contain novel and efficient plant cell wall degrading enzymes of biotechnological interest. We have used one-dimensional and two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization-time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS/MS), and quadrupole time-of-flight liquid chromatography-tandem mass spectrometry (Q-TOF LC-MS/MS) to identify proteins from the secretome of the coprophilous fungus Doratomyces stemonitis C8 (EU551185) isolated from koala feces. As the genome of D. stemonitis has not been sequenced, cross-species identification, de novo sequencing, and zymography formed an integral part of the analysis. A broad range of enzymes involved in the degradation of cellulose, hemicellulose, pectin, lignin, and protein were revealed, dominated by cellobiohydrolase of the glycosyl hydrolase family 7 and endo-1,4-β-xylanase of the glycosyl hydrolase family 10. A high degree of specialization for pectin degradation in the D. stemonitis C8 secretome distinguishes it from the secretomes of some other saprophytic fungi, such as the industrially exploited T. reesei. In the first proteomic analysis of the secretome of a coprophilous fungus reported to date, the identified enzymes provide valuable insight into how coprophilous fungi subsist on herbivore feces, and these findings hold potential for increasing the efficiency of plant biomass degradation in industrial processes such as biofuel production in the future.
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48
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Paul R, Teli MD. Effect of swelling and reactive dyeing on the accessibility of cotton to cellulase enzymes. J Appl Polym Sci 2011. [DOI: 10.1002/app.33772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Nakagame S, Chandra RP, Kadla JF, Saddler JN. The isolation, characterization and effect of lignin isolated from steam pretreated Douglas-fir on the enzymatic hydrolysis of cellulose. BIORESOURCE TECHNOLOGY 2011; 102:4507-17. [PMID: 21256740 DOI: 10.1016/j.biortech.2010.12.082] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 12/22/2010] [Accepted: 12/22/2010] [Indexed: 05/02/2023]
Abstract
Douglas-fir was SO(2)-steam pretreated at different severities (190, 200, and 210°C) to assess the possible negative effect of the residual and isolated lignins on the enzymatic hydrolysis of the steam pretreated substrates. When various isolated lignins were added to the Avicel hydrolysis reactions, the decrease in glucose yields ranged from 15.2% to 29.0% after 72 h. It was apparent that the better hydrolysis yields obtained at higher pretreatment severities were more a result of the greater accessibly of the cellulose rather than any specific change in the non-productive binding of the lignin to the enzymes. FTIR and (13)C NMR characterization indicated that the lignin in the steam pretreated substrates became more condensed with increasing severity, suggesting that the cellulases were adsorbed to the lignin by hydrophobic interactions. Electrostatic interactions were also involved as the positively charged cellulase components were preferentially adsorbed to the lignins.
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Affiliation(s)
- Seiji Nakagame
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, Canada
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50
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Gusakov AV, Semenova MV, Sinitsyn AP. Mass spectrometry in the study of extracellular enzymes produced by filamentous fungi. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810140030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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