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Zhu W, Qin L, Xu Y, Lu H, Wu Q, Li W, Zhang C, Li X. Three Molecular Modification Strategies to Improve the Thermostability of Xylanase XynA from Streptomyces rameus L2001. Foods 2023; 12:foods12040879. [PMID: 36832954 PMCID: PMC9957083 DOI: 10.3390/foods12040879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Glycoside hydrolase family 11 (GH11) xylanases are the preferred candidates for the production of functional oligosaccharides. However, the low thermostability of natural GH11 xylanases limits their industrial applications. In this study, we investigated the following three strategies to modify the thermostability of xylanase XynA from Streptomyces rameus L2001 mutation to reduce surface entropy, intramolecular disulfide bond construction, and molecular cyclization. Changes in the thermostability of XynA mutants were analyzed using molecular simulations. All mutants showed improved thermostability and catalytic efficiency compared with XynA, except for molecular cyclization. The residual activities of high-entropy amino acid-replacement mutants Q24A and K104A increased from 18.70% to more than 41.23% when kept at 65 °C for 30 min. The catalytic efficiencies of Q24A and K143A increased to 129.99 and 92.26 mL/s/mg, respectively, compared with XynA (62.97 mL/s/mg) when using beechwood xylan as the substrate. The mutant enzyme with disulfide bonds formed between Val3 and Thr30 increased the t1/260 °C by 13.33-fold and the catalytic efficiency by 1.80-fold compared with the wild-type XynA. The high thermostabilities and hydrolytic activities of XynA mutants will be useful for enzymatic production of functional xylo-oligosaccharides.
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Affiliation(s)
- Weijia Zhu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Liqin Qin
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongyun Lu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Qiuhua Wu
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Chengnan Zhang
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Xiuting Li
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, China General Chamber of Commerce, Beijing 100048, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
- Correspondence:
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Li Y, Song W, Han X, Wang Y, Rao S, Zhang Q, Zhou J, Li J, Liu S, Du G. Recent progress in key lignocellulosic enzymes: Enzyme discovery, molecular modifications, production, and enzymatic biomass saccharification. BIORESOURCE TECHNOLOGY 2022; 363:127986. [PMID: 36126851 DOI: 10.1016/j.biortech.2022.127986] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 05/15/2023]
Abstract
Lignocellulose, the most prevalent biomass on earth, can be enzymatically converted into carbohydrates for bioethanol production and other uses. Among lignocellulosic enzymes, endoglucanase, xylanase, and laccase are the key enzymes, owing to their ability to disrupt the main structure of lignocellulose. Recently, new discovery methods have been established to obtain key lignocellulosic enzymes with excellent enzymatic properties. Molecular modification of enzymes to modulate their thermostability, catalytic activity, and substrate specificity has been performed with protein engineering technology. In addition, the enzyme expression has been effectively improved through expression element screening and host modification, as well as fermentation optimization. Immobilization of enzymes, use of surfactants, synergistic degradation, and optimization of reaction conditions have addressed the inefficiency of enzymatic saccharification. In this review, recent advances in key lignocellulosic enzymes are summarized, along with future prospects for the development of super-engineered strains and integrative technologies for enzymatic biomass saccharification.
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Affiliation(s)
- Yangyang Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Weiyan Song
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xuyue Han
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yachan Wang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Shengqi Rao
- College of Food Science and Engineering, Yangzhou University, Yangzhou 214122, China
| | - Quan Zhang
- Dalian Research Institute of Petroleum and Petrochemicals, SINOPEC, Dalian 116000, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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3
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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4
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Li L, Li W, Gong J, Xu Y, Wu Z, Jiang Z, Cheng YS, Li Q, Ni H. An effective computational-screening strategy for simultaneously improving both catalytic activity and thermostability of α-l-rhamnosidase. Biotechnol Bioeng 2021; 118:3409-3419. [PMID: 33742693 DOI: 10.1002/bit.27758] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/04/2021] [Accepted: 03/18/2021] [Indexed: 12/21/2022]
Abstract
Catalytic efficiency and thermostability are the two most important characteristics of enzymes. However, it is always tough to improve both catalytic efficiency and thermostability of enzymes simultaneously. In the present study, a computational strategy with double-screening steps was proposed to simultaneously improve both catalysis efficiency and thermostability of enzymes; and a fungal α-l-rhamnosidase was used to validate the strategy. As the result, by molecular docking and sequence alignment analysis within the binding pocket, seven mutant candidates were predicted with better catalytic efficiency. By energy variety analysis, A355N, S356Y, and D525N among the seven mutant candidates were predicted with better thermostability. The expression and characterization results showed the mutant D525N had significant improvements in both enzyme activity and thermostability. Molecular dynamics simulations indicated that the mutations located within the 5 Å range of the catalytic domain, which could improve root mean squared deviation, electrostatic, Van der Waal interaction, and polar salvation values, and formed water bridge between the substrate and the enzyme. The study indicated that the computational strategy based on the binding energy, conservation degree and mutation energy analyses was effective to develop enzymes with better catalysis and thermostability, providing practical approach for developing industrial enzymes.
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Affiliation(s)
- Lijun Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Wenjing Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Jianye Gong
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Yanyan Xu
- Tan Kah Kee College, Xiamen University, Zhangzhou, China
| | - Zheyu Wu
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Yi-Sheng Cheng
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
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5
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Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
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Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
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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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7
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Damis SIR, Murad AMA, Diba Abu Bakar F, Rashid SA, Jaafar NR, Illias RM. Protein engineering of GH11 xylanase from Aspergillus fumigatus RT-1 for catalytic efficiency improvement on kenaf biomass hydrolysis. Enzyme Microb Technol 2019; 131:109383. [DOI: 10.1016/j.enzmictec.2019.109383] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 06/30/2019] [Accepted: 07/16/2019] [Indexed: 11/15/2022]
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8
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Liu MQ, Li JY, Rehman AU, Xu X, Gu ZJ, Wu RC. Laboratory Evolution of GH11 Endoxylanase Through DNA Shuffling: Effects of Distal Residue Substitution on Catalytic Activity and Active Site Architecture. Front Bioeng Biotechnol 2019; 7:350. [PMID: 31824938 PMCID: PMC6883096 DOI: 10.3389/fbioe.2019.00350] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/06/2019] [Indexed: 11/15/2022] Open
Abstract
Endoxylanase with high specific activity, thermostability, and broad pH adaptability is in huge demand. The mutant library of GH11 endoxylanase was constructed via DNA shuffling by using the catalytic domain of Bacillus amyloliquefaciens xylanase A (BaxA) and Thermomonospora fusca TF xylanase A (TfxA) as parents. A total of 2,250 colonies were collected and 756 of them were sequenced. Three novel mutants (DS153: N29S, DS241: S31R and DS428: I51V) were identified and characterized in detail. For these mutants, three residues of BaxA were substituted by the corresponding one of TfxA_CD. The specific activity of DS153, DS241, and DS428 in the optimal condition was 4.54, 4.35, and 3.9 times compared with the recombinant BaxA (reBaxA), respectively. The optimum temperature of the three mutants was 50°C. The optimum pH for DS153, DS241, and DS428 was 6.0, 7.0, and 6.0, respectively. The catalytic efficiency of DS153, DS241, and DS428 enhanced as well, while their sensitivity to recombinant rice xylanase inhibitor (RIXI) was lower than that of reBaxA. Three mutants have identical hydrolytic function as reBaxA, which released xylobiose–xylopentaose from oat spelt, birchwood, and beechwood xylan. Furthermore, molecular dynamics simulations were performed on BaxA and three mutants to explore the precise impact of gain-of-function on xylanase activity. The tertiary structure of BaxA was not altered under the substitution of distal residues (N29S, S31R, and I51V); it induced slightly changes in active site architecture. The distal impact rescued the BaxA from native conformation (“closed state”) through weakening interactions between “gate” residues (R112, N35 in DS241 and DS428; W9, P116 in DS153) and active site residues (E78, E172, Y69, and Y80), favoring conformations with an “open state” and providing improved activity. The current findings would provide a better and more in-depth understanding of how distal single residue substitution improved the catalytic activity of xylanase at the atomic level.
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Affiliation(s)
- Ming-Qi Liu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Jia-Yi Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Xu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Zhu-Jun Gu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Ruo-Chen Wu
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
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9
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Abdul Wahab MKH, El-Enshasy HA, Bakar FDA, Murad AMA, Jahim JM, Illias RM. Improvement of cross-linking and stability on cross-linked enzyme aggregate (CLEA)-xylanase by protein surface engineering. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.07.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Shukla P. Synthetic Biology Perspectives of Microbial Enzymes and Their Innovative Applications. Indian J Microbiol 2019; 59:401-409. [PMID: 31762501 DOI: 10.1007/s12088-019-00819-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are high in demand and there is focus on their efficient, cost effective and eco-friendly production. The relevant microbial enzymes for respective industries needs to be identified but the conventional technologies don't have much edge over it. So, there is more attention towards high throughput methods for production of efficient enzymes. The enzymes produced by microbes need to be modified to bear the extreme conditions of the industries in order to get prolific outcomes and here the synthetic biology tools may be augmented to modify such microbes and enzymes. These tools are applied to synthesize novel and efficient enzymes. Use of computational tools for enzyme modification has provided new avenues for faster and specific modification of enzymes in a shorter time period. This review focuses on few important enzymes and their modification through synthetic biology tools including genetic modification, nanotechnology, post translational modification.
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Affiliation(s)
- Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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Improving the thermostability and catalytic efficiency of GH11 xylanase PjxA by adding disulfide bridges. Int J Biol Macromol 2019; 128:354-362. [DOI: 10.1016/j.ijbiomac.2019.01.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 11/24/2022]
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12
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Han H, Ling Z, Khan A, Virk AK, Kulshrestha S, Li X. Improvements of thermophilic enzymes: From genetic modifications to applications. BIORESOURCE TECHNOLOGY 2019; 279:350-361. [PMID: 30755321 DOI: 10.1016/j.biortech.2019.01.087] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Thermozymes (from thermophiles or hyperthermophiles) offer obvious advantages due to their excellent thermostability, broad pH adaptation, and hydrolysis ability, resulting in diverse industrial applications including food, paper, and textile processing, biofuel production. However, natural thermozymes with low yield and poor adaptability severely hinder their large-scale applications. Extensive studies demonstrated that using genetic modifications such as directed evolution, semi-rational design, and rational design, expression regulations and chemical modifications effectively improved enzyme's yield, thermostability and catalytic efficiency. However, mechanism-based techniques for thermozymes improvements and applications need more attention. In this review, stabilizing mechanisms of thermozymes are summarized for thermozymes improvements, and these improved thermozymes eventually have large-scale industrial applications.
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Affiliation(s)
- Huawen Han
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Zhenmin Ling
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China
| | - Amanpreet Kaur Virk
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229, India
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, People's Republic of China.
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13
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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14
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Kumar V, Dangi AK, Shukla P. Engineering Thermostable Microbial Xylanases Toward its Industrial Applications. Mol Biotechnol 2018; 60:226-235. [DOI: 10.1007/s12033-018-0059-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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15
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Site-directed mutagenesis of GH10 xylanase A from Penicillium canescens for determining factors affecting the enzyme thermostability. Int J Biol Macromol 2017. [DOI: 10.1016/j.ijbiomac.2017.06.079] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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16
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Miller SR. An appraisal of the enzyme stability‐activity trade‐off. Evolution 2017; 71:1876-1887. [DOI: 10.1111/evo.13275] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/09/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Scott R. Miller
- Division of Biological SciencesThe University of Montana Missoula Montana 59812
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