1
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Pasin TM, Lucas RC, de Oliveira TB, McLeish MJ, Polizeli MDLTM. A new halotolerant xylanase from Aspergillus clavatus expressed in Escherichia coli with catalytic efficiency improved by site-directed mutagenesis. 3 Biotech 2024; 14:178. [PMID: 38855145 PMCID: PMC11156621 DOI: 10.1007/s13205-024-04021-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Daily agro-industrial waste, primarily cellulose, lignin, and hemicellulose, poses a significant environmental challenge. Harnessing lignocellulolytic enzymes, particularly endo-1,4-β-xylanases, for efficient saccharification is a cost-effective strategy, transforming biomass into high-value products. This study focuses on the cloning, expression, site-directed mutagenesis, purification, three-dimensional modeling, and characterization of the recombinant endo-1,4-β-xylanase (XlnA) from Aspergillus clavatus in Escherichia coli. This work includes evaluation of the stability at varied NaCl concentrations, determining kinetic constants, and presenting the heterologous expression of XlnAΔ36 using pET22b(+). The expression led to purified enzymes with robust stability across diverse pH levels, exceptional thermostability at 50 °C, and 96-100% relative stability after 24 h in 3.0 M NaCl. Three-dimensional modeling reveals a GH11 architecture with catalytic residues Glu 132 and 22. XlnAΔ36 demonstrates outstanding kinetic parameters compared to other endo-1,4-β-xylanases, indicating its potential for industrial enzymatic cocktails, enhancing saccharification. Moreover, its ability to yield high-value compounds, such as sugars, suggests a promising and ecologically positive alternative for the food and biotechnology industries.
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Affiliation(s)
- Thiago M. Pasin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Rosymar C. Lucas
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Biochemistry, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, MG 37130-001 Brazil
| | - Tássio B. de Oliveira
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901 Brazil
- Department of Systematics and Ecology, Center for Exact and Nature Sciences, Federal University of Paraíba, João Pessoa, PB 58051-900 Brazil
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
| | - Maria de Lourdes T. M. Polizeli
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901 Brazil
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2
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Li Y, Zhang H, Fu Y, Zhou Z, Yu W, Zhou J, Li J, Du G, Liu S. Enhancing Acid Resistance of Aspergillus niger Pectin Lyase through Surface Charge Design for Improved Application in Juice Clarification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11652-11662. [PMID: 38738910 DOI: 10.1021/acs.jafc.4c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Pectin lyases (PNLs) can enhance juice clarity and flavor by degrading pectin in highly esterified fruits, but their inadequate acid resistance leads to rapid activity loss in juice. This study aimed to improve the acid resistance of Aspergillus niger PNL pelA through surface charge design. A modification platform was established by fusing pelA with a protein tag and expressing the fusion enzyme in Escherichia coli. Four single-point mutants were identified to increase the surface charge using computational tools. Moreover, the combined mutant M6 (S514D/S538E) exhibited 99.8% residual activity at pH 3.0. The M6 gene was then integrated into the A. niger genome using a multigene integration system to obtain the recombinant PNL AM6. Notably, AM6 improved the light transmittance of orange juice to 45.3%, which was 8.39 times higher than that of pelA. In conclusion, AM6 demonstrated the best-reported acid resistance, making it a promising candidate for industrial juice clarification.
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Affiliation(s)
- Yangyang Li
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Haiyun Zhang
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yishan Fu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Zhitong Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Wenwen Yu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, 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
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Guocheng Du
- Science Center for Future Foods, 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
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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3
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Li Q, Qin C, Chen X, Hu K, Li J, Liu A, Liu S. Enhancing the acid stability of the recombinant GH11 xylanase xynA through N-terminal substitution to facilitate its application in apple juice clarification. Int J Biol Macromol 2024; 268:131857. [PMID: 38670187 DOI: 10.1016/j.ijbiomac.2024.131857] [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: 02/19/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
The utilization of xylanase in juice clarification is contingent upon its stability within acidic environments. We generated a mutant xynA-1 by substituting the N-terminal segment of the recombinant xylanase xynA to investigate the correlation between the N-terminal region of xylanase and its acid stability. The enzymatic activity of xynA-1 was found to be superior under acidic conditions (pH 5.0). It exhibited enhanced acid stability, surpassing the residual enzyme activity values of xynA at pH 4.0 (53.07 %), pH 4.5 (69.8 %), and pH 5.0 (82.4 %), with values of 60.16 %, 77.74 %, and 87.3 %, respectively. Additionally, the catalytic efficiency of xynA was concurrently improved. Through molecular dynamics simulation, we observed that N-terminal shortening induced a reduction in motility across most regions of the protein structure while enhancing its stability, particularly Lys131-Phe146 and Leu176-Gly206. Furthermore, the application of treated xynA-1 in the process of apple juice clarification led to a significant increase in clarity within a short duration of 20 min at 35 °C while ensuring the quality of the apple juice. This study not only enhances the understanding of the N-terminal region of xylanase but also establishes a theoretical basis for augmenting xylanase resources employed in fruit juice clarification.
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Affiliation(s)
- Qin Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China.
| | - Chi Qin
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China
| | - Xingziyi Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China
| | - Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China.
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4
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Hasan WANBW, Nezhad NG, Yaacob MA, Salleh AB, Rahman RNZRA, Leow TC. Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy. World J Microbiol Biotechnol 2024; 40:106. [PMID: 38386107 DOI: 10.1007/s11274-024-03927-x] [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: 11/11/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues affecting the optimum pH of Staphylococcal lipases, chimeric lipases from homologous lipases were generated via a DNA shuffling strategy. Chimeric 1 included mutations of G166S, K212E, T243A, H271Y. Chimeric 2 consisted of substitutions of K212E, T243A, H271Y. Chimeric 3 contained substitutions of K212E, R359L. From the screening results, the pH profiles for chimeric 1 and 2 lipases were shifted from pH 7 to 6. While the pH of chimeric 3 was shifted to 8. It seems the mutation of K212E in chimeric 1 and 2 decreased the pH to 6 by changing the electrostatic potential surface. Furthermore, chimeric 3 showed 10 ˚C improvement in the optimum temperature due to the rigidification of the catalytic loop through the hydrophobic interaction network. Moreover, the substrate specificity of chimeric 1 and 2 was increased towards the longer carbon length chains due to the mutation of T243A adjacent to the lid region through increasing the flexibility of the lid. Current study illustrated that directed evolution successfully modified lipase properties including optimum pH, temperature and substrate specificity through mutations, especially near catalytic and lid regions.
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Affiliation(s)
- Wan Atiqah Najiah Binti Wan Hasan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Mohd Adilin Yaacob
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
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5
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Zhang Z, Zhao Z, Huang K, Liang Z. Acid-resistant enzymes: the acquisition strategies and applications. Appl Microbiol Biotechnol 2023; 107:6163-6178. [PMID: 37615723 DOI: 10.1007/s00253-023-12702-1] [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: 06/05/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Enzymes have promising applications in chemicals, food, pharmaceuticals, and other variety products because of their high efficiency, specificity, and environmentally friendly properties. However, due to the complexity of raw materials, pH, temperature, solvents, etc., the application range of enzymes is greatly limited in the industry. Protein engineering and enzyme immobilization are classical strategies to overcome the limitations of industrial applications. Although the pH tendency of enzymes has been extensively researched, the mechanism underlying enzyme acid resistance is unclear, and a less practical strategy for altering the pH propensity of enzymes has been suggested. This review proposes that the optimum pH of enzyme is determined by the pKa values of active center ionizable amino acid residues. Three levels of acquiring acid-resistant enzymes are summarized: mining from extreme environments and enzyme databases, modification with protein engineering and enzyme microenvironment engineering, and de novo synthesis. The industrial applications of acid-resistant enzymes in chemicals, food, and pharmaceuticals are also summarized. KEY POINTS: • The mechanism of enzyme acid resistance is fundamentally determined. • The three aspects of the method for acquiring acid-resistant enzymes are summarized. • Computer-aided strategies and artificial intelligence are used to obtain acid-resistant enzymes.
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Affiliation(s)
- Zhenzhen Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zitong Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China
- Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Zhihong Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.
- The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing, China.
- Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China.
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6
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Wu Q, Zhang C, Dong W, Lu H, Yang Y, Li W, Xu Y, Li X. Simultaneously Enhanced Thermostability and Catalytic Activity of Xylanase from Streptomyces rameus L2001 by Rigidifying Flexible Regions in Loop Regions of the N-Terminus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12785-12796. [PMID: 37590476 DOI: 10.1021/acs.jafc.3c03871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
The GH11 xylanase XynA from Streptomyces rameus L2001 has favorable hydrolytic properties. However, its poor thermal stability hinders its widespread application in industry. In this study, mutants Mut1 and Mut2 were constructed by rationally combining the mutations 11YHDGYF16, 23AP24/23SP24, and 32GP33. The residual enzyme activity of these combinational mutants was more than 85% when incubated at 80 and 90 °C for 12 h, and thus are the most thermotolerant xylanases known to date. The reduced flexibility of the N-terminus, increased overall rigidity, as well as the surface net charge of Mut1 and Mut2 may be partially responsible for the improved thermal stability. In addition, the specific activity and catalytic efficiency of Mut1 and Mut2 were improved compared with those of wild-type XynA. The broader catalytic cleft and enhanced flexibility of the "thumb" of Mut1 and Mut2 may be partially responsible for the improved specific activity and catalytic efficiency.
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Affiliation(s)
- Qiuhua Wu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Chengnan Zhang
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Wenqi Dong
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Hongyun Lu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Yue Yang
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Weiwei Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Youqiang Xu
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xiuting Li
- Ministry of Education, Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Beijing 100048, China
- China General Chamber of Commerce, Key Laboratory of Brewing Microbiome and Enzymatic Molecular Engineering, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
- Beijing Association for Science and Technology-Food Nutrition and Safety Professional Think Tank Base, Beijing 100048, China
- School of Food and Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
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7
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Yip YS, Manas NHA, Jaafar NR, Rahman RA, Puspaningsih NNT, Illias RM. Combined cross-linked enzyme aggregates of cyclodextrin glucanotransferase and maltogenic amylase from Bacillus lehensis G1 for maltooligosaccharides synthesis. Int J Biol Macromol 2023; 242:124675. [PMID: 37127056 DOI: 10.1016/j.ijbiomac.2023.124675] [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: 01/10/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/03/2023]
Abstract
Maltooligosaccharides (MOS) are functional oligosaccharides that can be synthesized through enzymatic cascade reaction between cyclodextrin glucanotransferase (CGTase) and maltogenic amylase (Mag1) from Bacillus lehensis G1. To address the problems of low operational stability and non-reusability of free enzymes, both enzymes were co-immobilized as combined cross-linked enzyme aggregates (Combi-CLEAs-CM) with incorporation of bovine serum albumin (BSA) and Tween 80 (Combi-CLEAs-CM-add). Combi-CLEAs-CM and Combi-CLEAs-CM-add showed activity recoveries of 54.12 % and 69.44 %, respectively after optimization. Combi-CLEAs-CM-add showed higher thermal stability at higher temperatures (40 °C) with longer half-life (46.20 min) as compared to those of free enzymes (36.67 min) and Combi-CLEAs-CM (41.51 min). Both combi-CLEAs also exhibited higher pH stability over pH 5 to pH 9, and displayed excellent reusability with >50 % of initial activity retained after four cycles. The reduction in Km value of about 22.80 % and 1.76-fold increase in starch hydrolysis in comparison to Combi-CLEAs-CM attested the improvement of enzyme-substrate interaction by Tween 80 and pores formation by BSA in Combi-CLEAs-CM-add. The improved product specificity of Combi-CLEAs-CM-add also produced the highest yield of MOS (492 mg/g) after 3 h. Therefore, Combi-CLEAs-CM-add with ease of preparation, excellent reusability and high operational stability is believed to be highly efficacious biocatalyst for MOS production.
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Affiliation(s)
- Yee Seng Yip
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Nor Hasmaliana Abdul Manas
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia; Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Nardiah Rizwana Jaafar
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Roshanida A Rahman
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Ni Nyoman Tri Puspaningsih
- Laboratory of Proteomics, University-CoE Research Center for Bio-Molecule Engineering, Universitas Airlangga, Kampus C-UNAIR, Surabaya, East Java, Indonesia
| | - Rosli Md Illias
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia; Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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8
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Enhanced Thermal Stability of Polyphosphate-Dependent Glucomannokinase by Directed Evolution. Catalysts 2022. [DOI: 10.3390/catal12101112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Polyphosphate-dependent glucomannokinase (PPGMK) is able to utilize inorganic polyphosphate to synthesize mannose-6-phosphate (M6P) instead of highly costly ATP. This enzyme was modified and designed by combining error-prone PCR (EP-PCR) and site-directed saturation mutagenesis. Two mutants, H92L/A138V and E119V, were screened out from the random mutation library, and we used site-specific saturation mutations to find the optimal amino acid at each site. Finally, we found the optimal combination mutant, H92K/E119R. The thermal stability of H92K/E119R increased by 5.4 times at 50 °C, and the half-life at 50 °C increased to 243 min. Moreover, the enzyme activity of H92K/E119R increased to 16.6 U/mg, and its enzyme activity is twice that of WT. We analyzed the structure of the mutant using molecular dynamics simulation. We found that the shortening of the hydrogen bond distance and the formation of salt bridges can firmly connect the α-helix and β-sheet and improve the stability of the PPGMK structure.
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9
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Li Y, Li C, Huang H, Rao S, Zhang Q, Zhou J, Li J, Du G, Liu S. Significantly Enhanced Thermostability of Aspergillus niger Xylanase by Modifying Its Highly Flexible Regions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4620-4630. [PMID: 35404048 DOI: 10.1021/acs.jafc.2c01343] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this study, the thermostability of an acid-resistant GH11 xylanase (xynA) from Aspergillus niger AG11 was enhanced through systematic modification of its four highly flexible regions (HFRs) predicted using MD simulations. Among them, HFR I (residues 92-100) and HFR II (residues 121-130) were modified by iterative saturation mutagenesis (ISM), yielding mutants G92F/G97S/G100K and T121V/A124P/I126V/T129L/A130N, respectively. For HFR III, the N-(residues 1-37) and C-termini (residues 179-188) were, respectively, substituted with the corresponding sequences from thermophilic EvXyn11TS and Nesterenkonia xinjiangensis xylanase. N-Glycosylation was introduced into HFR IV (residues 50-70) through site-directed mutation (A55N/D57S/S61N) and the recombinant expression in A. niger AG11. Combining these positive mutations from each HFR yielded the variant xynAm1 with 137.6- and 1.3-fold increases in half-life at 50 °C and specific activity compared to the wild-type xynA, respectively. With the highest thermostability at 80 and 90 °C in reports, xynAm1 could be a robust candidate for industrial applications in functional foods, feed products, and bioethanol production.
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Affiliation(s)
- Yangyang Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Cen Li
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Hao Huang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, 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
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, 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
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Guocheng Du
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Song Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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Verma D. Extremophilic Prokaryotic Endoxylanases: Diversity, Applicability, and Molecular Insights. Front Microbiol 2021; 12:728475. [PMID: 34566933 PMCID: PMC8458939 DOI: 10.3389/fmicb.2021.728475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Extremophilic endoxylanases grabbed attention in recent years due to their applicability under harsh conditions of several industrial processes. Thermophilic, alkaliphilic, and acidophilic endoxylanases found their employability in bio-bleaching of paper pulp, bioconversion of lignocellulosic biomass into xylooligosaccharides, bioethanol production, and improving the nutritious value of bread and other bakery products. Xylanases obtained from extremophilic bacteria and archaea are considered better than fungal sources for several reasons. For example, enzymatic activity under broad pH and temperature range, low molecular weight, cellulase-free activity, and longer stability under extreme conditions of prokaryotic derived xylanases make them a good choice. In addition, a short life span, easy cultivation/harvesting methods, higher yield, and rapid DNA manipulations of bacterial and archaeal cells further reduces the overall cost of the product. This review focuses on the diversity of prokaryotic endoxylanases, their characteristics, and their functional attributes. Besides, the molecular mechanisms of their extreme behavior have also been presented here.
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Affiliation(s)
- Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Rahimian Gavaseraei H, Hasanzadeh R, Afsharnezhad M, Foroutan Kalurazi A, Shahangian SS, Aghamaali MR, Aminzadeh S. Identification, heterologous expression and biochemical characterization of a novel cellulase-free xylanase B from the thermophilic bacterium Cohnella sp.A01. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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12
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Zhao P, Ren SM, Liu F, Zheng YC, Xu N, Pan J, Yu HL, Xu JH. Protein engineering of thioether monooxygenase to improve its thermostability for enzymatic synthesis of chiral sulfoxide. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Cheng J, Tu W, Luo Z, Gou X, Li Q, Wang D, Zhou J. A High-Efficiency Artificial Synthetic Pathway for 5-Aminovalerate Production From Biobased L-Lysine in Escherichia coli. Front Bioeng Biotechnol 2021; 9:633028. [PMID: 33634090 PMCID: PMC7900509 DOI: 10.3389/fbioe.2021.633028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Bioproduction of 5-aminovalerate (5AVA) from renewable feedstock can support a sustainable biorefinery process to produce bioplastics, such as nylon 5 and nylon 56. In order to achieve the biobased production of 5AVA, a 2-keto-6-aminocaproate-mediated synthetic pathway was established. Combination of L-Lysine α-oxidase from Scomber japonicus, α-ketoacid decarboxylase from Lactococcus lactis and aldehyde dehydrogenase from Escherichia coli could achieve the biosynthesis of 5AVA from biobased L-Lysine in E. coli. The H2O2 produced by L-Lysine α-oxidase was decomposed by the expression of catalase KatE. Finally, 52.24 g/L of 5AVA were obtained through fed-batch biotransformation. Moreover, homology modeling, molecular docking and molecular dynamic simulation analyses were used to identify mutation sites and propose a possible trait-improvement strategy: the expanded catalytic channel of mutant and more hydrogen bonds formed might be beneficial for the substrates stretch. In summary, we have developed a promising artificial pathway for efficient 5AVA synthesis.
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Affiliation(s)
- Jie Cheng
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Wenying Tu
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Zhou Luo
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xinghua Gou
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qiang Li
- Key Laboratory of Meat Processing of Sichuan Province, Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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14
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Improvement of PersiXyn2 activity and stability in presence of Trehalose and proline as a natural osmolyte. Int J Biol Macromol 2020; 163:348-357. [DOI: 10.1016/j.ijbiomac.2020.06.288] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/04/2023]
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Zhu D, Adebisi WA, Ahmad F, Sethupathy S, Danso B, Sun J. Recent Development of Extremophilic Bacteria and Their Application in Biorefinery. Front Bioeng Biotechnol 2020; 8:483. [PMID: 32596215 PMCID: PMC7303364 DOI: 10.3389/fbioe.2020.00483] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.
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Affiliation(s)
- Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Wasiu Adewale Adebisi
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Fiaz Ahmad
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Blessing Danso
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
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Ma C, Liu M, You C, Zhu Z. Engineering a diaphorase via directed evolution for enzymatic biofuel cell application. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00311-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Background
Diaphorase (DI) has received wide attention as the key anodic enzyme mediating the electron transfer and electric energy generation in enzymatic biofuel cells (EBFCs). Lowering the anodic pH may be a useful strategy for constructing high-performance in EBFCs. However, most DI suffered from the poor activity at low pHs. Therefore, it is necessary to modify the activity and its acidic tolerance to further improve the performance of the EBFC.
Results
This paper attempts to improve the enzyme activity of DI originated from Geobacillus stearothermophilus under acidic conditions through directed evolution. Three rounds of random mutagenesis by error-prone PCR of the GsDI gene followed by high-throughput screening allowed the identification of the mutant 3–8 (H37Q, S73T, F105L, S68T, G61S, D74V) exhibiting a 4- or 7-fold increase in the catalytic activity at pH 5.4 or 4.5 compared to that of the wild type. And the pH stability of mutant 3–8 was significantly better than that of wild type and showed a 1.3 times higher in the stability at pH 5.4. The EBFC anode equipped with 0.5 mg of mutant 3–8 achieved a maximum current of 40 μA at pH 5.4, much higher than that with the same loading of the wild type enzyme.
Conclusion
The GsDI has been improved in the specific activity and pH stability by directed evolution which leads to the improvement of the EBFC performance. Also, the enlarged catalytic channel of mutant and decreased B-factor may be beneficial for the activity and stability. These results suggest that this engineered DI will be a useful candidate for the construction of enhanced EBFCs.
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