1
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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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2
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Leadbeater DR, Bruce NC. Functional characterisation of a new halotolerant seawater active glycoside hydrolase family 6 cellobiohydrolase from a salt marsh. Sci Rep 2024; 14:3205. [PMID: 38332324 PMCID: PMC10853513 DOI: 10.1038/s41598-024-53886-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Realising a fully circular bioeconomy requires the valorisation of lignocellulosic biomass. Cellulose is the most attractive component of lignocellulose but depolymerisation is inefficient, expensive and resource intensive requiring substantial volumes of potable water. Seawater is an attractive prospective replacement, however seawater tolerant enzymes are required for the development of seawater-based biorefineries. Here, we report a halophilic cellobiohydrolase SMECel6A, identified and isolated from a salt marsh meta-exo-proteome dataset with high sequence divergence to previously characterised cellobiohydrolases. SMECel6A contains a glycoside hydrolase family 6 (GH6) domain and a carbohydrate binding module family 2 (CBM2) domain. Characterisation of recombinant SMECel6A revealed SMECel6A to be active upon crystalline and amorphous cellulose. Mono- and oligosaccharide product profiles revealed cellobiose as the major hydrolysis product confirming SMECel6A as a cellobiohydrolase. We show SMECel6A to be halophilic with optimal activity achieved in 0.5X seawater displaying 80.6 ± 6.93% activity in 1 × seawater. Structural predictions revealed similarity to a characterised halophilic cellobiohydrolase despite sharing only 57% sequence identity. Sequential thermocycling revealed SMECel6A had the ability to partially reversibly denature exclusively in seawater retaining significant activity. Our study confirms that salt marsh ecosystems harbour enzymes with attractive traits with biotechnological potential for implementation in ionic solution based bioprocessing systems.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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3
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Ordeñana Manso J, Nielsen MB, Balaguer Moya E, Sandri JP, Yamakawa CK, Mussatto SI. Intensification of corn fiber saccharification using a tailor made enzymatic cocktail. Enzyme Microb Technol 2024; 172:110347. [PMID: 37931383 DOI: 10.1016/j.enzmictec.2023.110347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023]
Abstract
The transition from an economic model based on resource extraction to a more sustainable and circular economy requires the development of innovative methods to unlock the potential of raw materials such as lignocellulosic biomasses. Corn fiber differs from more traditional lignocellulosic biomasses due to its high starch content, which provides additional carbohydrates for fermentation-based biomanufacturing processes. Due to its unique chemical composition, this study focused on the development of a tailor made enzymatic cocktail for corn fiber saccharification into monosaccharides. Three commercially available hydrolytic enzymes (Cellic® CTec2, Pentopan® Mono BG, and Termamyl® 300 L) were combined to hydrolyze the polysaccharide structure of the three main carbohydrate fractions of corn fiber (cellulose, hemicellulose and starch, respectively). Prior to saccharification, corn fiber was submitted to a mild hydrothermal pretreatment (30 min at 100 °C). Then, two experimental designs were used to render an enzymatic cocktail capable of providing efficient release of monosaccharides. Using 60 FPU/g DM of Cellic® CTec2 and 4.62 U/g DM of Termamyl® 300 L, without addition of Pentopan® Mono BG, resulted in the highest efficiencies for glucose and xylose release (66% and 30%, respectively). While higher enzyme dosages could enhance the saccharification efficiency, adding more enzymes would have a more pronounced effect on the overall process costs rather than in increasing the efficiency for monosaccharides release. The results revealed that the recalcitrance of corn fiber poses a problem for its full enzymatic degradation. This fact combined with the unique chemical composition of this material, justify the need for developing a tailor made enzymatic cocktail for its degradation. However, attention should also be given to the pretreatment step to reduce even more the recalcitrance of corn fiber and improve the performance of the tailored cocktail, as a consequence.
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Affiliation(s)
- Julen Ordeñana Manso
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800, Kongens Lyngby, Denmark
| | - Martin B Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800, Kongens Lyngby, Denmark
| | - Eva Balaguer Moya
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800, Kongens Lyngby, Denmark
| | - Juliana P Sandri
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, Km 235, 13565-905, São Carlos, SP, Brazil
| | - Celina K Yamakawa
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800, Kongens Lyngby, Denmark
| | - Solange I Mussatto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800, Kongens Lyngby, Denmark.
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4
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202309305. [PMID: 38516574 PMCID: PMC10952289 DOI: 10.1002/ange.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 03/23/2024]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - John Davidson
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center National Renewable Energy Laboratory Golden CO USA
- BOTTLE Consortium Golden CO USA
| | - Anthony P Green
- Department of Chemistry & Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M1 7DN UK
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Radley E, Davidson J, Foster J, Obexer R, Bell EL, Green AP. Engineering Enzymes for Environmental Sustainability. Angew Chem Int Ed Engl 2023; 62:e202309305. [PMID: 37651344 PMCID: PMC10952156 DOI: 10.1002/anie.202309305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/02/2023]
Abstract
The development and implementation of sustainable catalytic technologies is key to delivering our net-zero targets. Here we review how engineered enzymes, with a focus on those developed using directed evolution, can be deployed to improve the sustainability of numerous processes and help to conserve our environment. Efficient and robust biocatalysts have been engineered to capture carbon dioxide (CO2 ) and have been embedded into new efficient metabolic CO2 fixation pathways. Enzymes have been refined for bioremediation, enhancing their ability to degrade toxic and harmful pollutants. Biocatalytic recycling is gaining momentum, with engineered cutinases and PETases developed for the depolymerization of the abundant plastic, polyethylene terephthalate (PET). Finally, biocatalytic approaches for accessing petroleum-based feedstocks and chemicals are expanding, using optimized enzymes to convert plant biomass into biofuels or other high value products. Through these examples, we hope to illustrate how enzyme engineering and biocatalysis can contribute to the development of cleaner and more efficient chemical industry.
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Affiliation(s)
- Emily Radley
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - John Davidson
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Jake Foster
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Richard Obexer
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Elizabeth L. Bell
- Renewable Resources and Enabling Sciences CenterNational Renewable Energy LaboratoryGoldenCOUSA
- BOTTLE ConsortiumGoldenCOUSA
| | - Anthony P. Green
- Department of Chemistry & Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
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6
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Barghout RA, Xu Z, Betala S, Mahadevan R. Advances in generative modeling methods and datasets to design novel enzymes for renewable chemicals and fuels. Curr Opin Biotechnol 2023; 84:103007. [PMID: 37931573 DOI: 10.1016/j.copbio.2023.103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 11/08/2023]
Abstract
Biotechnology has revolutionized the development of sustainable energy sources by harnessing biomass as a feedstock for energy production. However, challenges such as recalcitrant feedstocks and inefficient metabolic pathways hinder the large-scale integration of renewable energy systems. Enzyme engineering has emerged as a powerful tool to address these challenges by enhancing enzyme activity, specificity, and stability. Generative machine learning (ML) models have shown great promise in accelerating protein design, allowing for the generation of novel protein sequences with desired properties by navigating vast spaces. This review paper aims to summarize the state of the art in generative models for protein design and how they can be applied to bioenergy applications, including the underlying architectures and training strategies. Additionally, it highlights the importance of high-quality datasets for training and evaluating generative models, organizes available datasets for generative protein design, and discusses the potential of applying generative models to strain design for bioenergy production.
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Affiliation(s)
- Rana A Barghout
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College St, Toronto, ON, Canada.
| | - Zhiqing Xu
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College St, Toronto, ON, Canada
| | - Siddharth Betala
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College St, Toronto, ON, Canada
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7
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Lu H, Xue M, Nie X, Luo H, Tan Z, Yang X, Shi H, Li X, Wang T. Glycoside hydrolases in the biodegradation of lignocellulosic biomass. 3 Biotech 2023; 13:402. [PMID: 37982085 PMCID: PMC10654287 DOI: 10.1007/s13205-023-03819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/15/2023] [Indexed: 11/21/2023] Open
Abstract
Lignocellulose is a plentiful and intricate biomass substance made up of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are polysaccharides characterized by different compositions and degrees of polymerization. As renewable resources, their applications are eco-friendly and can help reduce reliance on petrochemical resources. This review aims to illustrate cellulose, hemicellulose, and their structures and hydrolytic enzymes. To obtain desirable enzyme sources for the high hydrolysis of lignocellulose, highly stable, efficient and thermophilic enzyme sources, and new technologies, such as rational design and machine learning, have been introduced in detail. Generally, the efficient biodegradation of abundant natural biomass into fermentable sugars or other intermediates has great potential in practical applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03819-1.
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Affiliation(s)
- Honglin Lu
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Maoyuan Xue
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xinling Nie
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Hongzheng Luo
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Zhongbiao Tan
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xiao Yang
- Department of Poultry Science, The University of Georgia, Athens, GA 30602 USA
| | - Hao Shi
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Tao Wang
- Department of Microbiology, The University of Georgia, Athens, GA 30602 USA
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8
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Chaudhary N, Grover M. Bioindustrial applications of thermostable Endoglucanase purified from Trichoderma viride towards the conversion of agrowastes to value-added products. Protein Expr Purif 2023; 211:106324. [PMID: 37356677 DOI: 10.1016/j.pep.2023.106324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/27/2023]
Abstract
Importance of biocatalytic reactions and biotransformations mediated by fungal enzymes has increased tremendously in various industries. Endoglucanase obtained from Trichoderma viride has been utilized for bioconversion of agrowastes; wheat straw (WS) and corn stover (CS) as biomass into citric acid and single cell protein (SCP) as value-added products. The enzyme was purified to apparent homogeneity with Mr:44.67 kDa; purification-fold, yield, specific activity to be 19.5-, 29.2%, and 150.4 Units.mg-1, respectively, with thermostability up to 70 °C. The enzyme showed a novel N-terminal peptide and its computational analysis revealed a conserved 'SG' amino acid sequence alike microbial cellulases. The experimental results have shown the potential of endoglucanase for the conversion of agrowastes; wheat straw (WS) and corn stover (CS) into citric acid, maximum yield (KgM-3) found in submerged (WS:50;CS:45) fermentation process. Single-cell protein (SCP) production in WS (68 KgM-3) hydrolysate was superior to both CS hydrolysate (60 KgM-3) and YEPD (standard medium) (58 KgM-3).
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Affiliation(s)
- Nidhee Chaudhary
- Centre of Biotechnology and Biochemical Engineering, Amity Institute of Biotechnology, Amity University, Uttar Pradesh, Sector-125, Noida, 201313, India.
| | - Monendra Grover
- Centre for Agricultural Bioinformatics, ICAR-IASRI, Library Avenue Pusa, New Delhi, India
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9
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Wang M, Cui H, Gu C, Li A, Qiao J, Schwaneberg U, Zhang L, Wei J, Li X, Huang H. Engineering All-Round Cellulase for Bioethanol Production. ACS Synth Biol 2023; 12:2187-2197. [PMID: 37403343 DOI: 10.1021/acssynbio.3c00289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
One strategy to decrease both the consumption of crude oil and environmental damage is through the production of bioethanol from biomass. Cellulolytic enzyme stability and enzymatic hydrolysis play important roles in the bioethanol process. However, the gradually increased ethanol concentration often reduces enzyme activity and leads to inactivation, thereby limiting the final ethanol yield. Herein, we employed an optimized Two-Gene Recombination Process (2GenReP) approach to evolve the exemplary cellulase CBHI for practical bioethanol fermentation. Two all-round CBHI variants (named as R2 and R4) were obtained with simultaneously improved ethanol resistance, organic solvent inhibitor tolerance, and enzymolysis stability in simultaneous saccharification and fermentation (SSF). Notably, CBHI R4 had a 7.0- to 34.5-fold enhanced catalytic efficiency (kcat/KM) in the presence/absence of ethanol. Employing the evolved CBHI R2 and R4 in the 1G bioethanol process resulted in up to 10.27% (6.7 g/L) improved ethanol yield (ethanol concentration) than non-cellulase, which was far more beyond than other optimization strategies. Besides bioenergy fields, this transferable protein engineering routine holds the potential to generate all-round enzymes that meet the requirement in biotransformation and bioenergy fields.
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Affiliation(s)
- Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Chenlei Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Lihui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Junnan Wei
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
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10
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Ouyang B, Wang G, Zhang N, Zuo J, Huang Y, Zhao X. Recent Advances in β-Glucosidase Sequence and Structure Engineering: A Brief Review. Molecules 2023; 28:4990. [PMID: 37446652 DOI: 10.3390/molecules28134990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
β-glucosidases (BGLs) play a crucial role in the degradation of lignocellulosic biomass as well as in industrial applications such as pharmaceuticals, foods, and flavors. However, the application of BGLs has been largely hindered by issues such as low enzyme activity, product inhibition, low stability, etc. Many approaches have been developed to engineer BGLs to improve these enzymatic characteristics to facilitate industrial production. In this article, we review the recent advances in BGL engineering in the field, including the efforts from our laboratory. We summarize and discuss the BGL engineering studies according to the targeted functions as well as the specific strategies used for BGL engineering.
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Affiliation(s)
- Bei Ouyang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Guoping Wang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Nian Zhang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Jiali Zuo
- School of Computer and Information Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Yunhong Huang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
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11
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Qiao J, Sheng Y, Wang M, Li A, Li X, Huang H. Evolving Robust and Interpretable Enzymes for the Bioethanol Industry. Angew Chem Int Ed Engl 2023; 62:e202300320. [PMID: 36701239 DOI: 10.1002/anie.202300320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 01/27/2023]
Abstract
Obtaining a robust and applicable enzyme for bioethanol production is a dream for biorefinery engineers. Herein, we describe a general method to evolve an all-round and interpretable enzyme that can be directly employed in the bioethanol industry. By integrating the transferable protein evolution strategy InSiReP 2.0 (In Silico guided Recombination Process), enzymatic characterization for actual production, and computational molecular understanding, the model cellulase PvCel5A (endoglucanase II Cel5A from Penicillium verruculosum) was successfully evolved to overcome the remaining challenges of low ethanol and temperature tolerance, which primarily limited biomass transformation and bioethanol yield. Remarkably, application of the PvCel5A variants in both first- and second-generation bioethanol production processes (i. Conventional corn ethanol fermentation combined with the in situ pretreatment process; ii. cellulosic ethanol fermentation process) resulted in a 5.7-10.1 % increase in the ethanol yield, which was unlikely to be achieved by other optimization techniques.
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Affiliation(s)
- Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China.,School of Pharmaceutical Science, Nanjing Tech University, Nanjing, 211816, China
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12
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Chaudhari YB, Várnai A, Sørlie M, Horn SJ, Eijsink VGH. Engineering cellulases for conversion of lignocellulosic biomass. Protein Eng Des Sel 2023; 36:gzad002. [PMID: 36892404 PMCID: PMC10394125 DOI: 10.1093/protein/gzad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023] Open
Abstract
Lignocellulosic biomass is a renewable source of energy, chemicals and materials. Many applications of this resource require the depolymerization of one or more of its polymeric constituents. Efficient enzymatic depolymerization of cellulose to glucose by cellulases and accessory enzymes such as lytic polysaccharide monooxygenases is a prerequisite for economically viable exploitation of this biomass. Microbes produce a remarkably diverse range of cellulases, which consist of glycoside hydrolase (GH) catalytic domains and, although not in all cases, substrate-binding carbohydrate-binding modules (CBMs). As enzymes are a considerable cost factor, there is great interest in finding or engineering improved and robust cellulases, with higher activity and stability, easy expression, and minimal product inhibition. This review addresses relevant engineering targets for cellulases, discusses a few notable cellulase engineering studies of the past decades and provides an overview of recent work in the field.
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Affiliation(s)
- Yogesh B Chaudhari
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, NMBU-Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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14
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Agro-Industrial Food Waste as a Low-Cost Substrate for Sustainable Production of Industrial Enzymes: A Critical Review. Catalysts 2022. [DOI: 10.3390/catal12111373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The grave environmental, social, and economic concerns over the unprecedented exploitation of non-renewable energy resources have drawn the attention of policy makers and research organizations towards the sustainable use of agro-industrial food and crop wastes. Enzymes are versatile biocatalysts with immense potential to transform the food industry and lignocellulosic biorefineries. Microbial enzymes offer cleaner and greener solutions to produce fine chemicals and compounds. The production of industrially important enzymes from abundantly present agro-industrial food waste offers economic solutions for the commercial production of value-added chemicals. The recent developments in biocatalytic systems are designed to either increase the catalytic capability of the commercial enzymes or create new enzymes with distinctive properties. The limitations of low catalytic efficiency and enzyme denaturation in ambient conditions can be mitigated by employing diverse and inexpensive immobilization carriers, such as agro-food based materials, biopolymers, and nanomaterials. Moreover, revolutionary protein engineering tools help in designing and constructing tailored enzymes with improved substrate specificity, catalytic activity, stability, and reaction product inhibition. This review discusses the recent developments in the production of essential industrial enzymes from agro-industrial food trash and the application of low-cost immobilization and enzyme engineering approaches for sustainable development.
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15
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Ding Z, Kumar V, Sar T, Harirchi S, Dregulo AM, Sirohi R, Sindhu R, Binod P, Liu X, Zhang Z, Taherzadeh MJ, Awasthi MK. Agro waste as a potential carbon feedstock for poly-3-hydroxy alkanoates production: Commercialization potential and technical hurdles. BIORESOURCE TECHNOLOGY 2022; 364:128058. [PMID: 36191751 DOI: 10.1016/j.biortech.2022.128058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
The enormous production and widespread applications of non -biodegradable plastics lead to their accumulation and toxicity to animals and humans. The issue can be addressed by the development of eco-friendly strategies for the production of biopolymers by utilization of waste residues like agro residues. This will address two societal issues - waste management and the development of an eco-friendly biopolymer, poly-3-hydroxy alkanoates (PHAs). Strategies adopted for utilization of agro-residues, challenges and future perspectives are discussed in detail in this comprehensive review. The possibility of PHA properties improvements can be increased by preparation of blends.
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Affiliation(s)
- Zheli Ding
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan Province 571101, China
| | - Vinay Kumar
- Department of Community Medicine, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam 602105, India
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, Borås 50190, Sweden
| | - Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, Borås 50190, Sweden
| | - Andrei Mikhailovich Dregulo
- Institute for Regional Economy Problems of the Russian Academy of Sciences (IRES RAS), 38 Serpukhovskaya str, 190013 Saint-Petersburg, Russia
| | - Ranjna Sirohi
- Department of Food Technology, School of Health Sciences & Technology, University of Petroleum and Energy Studies, Dehradun 248 007, India
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 691505, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695019, Kerala, India
| | - Xiaodi Liu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, Hainan Province 571101, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | | | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China.
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16
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Qin X, Zou J, Yang K, Li J, Wang X, Tu T, Wang Y, Yao B, Huang H, Luo H. Deciphering the efficient cellulose degradation by the thermophilic fungus Myceliophthora thermophila focused on the synergistic action of glycoside hydrolases and lytic polysaccharide monooxygenases. BIORESOURCE TECHNOLOGY 2022; 364:128027. [PMID: 36174898 DOI: 10.1016/j.biortech.2022.128027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The thermophilic fungus Myceliophthora thermophila as an efficient decomposer secretes various glycoside hydrolases and auxiliary oxidation enzymes to deconstruct cellulose. However, the core enzymes critical for efficient cellulose degradation and their interactions with other cellulolytic enzymes remain unclear. Herein, the transcriptomic analysis of M. thermophila grown on Avicel exhibited that cellulases from GH5_5, GH6 and GH7, and lytic polysaccharide monooxygenases (LPMOs) from AA9 contributed to cellulose degradation. Moreover, the peptide mass fingerprinting analysis of major extracellular proteins and corresponding gene-knockout strains studies revealed that MtCel7A and MtCel5A were the core cellulolytic enzymes. Furthermore, synergistic experiments found that hydrolytic efficiencies of MtCel7A and MtCel5A were both improved by mixture C1/C4 oxidizing MtLPMO9H, but inhibited by C1 oxidizing MtLPMO9E and C4 oxidizing MtLPMO9J respectively. These results demonstrated the potential application of C1/C4 oxidizing LPMOs for future designing novel cellulolytic enzyme cocktails on the efficient conversion of cellulose into biofuels and biochemicals.
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Affiliation(s)
- Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahuan Zou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jinyang Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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17
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Zhai R, Hu J, Jin M. Towards efficient enzymatic saccharification of pretreated lignocellulose: Enzyme inhibition by lignin-derived phenolics and recent trends in mitigation strategies. Biotechnol Adv 2022; 61:108044. [PMID: 36152893 DOI: 10.1016/j.biotechadv.2022.108044] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/24/2022] [Accepted: 09/19/2022] [Indexed: 01/01/2023]
Abstract
Lignocellulosic biorefinery based on its sugar-platform has been considered as an efficient strategy to replace fossil fuel-based refinery. In the bioconversion process, pretreatment is an essential step to firstly open up lignocellulose cell wall structure and enhance the accessibility of carbohydrates to hydrolytic enzymes. However, various lignin and/or carbohydrates degradation products (e.g. phenolics, 5-hydroxymethylfurfural, furfural) also generated during pretreatment, which severely inhibit the following enzymatic hydrolysis and the downstream fermentation process. Among them, the lignin derived phenolics have been considered as the most inhibitory compounds and their inhibitory effects are highly dependent on the source of biomass and the type of pretreatment strategy. Although liquid-solid separation and subsequent washing can remove the lignin derived phenolics and other inhibitors, this is undesirable in the realistic industrial application where the whole slurry of pretreated biomass need to be directly used in the hydrolysis process. This review summarizes the phenolics formation mechanism for various commonly applied pretreatment methods and discusses the key factors that affect the inhibitory effect of phenolics on cellulose hydrolysis. In addition, the recent achievements on the rational design of inhibition mitigation strategies to boost cellulose hydrolysis for sugar-platform biorefinery are also introduced. This review also provides guidance for rational design detoxification strategies to facilitate whole slurry hydrolysis which helps to realize the industrialization of lignocellulose biorefinery.
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Affiliation(s)
- Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Jianguang Hu
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary T2N 1N4, Canada
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.
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18
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Qiao J, Cui H, Wang M, Fu X, Wang X, Li X, Huang H. Integrated biorefinery approaches for the industrialization of cellulosic ethanol fuel. BIORESOURCE TECHNOLOGY 2022; 360:127516. [PMID: 35764282 DOI: 10.1016/j.biortech.2022.127516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic biomass is an abundant and sustainable raw material, but its conversion into ethanol fuel has not yet achieved large-scale industrialization and economic benefits. Integrated biorefineries have been widely identified as the key to achieving this goal. Here, four promising routes were summarized to assemble the new industrial plants for cellulose-based fuels and chemicals, including 1) integration of cellulase production systems into current cellulosic ethanol processes; 2) combination of processes and facilities between cellulosic ethanol and first-generation ethanol; 3) application of enzyme-free saccharification processes and computational approaches to increase the bioethanol yield and optimize the integration process; 4) production of multiple products to maximize the value derived from the lignocellulosic biomass. Finally, the remaining challenges and perspectives of this field are also discussed.
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Affiliation(s)
- Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Haiyang Cui
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Xianshen Fu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing 210097, China; School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
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19
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Enhanced activity of hyperthermostable Pyrococcus horikoshii endoglucanase in superbase ionic liquids. Biotechnol Lett 2022; 44:961-974. [PMID: 35763164 PMCID: PMC9356960 DOI: 10.1007/s10529-022-03268-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022]
Abstract
Objectives Ionic liquids (ILs) that dissolve biomass are harmful to the enzymes that degrade lignocellulose. Enzyme hyperthermostability promotes a tolerance to ILs. Therefore, the limits of hyperthemophilic Pyrococcus horikoschii endoglucanase (PhEG) to tolerate 11 superbase ILs were explored. Results PhEG was found to be most tolerant to 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc) in soluble 1% carboxymethylcellulose (CMC) and insoluble 1% Avicel substrates. At 35% concentration, this IL caused an increase in enzyme activity (up to 1.5-fold) with CMC. Several ILs were more enzyme inhibiting with insoluble Avicel than with soluble CMC. Km increased greatly in the presence ILs, indicating significant competitive inhibition. Increased hydrophobicity of the IL cation or anion was associated with the strongest enzyme inhibition and activation. Surprisingly, PhEG activity was increased 2.0–2.5-fold by several ILs in 4% substrate. Cations exerted the main role in competitive inhibition of the enzyme as revealed by their greater binding energy to the active site. Conclusions These results reveal new ways to design a beneficial combination of ILs and enzymes for the hydrolysis of lignocellulose, and the strong potential of PhEG in industrial, high substrate concentrations in aqueous IL solutions. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-022-03268-5.
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20
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Cheng L, Wang W, Fan MZ. Characterization of in vitro stability for two processive endoglucanases as exogenous fibre biocatalysts in pig nutrition. Sci Rep 2022; 12:9135. [PMID: 35650308 PMCID: PMC9160044 DOI: 10.1038/s41598-022-13124-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Development of highly efficacious exogenous fibre degradation enzymes can enhance efficiency of dietary fibre utilization and sustainability of global pork production. The objectives of this study were to investigate in vitro stability for two processive endoglucanases, referred to as GH5-tCel5A1 and GH5-p4818Cel5_2A that were overexpressed in CLEARCOLIBL21(DE3). Three-dimensional models predicted presence of Cys residues on the catalytic site surfaces of GH5-tCel5A1 and GH5-p4818Cel5_2A; and time course experimental results shown that both cellulases were susceptible to auto-oxidation by airborne O2 and were unstable. Furthermore, we examined these endoglucanases' stability under the mimicked in vitro porcine gastric and the small intestinal pH and proteases' conditions. Eadie-Hofstee inhibition kinetic analyses showed that GH5-tCel5A1 and GH5-p4818Cel5_2A respectively lost 18 and 68% of their initial activities after 2-h incubations under the gastric conditions and then lost more than 90% of their initial activities after 2-3 h of incubations under the small intestinal conditions. Therefore, further enzyme protein engineering to improve resistance and alternatively post-fermentation enzyme processing such as coating to bypass the gastric-small intestinal environment will be required to enable these two processive endoglucanases as efficacious exogenous fibre enzymes in pig nutrition application.
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Affiliation(s)
- Laurence Cheng
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Weijun Wang
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Canadian Food Inspection Agency (CFIA) - Ontario Operation, Guelph, ON, N1G 2W1, Canada
| | - Ming Z Fan
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- One Health Institute, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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21
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Pang AP, Luo Y, Hu X, Zhang F, Wang H, Gao Y, Durrani S, Li C, Shi X, Wu FG, Li BZ, Lu Z, Lin F. Transmembrane transport process and endoplasmic reticulum function facilitate the role of gene cel1b in cellulase production of Trichoderma reesei. Microb Cell Fact 2022; 21:90. [PMID: 35590356 PMCID: PMC9118834 DOI: 10.1186/s12934-022-01809-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/30/2022] [Indexed: 11/16/2022] Open
Abstract
Background A total of 11 β-glucosidases are predicted in the genome of Trichoderma reesei, which are of great importance for regulating cellulase biosynthesis. Nevertheless, the relevant function and regulation mechanism of each β-glucosidase remained unknown. Results We evidenced that overexpression of cel1b dramatically decreased cellulase synthesis in T. reesei RUT-C30 both at the protein level and the mRNA level. In contrast, the deletion of cel1b did not noticeably affect cellulase production. Protein CEL1B was identified to be intracellular, being located in vacuole and cell membrane. The overexpression of cel1b reduced the intracellular pNPGase activity and intracellular/extracellular glucose concentration without inducing carbon catabolite repression. On the other hand, RNA-sequencing analysis showed the transmembrane transport process and endoplasmic reticulum function were affected noticeably by overexpressing cel1b. In particular, some important sugar transporters were notably downregulated, leading to a compromised cellular uptake of sugars including glucose and cellobiose. Conclusions Our data suggests that the cellulase inhibition by cel1b overexpression was not due to the β-glucosidase activity, but probably the dysfunction of the cellular transport process (particularly sugar transport) and endoplasmic reticulum (ER). These findings advance the knowledge of regulation mechanism of cellulase synthesis in filamentous fungi, which is the basis for rationally engineering T. reesei strains to improve cellulase production in industry. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01809-1.
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Affiliation(s)
- Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yongsheng Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaotong Shi
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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22
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Gao Y, Pang AP, Ma L, Wang H, Durrani S, Li B, Wu FG, Lin F. Intron retention coupled with nonsense-mediated decay is involved in cellulase biosynthesis in cellulolytic fungi. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:53. [PMID: 35590374 PMCID: PMC9118705 DOI: 10.1186/s13068-022-02141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Knowledge on regulatory networks associated with cellulase biosynthesis is prerequisite for exploitation of such regulatory systems in enhancing cellulase production with low cost. The biological functions of intron retention (IR) and nonsense-mediated mRNA decay (NMD) in filamentous fungi is lack of study, let alone their roles in cellulase biosynthesis. RESULTS We found that major cellulase genes (cel7a, cel7b, and cel3a) exhibited concomitant decrease in IR rates and increase in their gene expression in T. reesei under cellulase-producing condition (cellulose and lactose) that was accompanied with a more active NMD pathway, as compared to cellulase non-producing condition (glucose). In the presence of the NMD pathway inhibitor that successfully repressed the NMD pathway, the mRNA levels of cellulase genes were sharply down-regulated, but the rates of IR in these genes were significantly up-regulated. Consistently, the cellulase activities were severely inhibited. In addition, the NMD pathway inhibitor caused the downregulated mRNA levels of two important genes of the target of rapamycin (TOR) pathway, trfkbp12 and trTOR1. The absence of gene trfkbp12 made the cellulase production in T. reesei more sensitive to the NMD pathway inhibitor. CONCLUSIONS All these findings suggest that the IR of cellulase genes regulates their own gene expression by coupling with the NMD pathway, which might involve the TOR pathway. Our results provide better understanding on intron retention, the NMD pathway, and cellulase production mechanism in filamentous fungi.
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Affiliation(s)
- Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Leyao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haiyan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bingzhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
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23
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Ranganathan S, Mahesh S, Suresh S, Nagarajan A, Z Sen T, M Yennamalli R. Experimental and computational studies of cellulases as bioethanol enzymes. Bioengineered 2022; 13:14028-14046. [PMID: 35730402 PMCID: PMC9345620 DOI: 10.1080/21655979.2022.2085541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bioethanol industries and bioprocesses have many challenges that constantly impede commercialization of the end product. One of the bottlenecks in the bioethanol industry is the challenge of discovering highly efficient catalysts that can improve biomass conversion. The current promising bioethanol conversion catalysts are microorganism-based cellulolytic enzymes, but lack optimization for high bioethanol conversion, due to biological and other factors. A better understanding of molecular underpinnings of cellulolytic enzyme mechanisms and significant ways to improve them can accelerate the bioethanol commercial production process. In order to do this, experimental methods are the primary choice to evaluate and characterize cellulase’s properties, but they are time-consuming and expensive. A time-saving, complementary approach involves computational methods that evaluate the same properties and improves our atomistic-level understanding of enzymatic mechanism of action. Theoretical methods in many cases have proposed research routes for subsequent experimental testing and validation, reducing the overall research cost. Having a plethora of tools to evaluate cellulases and the yield of the enzymatic process will aid in planning more optimized experimental setups. Thus, there is a need to connect the computational evaluation methods with the experimental methods to overcome the bottlenecks in the bioethanol industry. This review discusses various experimental and computational methods and their use in evaluating the multiple properties of cellulases.
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Affiliation(s)
- Shrivaishnavi Ranganathan
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Sankar Mahesh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Sruthi Suresh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Ayshwarya Nagarajan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
| | - Taner Z Sen
- S. Department of Agriculture, Agricultural Research Service, Crop Improvement and Genetics Research UnitU., California, USA
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Tirumalaisamudram, Thanjavur, India
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Wu M, Lv K, Li J, Wu B, He B. Coevolutionary analysis reveals a distal amino acid residue pair affecting the catalytic activity of GH5 processive endoglucanase from Bacillus subtilis BS-5. Biotechnol Bioeng 2022; 119:2105-2114. [PMID: 35438195 DOI: 10.1002/bit.28113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022]
Abstract
EG5C-1, processive endoglucanase from Bacillus subtilis, is a typical bifunctional cellulase with endoglucanase and exoglucanase activities. The engineering of processive endoglucanase focuses on the catalytic pocket or carbohydrate-binding module tailoring based on sequence/structure information. Herein, a computational strategy was applied to identify the desired mutants in the enzyme molecule by evolutionary coupling analysis; subsequently, four residue pairs were selected as evolutionary mutational hotspots. Based on iterative-saturation mutagenesis and subsequent enzymatic activity analysis, a superior mutant K51T/L93T was identified away from the active center. This variant had increased specific activity from 4170 U/µmol of wild-type (WT) to 5678 U/µmol towards CMC-Na and an increase towards the substrate Avicel from 320 U/µmol in WT to 521 U/µmol. In addition, kinetic measurements suggested that superior mutant K51T/L93T had a high substrate affinity (Km ) and a remarkable improvement in catalytic efficiency (kcat /Km ). Furthermore, molecular dynamics simulations revealed that the K51T/L93T mutation altered the spatial conformation at the active site cleft, enhancing the interaction frequency between active site residues and substrate, improving catalytic efficiency and substrate affinity. The current studies provided some perspectives on the effects of distal residue substitution, which might assist in the engineering of processive endoglucanase or other glycoside hydrolases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mujunqi Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Kemin Lv
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
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25
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Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
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Structural and Biochemical Characterization of Endo-β-1,4-glucanase from Dictyoglomus thermophilum, a Hyperthermostable and Halotolerant Cellulase. Catalysts 2022. [DOI: 10.3390/catal12030302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enzymatic conversion of polysaccharides in the lignocellulosic biomass is currently the subject of intensive research and will be a key technology in future biorefineries. Using a bioinformatics approach, we previously identified a putative endo-β-1,4-glucanase (DtCel5A) from Dictyoglomus thermophilum, a chemoorganotrophic and thermophilic bacterium. Here, we structurally and functionally characterize DtCel5A and show that it is endowed with remarkable thermal and chemical stability. The structural features of DtCel5A and of its complex with cellobiose have been investigated by combining X-ray crystallography and other biophysical studies. Importantly, biochemical assays show that DtCel5A retains its activity on cellulose at high temperatures and at elevated salt concentrations. These features make DtCel5A an enzyme with interesting biotechnological applications for biomass degradation.
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The Linker Region Promotes Activity and Binding Efficiency of Modular LPMO towards Polymeric Substrate. Microbiol Spectr 2022; 10:e0269721. [PMID: 35080440 PMCID: PMC8791183 DOI: 10.1128/spectrum.02697-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) mediate oxidative degradation of plant polysaccharides. The genes encoding LPMOs are most commonly arranged with one catalytic domain, while a few are found tethered to additional noncatalytic units, i.e., cellulase linker and carbohydrate-binding module (CBM). The presence of CBM is known to facilitate catalysis by directing the enzymes toward cellulosic polymer, while the role of linkers is poorly understood. Based on limited experimental evidence, linkers are believed to serve merely as flexible spacers between the structured domains. Thus, this study aims to unravel the role of the linker regions present in LPMO sequences. For this, we analyzed the genome of Botrytis cinerea and found 9 genes encoding cellulose lytic monooxygenases (AA9 family), of which BcAA9C was overexpressed in cellulose-inducible conditions. We designed variants of flLPMO (full-length enzyme) with truncation of either linker or CBM to examine the role of linker in activity, binding, and thermal stability of the associated monooxygenase. Biochemical assays predicted that the deletion of linker does not impact the potential of flLPMO for catalyzing the oxidation of Amplex Red, but that it does have a major influence on the capability of flLPMO to degrade recalcitrant polysaccharide substrate. Langmuir isotherm and SEM analysis demonstrated that linker domain aids in polysaccharide binding during flLPMO-mediated deconstruction of plant cell wall. Interestingly, linker domain was also found to contribute toward the thermostability of flLPMO. Overall, our study reveals that linker is not merely a spacer, but plays a key role in LPMO-mediated biomass fibrillation; these findings are broadly applicable to other polysaccharide-degrading enzymes. IMPORTANCE The polysaccharide-disintegrating carbohydrate-active enzymes (CAZymes) are often found with multimodular architecture, where the catalytic domain is connected to an accessory CBM domain with the help of a flexible linker region. So far, the linker has been understood merely as a flexible spacer between the two domains. Therefore, the current study is designed to determine the role of linker in polysaccharide fibrillation. To conceive this study, we have selected LPMO as a model enzyme, as it is not only an industrially relevant enzyme but it also harbors a catalytic domain, linker region, and CBM domain. The present study highlighted the crucial and indispensable role of the linker region in mediating polysaccharide disintegration. Considering its role in binding, thermostability, and activity toward polysaccharide substrate, we propose linker as a potential candidate for future CAZyme engineering.
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Dey N, Kumar G, Vickram AS, Mohan M, Singhania RR, Patel AK, Dong CD, Anbarasu K, Thanigaivel S, Ponnusamy VK. Nanotechnology-assisted production of value-added biopotent energy-yielding products from lignocellulosic biomass refinery - A review. BIORESOURCE TECHNOLOGY 2022; 344:126171. [PMID: 34695586 DOI: 10.1016/j.biortech.2021.126171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/13/2021] [Accepted: 10/17/2021] [Indexed: 05/22/2023]
Abstract
The need to develop sustainable alternatives for pretreatment and hydrolysis of lignocellulosic biomass (LCB) is a massive concern in the industrial sector today. Breaking down of LCB yields sugars and fuel in the bulk scale. If explored under nanotechnology, LCB can be refined to yield high-performance fuel sources. The toxicity and cost of conventional methods can be reduced by applying nanoparticles (NPs) in refining LCB. Immobilization of enzymes onto NPs or used in conjugation with nanomaterials would instill specific and eco-friendly options for hydrolyzing LCB. Nanomaterials increase the proficiency, reusability, and stability of enzymes. Notably, magnetic NPs have bagged their place in the downstream processing of LCB effluents due to their efficient separation and cost-effectiveness. The current review highlights the role of nanotechnology and its particles in refining LCB into various commercial precursors and value-added products. The relationship between nanotechnology and LCB refinery is portrayed effectively in the present study.
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Affiliation(s)
- Nibedita Dey
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai City, India
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, Box 8600 Forus 4036, Stavanger, Norway
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai City, India
| | - Monisha Mohan
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai City, India
| | - Reeta Rani Singhania
- Program of Aquatic Science and Technology, & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City 811, Taiwan
| | - Anil Kumar Patel
- Program of Aquatic Science and Technology, & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City 811, Taiwan
| | - Cheng-Di Dong
- Program of Aquatic Science and Technology, & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City 811, Taiwan
| | - K Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai City, India
| | - S Thanigaivel
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai City, India
| | - Vinoth Kumar Ponnusamy
- Program of Aquatic Science and Technology, & Department of Marine Environmental Engineering, College of Hydrosphere Science, National Kaohsiung University of Science and Technology (NKUST), Kaohsiung City 811, Taiwan; Department of Medicinal and Applied Chemistry. & Research Center for Environmental Medicine, Kaohsiung Medical University (KMU), Kaohsiung City 807, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital (KMUH), Kaohsiung City 807, Taiwan.
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Scapini T, Dalastra C, Camargo AF, Kubeneck S, Modkovski TA, Júnior SLA, Treichel H. Seawater-based biorefineries: A strategy to reduce the water footprint in the conversion of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 344:126325. [PMID: 34785329 DOI: 10.1016/j.biortech.2021.126325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biorefineries are an essential step towards implementing a circular economy in the long term. They are based on renewable raw materials and must be designed holistically, recovering building blocks from being converted into several products. Lignocellulosic biomass is considered a critical pillar for a biologically based economy and a high value-added feedstock. The separation of the structural complexity that makes up the biomass allows the development of different product flows. Chemical, physical, and biological processes are evaluated for fractionation, hydrolysis, and fermentation processes in biorefineries; however, the volume of freshwater used affects water safety and increases the economic costs. Non-potable-resources-based technologies for biomass bioconversion are essential for biorefineries to become environmentally and economically sustainable systems. Studies are being carried out to substitute freshwater with seawater to reduce the water footprint. Accordingly, this review addresses a comprehensive discussion about seawater-based biorefineries focusing on lignocellulosic biomass conversion in biofuel and value-added products.
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Affiliation(s)
- Thamarys Scapini
- Laboratory of Microbiology and Bioprocess (LAMIBI), Federal University of Fronteira Sul, Erechim, RS, Brazil; Bioprocess Engineering and Biotechnology Department, Federal University of Paraná, Curitiba, PR, Brazil
| | - Caroline Dalastra
- Laboratory of Microbiology and Bioprocess (LAMIBI), Federal University of Fronteira Sul, Erechim, RS, Brazil
| | - Aline Frumi Camargo
- Laboratory of Microbiology and Bioprocess (LAMIBI), Federal University of Fronteira Sul, Erechim, RS, Brazil; Department of Biological Science, Graduate Program in Biotechnology and Bioscience, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Simone Kubeneck
- Laboratory of Microbiology and Bioprocess (LAMIBI), Federal University of Fronteira Sul, Erechim, RS, Brazil
| | | | - Sérgio Luiz Alves Júnior
- Laboratory of Biochemistry and Genetics, Federal University of Fronteira Sul, Chapecó, SC, Brazil
| | - Helen Treichel
- Laboratory of Microbiology and Bioprocess (LAMIBI), Federal University of Fronteira Sul, Erechim, RS, Brazil; Department of Biological Science, Graduate Program in Biotechnology and Bioscience, Federal University of Santa Catarina, Florianópolis, SC, Brazil.
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30
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De Jesus R, Alkendi R. A minireview on the bioremediative potential of microbial enzymes as solution to emerging microplastic pollution. Front Microbiol 2022; 13:1066133. [PMID: 36938133 PMCID: PMC10018190 DOI: 10.3389/fmicb.2022.1066133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/29/2022] [Indexed: 03/06/2023] Open
Abstract
Accumulating plastics in the biosphere implicates adverse effects, raising serious concern among scientists worldwide. Plastic waste in nature disintegrates into microplastics. Because of their minute appearance, at a scale of <5 mm, microplastics easily penetrate different pristine water bodies and terrestrial niches, posing detrimental effects on flora and fauna. The potential bioremediative application of microbial enzymes is a sustainable solution for the degradation of microplastics. Studies have reported a plethora of bacterial and fungal species that can degrade synthetic plastics by excreting plastic-degrading enzymes. Identified microbial enzymes, such as IsPETase and IsMHETase from Ideonella sakaiensis 201-F6 and Thermobifida fusca cutinase (Tfc), are able to depolymerize plastic polymer chains producing ecologically harmless molecules like carbon dioxide and water. However, thermal stability and pH sensitivity are among the biochemical limitations of the plastic-degrading enzymes that affect their overall catalytic activities. The application of biotechnological approaches improves enzyme action and production. Protein-based engineering yields enzyme variants with higher enzymatic activity and temperature-stable properties, while site-directed mutagenesis using the Escherichia coli model system expresses mutant thermostable enzymes. Furthermore, microalgal chassis is a promising model system for "green" microplastic biodegradation. Hence, the bioremediative properties of microbial enzymes are genuinely encouraging for the biodegradation of synthetic microplastic polymers.
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Affiliation(s)
- Rener De Jesus
- College of Graduate Studies, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ruwaya Alkendi
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- *Correspondence: Ruwaya Alkendi,
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31
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Neis A, da Silva Pinto L. Glycosyl hydrolases family 5, subfamily 5: Relevance and structural insights for designing improved biomass degrading cocktails. Int J Biol Macromol 2021; 193:980-995. [PMID: 34666133 DOI: 10.1016/j.ijbiomac.2021.10.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Endoglucanases are carbohydrate-degrading enzymes widely used for bioethanol production as part of the enzymatic cocktail. However, family 5 subfamily 5 (GH5_5) endoglucanases are still poorly explored in depth. The Trichoderma reesei representative is the most studied enzyme, presenting catalytic activity in acidic media and mild temperature conditions. Though biochemically similar, its modular structure and synergy with other components vary greatly compared to other GH5_5 members and there is still a lack of specific studies regarding their interaction with other cellulases and application on novel and better mixtures. In this regard, the threedimensional structure elucidation is a highly valuable tool to both uncover basic catalytic mechanisms and implement engineering techniques, proved by the high success rate GH5_5 endoglucanases show. GH5_5 enzymes must be carefully evaluated to fully uncover their potential in biomass-degrading cocktails: the optimal industrial conditions, synergy with other cellulases, structural studies, and enzyme engineering approaches. We aimed to provide the current understanding of these main topics, collecting all available information about characterized GH5_5 endoglucanases function, structure, and bench experiments, in order to suggest future directions to a better application of these enzymes in the industry.
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Affiliation(s)
- Alessandra Neis
- Laboratório de Bioinformática e Proteômica (BioPro Lab), Centro de Desenvolvimento Tecnológico, Campus Universitário, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Caixa Postal 96010-900, Brazil.
| | - Luciano da Silva Pinto
- Laboratório de Bioinformática e Proteômica (BioPro Lab), Centro de Desenvolvimento Tecnológico, Campus Universitário, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Caixa Postal 96010-900, Brazil.
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32
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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33
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Roy S, Dikshit PK, Sherpa KC, Singh A, Jacob S, Chandra Rajak R. Recent nanobiotechnological advancements in lignocellulosic biomass valorization: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 297:113422. [PMID: 34351298 DOI: 10.1016/j.jenvman.2021.113422] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 05/22/2023]
Abstract
Increase in human population, rapid industrialization, excessive utilization of fossil fuel utilization and anthropogenic activities have caused serious threats to the environment in terms of greenhouse gas emissions (GHGs), global warming, air pollution, acid rain, etc. This destruction in sustainability can be averted by a paradigm shift in the fuel production from fossil resources to bioenergy. Amongst different forms of bioenergy, lignocellulosic biomass can be utilized as an attractive substrate for the production of several high-value products owing to its renewability, easy availability, and abundance. Additionally, utilization of these waste biomasses reduces the environmental hazards associated with its disposal. Impedance of lignin and crystalline nature of cellulose pose major bottlenecks in biomass based energy. Though, several physio-chemicals processes are recommended as mitigation route but none of them seems to be promising for large scale application. In recent years, a right fusion of biological treatment combined with nanotechnology for efficient pretreatment and subsequent hydrolysis of biomass by ubiquitous enzymes seems to be promising alternative. In addition, to overcome these difficulties, nanotechnology-based methods have been recently adopted in catalytic valorization of lignocellulosic biomass. The present review has critically discussed the application of nano-biotechnology in lignocellulosic biomass valorization in terms of pretreatment and hydrolysis. A detailed discussion on the application of various nanoparticles in these processes, enzyme immobilization and end-production utilization is presented in this review. Finally, the review emphasizes the major challenges of this process along with different routes and recommendations to address the issues.
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Affiliation(s)
- Sharmili Roy
- Division of Oncology, School of Medicine, Stanford University, CA, 94305, USA
| | - Pritam Kumar Dikshit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, India
| | - Knawang Chhunji Sherpa
- Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur, 721302, India
| | - Anshu Singh
- Agricultural and Food Engineering Department, Indian Institute of Technology, Kharagpur, 721302, India
| | - Samuel Jacob
- Department of Biotechnology, School of Engineering, SRM Institute of Science and Technology, Kattankulathur, India
| | - Rajiv Chandra Rajak
- Department of Botany, Marwari College, Ranchi University, Ranchi, 834008, India.
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den Haan R, Rose SH, Cripwell RA, Trollope KM, Myburgh MW, Viljoen-Bloom M, van Zyl WH. Heterologous production of cellulose- and starch-degrading hydrolases to expand Saccharomyces cerevisiae substrate utilization: Lessons learnt. Biotechnol Adv 2021; 53:107859. [PMID: 34678441 DOI: 10.1016/j.biotechadv.2021.107859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Selected strains of Saccharomyces cerevisiae are used for commercial bioethanol production from cellulose and starch, but the high cost of exogenous enzymes for substrate hydrolysis remains a challenge. This can be addressed through consolidated bioprocessing (CBP) where S. cerevisiae strains are engineered to express recombinant glycoside hydrolases during fermentation. Looking back at numerous strategies undertaken over the past four decades to improve recombinant protein production in S. cerevisiae, it is evident that various steps in the protein production "pipeline" can be manipulated depending on the protein of interest and its anticipated application. In this review, we briefly introduce some of the strategies and highlight lessons learned with regards to improved transcription, translation, post-translational modification and protein secretion of heterologous hydrolases. We examine how host strain selection and modification, as well as enzyme compatibility, are crucial determinants for overall success. Finally, we discuss how lessons from heterologous hydrolase expression can inform modern synthetic biology and genome editing tools to provide process-ready yeast strains in future. However, it is clear that the successful expression of any particular enzyme is still unpredictable and requires a trial-and-error approach.
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Affiliation(s)
- Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shaunita H Rose
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Kim M Trollope
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marthinus W Myburgh
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | | | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa.
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35
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Behle E, Raguin A. Stochastic model of lignocellulosic material saccharification. PLoS Comput Biol 2021; 17:e1009262. [PMID: 34516546 PMCID: PMC8460048 DOI: 10.1371/journal.pcbi.1009262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 09/23/2021] [Accepted: 07/09/2021] [Indexed: 12/03/2022] Open
Abstract
The processing of agricultural wastes towards extraction of renewable resources is recently being considered as a promising alternative to conventional biofuel production. The degradation of agricultural residues is a complex chemical process that is currently time intensive and costly. Various pre-treatment methods are being investigated to determine the subsequent modification of the material and the main obstacles in increasing the enzymatic saccharification. In this study, we present a computational model that complements the experimental approaches. We decipher how the three-dimensional structure of the substrate impacts the saccharification dynamics. We model a cell wall microfibril composed of cellulose and surrounded by hemicellulose and lignin, with various relative abundances and arrangements. This substrate is subjected to digestion by different cocktails of well characterized enzymes. The saccharification dynamics is simulated in silico using a stochastic procedure based on a Gillespie algorithm. As we additionally implement a fitting procedure that optimizes the parameters of the simulation runs, we are able to reproduce experimental saccharification time courses for corn stover. Our model highlights the synergistic action of enzymes, and confirms the linear decrease of sugar conversion when either lignin content or crystallinity of the substrate increases. Importantly, we show that considering the crystallinity of cellulose in addition to the substrate composition is essential to interpret experimental saccharification data. Finally, our findings support the hypothesis of xylan being partially crystalline. Leftover wastes generated by agriculture, such as inedible leaves and stalks of plants, represent an abundant and unexploited raw material that contains energy in the form of sugar polymers. Their breakdown and processing into bio-ethanol is recently being considered as a promising candidate for renewable fuel production. However, it is still poorly understood, how the microscopic structure and composition of plant waste materials impact their enzymatic digestion. Various experimental pre-processing methods are currently being tested to determine their effect on the material composition and structure, and the sugar conversion. In this study, we present a computational model to complement such experimental approaches. We simulate a microscopic plant fragment typically found in plant waste materials, whose structure and composition can be tailored. This fragment is then subjected to enzymatic digestion, whose dynamics is tracked in silico. The model reproduces experimentally observed time courses for plant fragments of known composition. It additionally provides new hypotheses for interpreting complex experimental results.
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Affiliation(s)
- Eric Behle
- Department of Biology, Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf, Germany
| | - Adélaïde Raguin
- Department of Biology, Cluster of Excellence on Plant Sciences, Institute of Quantitative and Theoretical Biology, Heinrich-Heine University, Düsseldorf, Germany
- * E-mail:
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36
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Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications. Int J Biol Macromol 2021; 188:226-244. [PMID: 34371052 DOI: 10.1016/j.ijbiomac.2021.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.
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Pramanik S, Semenova MV, M Rozhkova A, Zorov IN, Korotkova O, Sinitsyn AP, Davari MD. An engineered cellobiohydrolase I for sustainable degradation of lignocellulosic biomass. Biotechnol Bioeng 2021; 118:4014-4027. [PMID: 34196389 DOI: 10.1002/bit.27877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/29/2021] [Accepted: 06/20/2021] [Indexed: 11/11/2022]
Abstract
This study provides computational-assisted engineering of the cellobiohydrolase I (CBH-I) from Penicillium verruculosum with simultaneous enhanced thermostability and tolerance in ionic liquids, deep eutectic solvent, and concentrated seawater without affecting its wild-type activity. Engineered triple variant CBH-I R1 (A65R-G415R-S181F) showed 2.48-fold higher thermostability in terms of relative activity at 65°C after 1 h of incubation when compared with CBH-I wild type. CBH-I R1 exhibited 1.87-fold, 1.36-fold, and 1.57-fold higher specific activities compared with CBH-I wild type in [Bmim]Cl (50 g/L), [Ch]Cl (50 g/L), and two-fold concentrated seawater, respectively. In the multicellulases mixture, CBH-I R1 showed higher hydrolytic efficiency to hydrolyze aspen wood compared with CBH-I wild type in the buffer, [Bmim]Cl (50 g/L), and two-fold concentrated seawater, respectively. Structural analysis revealed a molecular basis for the higher stability of the CBH-I structure in which A65R and G415R substitutions form salt bridges (D64 … R65, E411 … R415) and S181F forms π-π interaction (Y155 … F181), leading to stabilize surface-exposed flexible α-helixes and loop in the multidomain β-jelly roll fold structure, respectively. In conclusion, the variant CBH-I R1 could enable efficient lignocellulosic biomass degradation as a cost-effective alternative for the sustainable production of biofuels and value-added chemicals.
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Affiliation(s)
- Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Margarita V Semenova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra M Rozhkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Ivan N Zorov
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Arkady P Sinitsyn
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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Lim SJ, Oslan SN. Native to designed: microbial -amylases for industrial applications. PeerJ 2021; 9:e11315. [PMID: 34046253 PMCID: PMC8139272 DOI: 10.7717/peerj.11315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Background -amylases catalyze the endo-hydrolysis of -1,4-D-glycosidic bonds in starch into smaller moieties. While industrial processes are usually performed at harsh conditions, -amylases from mainly the bacteria, fungi and yeasts are preferred for their stabilities (thermal, pH and oxidative) and specificities (substrate and product). Microbial -amylases can be purified and characterized for industrial applications. While exploring novel enzymes with these properties in the nature is time-costly, the advancements in protein engineering techniques including rational design, directed evolution and others have privileged their modifications to exhibit industrially ideal traits. However, the commentary on the strategies and preferably mutated residues are lacking, hindering the design of new mutants especially for enhanced substrate specificity and oxidative stability. Thus, our review ensures wider accessibility of the previously reported experimental findings to facilitate the future engineering work. Survey methodology and objectives A traditional review approach was taken to focus on the engineering of microbial -amylases to enhance industrially favoured characteristics. The action mechanisms of - and -amylases were compared to avoid any bias in the research background. This review aimed to discuss the advances in modifying microbial -amylases via protein engineering to achieve longer half-life in high temperature, improved resistance (acidic, alkaline and oxidative) and enhanced specificities (substrate and product). Captivating results were discussed in depth, including the extended half-life at 100C, pH 3.5 and 10, 1.8 M hydrogen peroxide as well as enhanced substrate (65.3%) and product (42.4%) specificities. These shed light to the future microbial -amylase engineering in achieving paramount biochemical traits ameliorations to apt in the industries. Conclusions Microbial -amylases can be tailored for specific industrial applications through protein engineering (rational design and directed evolution). While the critical mutation points are dependent on respective enzymes, formation of disulfide bridge between cysteine residues after mutations is crucial for elevated thermostability. Amino acids conversion to basic residues was reported for enhanced acidic resistance while hydrophobic interaction resulted from mutated hydrophobic residues in carbohydrate-binding module or surface-binding sites is pivotal for improved substrate specificity. Substitution of oxidation-prone methionine residues with non-polar residues increases the enzyme oxidative stability. Hence, this review provides conceptual advances for the future microbial -amylases designs to exhibit industrially significant characteristics. However, more attention is needed to enhance substrate specificity and oxidative stability since they are least reported.
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Affiliation(s)
- Si Jie Lim
- Enzyme Technology Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme Technology Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Sinitsyn AP, Sinitsyna OA. Bioconversion of Renewable Plant Biomass. Second-Generation Biofuels: Raw Materials, Biomass Pretreatment, Enzymes, Processes, and Cost Analysis. BIOCHEMISTRY (MOSCOW) 2021; 86:S166-S195. [PMID: 33827407 DOI: 10.1134/s0006297921140121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses various aspects of renewable plant biomass conversion and production of the second-generation biofuels, including the types of plant biomass, its composition and reaction ability in the enzymatic hydrolysis, and various pretreatment methods for increasing the biomass reactivity. Conversion of plant biomass into sugars requires the use of a complex of enzymes, the composition of which should be adapted to the biomass type and the pretreatment method. The efficiency of enzymatic hydrolysis can be increased by optimizing the composition of the enzymatic complex and by increasing the catalytic activity and operational stability of its constituent enzymes. The availability of active enzyme producers also plays an important role. Examples of practical implementation and scaling of processes for the production of second-generation biofuels are presented together with the cost analysis of bioethanol production.
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Affiliation(s)
- Arkadij P Sinitsyn
- Bakh Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia. .,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga A Sinitsyna
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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Li H, Hu Q, Hong X, Jiang Z, Ni H, Li Q, Zhu Y. Molecular cloning and characterization of a thermostable and halotolerant endo-β-1,4-glucanase from Microbulbifer sp. ALW1. 3 Biotech 2021; 11:250. [PMID: 33968593 PMCID: PMC8088414 DOI: 10.1007/s13205-021-02801-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/19/2021] [Indexed: 01/20/2023] Open
Abstract
The bacterium Microbulbifer sp. ALW1 was previously characterized with the capability to break down the cell wall of brown algae into fine pieces. The biological functions of strain ALW1 were yet to be elucidated. In this study, a gene, namely MaCel5A, was isolated from the ALW1 strain genome, encoding an endo-β-1,4-glucanase. MaCel5A was phylogenetically categorized under the glycoside hydrolase family GH5, with the highest identity to a putative cellulase of Microbulbifer thermotolerans. The recombinant MaCel5A protein purified from heterologous expression in E. coli exhibited maximum activity at 50 °C and pH 6.0, respectively, and functioned selectively toward carboxymethyl cellulose and barley β-glucan. Recombinant MaCel5A demonstrated considerable tolerance to the exposure to high temperature up to 80 °C for 30 min retaining 49% residual activity. In addition, MaCel5A showed moderate stability against pH 5.0-11.0 and strong stability in the presence of nonionic surfactant. MaCel5A exhibited strong halo-stability and halotolerance. The activity of the enzyme increased about tenfold at 0.5 M NaCl, and about fivefold even at 4.0 M NaCl compared to the enzyme activity without the addition of salt. The two conserved glutamic acid residues in MaCel5A featured the typical catalytic acid/base and nucleophile machinery of glycoside hydrolases. These characteristics highlight the industrial application potential of MaCel5A.
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Affiliation(s)
- Hebin Li
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361008 China
| | - Qingsong Hu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
| | - Xuan Hong
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361008 China
| | - Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
| | - Yanbing Zhu
- College of Food and Biological Engineering, Jimei University, Xiamen, 361021 China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, 361021 China
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Ning P, Yang G, Hu L, Sun J, Shi L, Zhou Y, Wang Z, Yang J. Recent advances in the valorization of plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:102. [PMID: 33892780 PMCID: PMC8063360 DOI: 10.1186/s13068-021-01949-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/07/2021] [Indexed: 05/28/2023]
Abstract
Plant biomass is a highly abundant renewable resource that can be converted into several types of high-value-added products, including chemicals, biofuels and advanced materials. In the last few decades, an increasing number of biomass species and processing techniques have been developed to enhance the application of plant biomass followed by the industrial application of some of the products, during which varied technologies have been successfully developed. In this review, we summarize the different sources of plant biomass, the evolving technologies for treating it, and the various products derived from plant biomass. Moreover, the challenges inherent in the valorization of plant biomass used in high-value-added products are also discussed. Overall, with the increased use of plant biomass, the development of treatment technologies, and the solution of the challenges raised during plant biomass valorization, the value-added products derived from plant biomass will become greater in number and more valuable.
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Affiliation(s)
- Peng Ning
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lihong Hu
- Institute of Chemical Industry of Forest Products, Key Laboratory of Biomass Energy and Material, CAF, Nanjing, China
| | - Jingxin Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Lina Shi
- Agricultural Integrated Service Center of Zhuyouguan, Longkou, Yantai, China
| | - Yonghong Zhou
- Institute of Chemical Industry of Forest Products, Key Laboratory of Biomass Energy and Material, CAF, Nanjing, China
| | - Zhaobao Wang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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Rozhkova AM, Kislitsin VY. CRISPR/Cas Genome Editing in Filamentous Fungi. BIOCHEMISTRY (MOSCOW) 2021; 86:S120-S139. [PMID: 33827404 DOI: 10.1134/s0006297921140091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The review describes the CRISPR/CAS system and its adaptation for the genome editing in filamentous fungi commonly used for production of enzyme complexes, enzymes, secondary metabolites, and other compounds used in industrial biotechnology and agriculture. In the second part of this review, examples of the CRISPR/CAS technology application for improving properties of the industrial strains of fungi from the Trichoderma, Aspergillus, Penicillium, and other genera are presented. Particular attention is given to the efficiency of genome editing, as well as system optimization for specific industrial producers.
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Affiliation(s)
- Aleksandra M Rozhkova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Valeriy Yu Kislitsin
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
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Geem KR, Song Y, Hwang I, Bae HJ, Lee DW. Production of Gloeophyllum trabeum Endoglucanase Cel12A in Nicotiana benthamiana for Cellulose Degradation. FRONTIERS IN PLANT SCIENCE 2021; 12:696199. [PMID: 34262588 PMCID: PMC8273430 DOI: 10.3389/fpls.2021.696199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/02/2021] [Indexed: 05/06/2023]
Abstract
Lignocellulosic biomass from plants has been used as a biofuel source and the potent acidic endoglucanase GtCel12A has been isolated from Gloeophyllum trabeum, a filamentous fungus. In this study, we established a plant-based platform for the production of active GtCel12A fused to family 3 cellulose-binding module (CBM3). We used the signal sequence of binding immunoglobulin protein (BiP) and the endoplasmic reticulum (ER) retention signal for the accumulation of the produced GtCel12A in the ER. To achieve enhanced enzyme expression, we incorporated the M-domain of the human receptor-type tyrosine-protein phosphatase C into the construct. In addition, to enable the removal of N-terminal domains that are not necessary after protein expression, we further incorporated the cleavage site of Brachypodium distachyon small ubiquitin-like modifier. The GtCel12A-CBM3 fusion protein produced in the leaves of Nicotiana benthamiana exhibited not only high solubility but also efficient endoglucanase activity on the carboxymethyl cellulose substrate as determined by 3,5-dinitrosalicylic acid assay. The endoglucanase activity of GtCel12A-CBM3 was maintained even when immobilized on microcrystalline cellulose beads. Taken together, these results indicate that GtCel12A endoglucanase produced in plants might be used to provide monomeric sugars from lignocellulosic biomass for bioethanol production.
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Affiliation(s)
- Kyoung Rok Geem
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea
| | - Younho Song
- Bio-Energy Research Center, Chonnam National University, Gwangju, South Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
| | - Hyeun-Jong Bae
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea
- Bio-Energy Research Center, Chonnam National University, Gwangju, South Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Dong Wook Lee
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, South Korea
- Bio-Energy Research Center, Chonnam National University, Gwangju, South Korea
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- *Correspondence: Dong Wook Lee
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Arnthong J, Siamphan C, Chuaseeharonnachai C, Boonyuen N, Suwannarangsee S. Towards a Miniaturized Culture Screening for Cellulolytic Fungi and Their Agricultural Lignocellulosic Degradation. J Microbiol Biotechnol 2020; 30:1670-1679. [PMID: 32876068 PMCID: PMC9728337 DOI: 10.4014/jmb.2007.07005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022]
Abstract
The substantial use of fungal enzymes to degrade lignocellulosic plant biomass has widely been attributed to the extensive requirement of powerful enzyme-producing fungal strains. In this study, a two-step screening procedure for finding cellulolytic fungi, involving a miniaturized culture method with shake-flask fermentation, was proposed and demonstrated. We isolated 297 fungal strains from several cellulose-containing samples found in two different locations in Thailand. By using this screening strategy, we then selected 9 fungal strains based on their potential for cellulase production. Through sequence-based identification of these fungal isolates, 4 species in 4 genera were identified: Aspergillus terreus (3 strains: AG466, AG438 and AG499), Penicillium oxalicum (4 strains: AG452, AG496, AG498 and AG559), Talaromyces siamensis (1 strain: AG548) and Trichoderma afroharzianum (1 strain: AG500). After examining their lignocellulose degradation capacity, our data showed that P. oxalicum AG452 exhibited the highest glucose yield after saccharification of pretreated sugarcane trash, cassava pulp and coffee silverskin. In addition, Ta. siamensis AG548 produced the highest glucose yield after hydrolysis of pretreated sugarcane bagasse. Our study demonstrated that the proposed two-step screening strategy can be further applied for discovering potential cellulolytic fungi isolated from various environmental samples. Meanwhile, the fungal strains isolated in this study will prove useful in the bioconversion of agricultural lignocellulosic residues into valuable biotechnological products.
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Affiliation(s)
- Jantima Arnthong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Chatuphon Siamphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Charuwan Chuaseeharonnachai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Nattawut Boonyuen
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand
| | - Surisa Suwannarangsee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Klong Luang, Pathumthani 12120, Thailand,Corresponding author Phone: +66-2564 6700 Fax: +66-2564-6700 E-mail:
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Storani A, Guerrero SA, Iglesias AA. On the functionality of the N-terminal domain in xylanase 10A from Ruminococcus albus 8. Enzyme Microb Technol 2020; 142:109673. [PMID: 33220861 DOI: 10.1016/j.enzmictec.2020.109673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/02/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
We analyzed the structure to function relationships in Ruminococcus albus 8 xylanase 10A (RalXyn10A) finding that the N-terminus 34-amino acids sequence (N34) in the protein is particularly functional. We performed the recombinant wild type enzyme's characterization and that of the truncated mutant lacking the N34 extreme (RalΔN34Xyn10A). The truncated enzyme exhibited about half of the activity and reduced affinity for binding to insoluble saccharides. These suggest a (CBM)-like function for the N34 motif. Besides, RalXyn10A activity was diminished by redox agent dithiothreitol, a characteristic absent in RalΔN34Xyn10A. The N34 sequence exhibited a significant similarity with protein components of the ABC transporter of the bacterial membrane, and this motif is present in other proteins of R. albus 8. Data suggest that N34 would confer RalXyn10A the capacity to interact with polysaccharides and components of the cell membrane, enhancing the degradation of the substrate and uptake of the products by the bacterium.
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Affiliation(s)
- Alem Storani
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL). Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Sergio A Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL). Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Alberto A Iglesias
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral (CONICET - UNL). Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina.
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Molecular engineering to improve lignocellulosic biomass based applications using filamentous fungi. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:73-109. [PMID: 33934853 DOI: 10.1016/bs.aambs.2020.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.
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Biocatalysis of Industrial Kraft Pulps: Similarities and Differences between Hardwood and Softwood Pulps in Hydrolysis by Enzyme Complex of Penicillium verruculosum. Catalysts 2020. [DOI: 10.3390/catal10050536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Kraft pulp enzymatic hydrolysis is a promising method of woody biomass bioconversion. The influence of composition and structure of kraft fibers on their hydrolysis efficiency was evaluated while using four substrates, unbleached hardwood pulp (UHP), unbleached softwood pulp (USP), bleached hardwood pulp (BHP), and bleached softwood pulp (BSP). Hydrolysis was carried out with Penicillium verruculosum enzyme complex at a dosage of 10 filter paper units (FPU)/g pulp. The changes in fiber morphology and structure were visualized while using optical and electron microscopy. Fiber cutting and swelling and quick xylan destruction were the main processes at the beginning of hydrolysis. The negative effect of lignin content was more pronounced for USP. Drying decreased the sugar yield of dissolved hydrolysis products for all kraft pulps. Fiber morphology, different xylan and mannan content, and hemicelluloses localization in kraft fibers deeply affected the hydrolyzability of bleached pulps. The introduction of additional xylobiase, mannanase, and cellobiohydrolase activities to enzyme mixture will further improve the hydrolysis of bleached pulps. A high efficiency of never-dried bleached pulp bioconversion was shown. At 10% substrate concentration, hydrolysates with more than 50 g/L sugar concentration were obtained. The bioconversion of never-dried BHP and BSP could be integrated into working kraft pulp mills.
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