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Wang L, Meng J, Yu X, Wang J, Zhang Y, Zhang M, Zhang Y, Wang H, Feng H, Tian Q, Zhang L, Liu H. Construction of highly active and stable recombinant nattokinase by engineered bacteria and computational design. Arch Biochem Biophys 2024; 760:110126. [PMID: 39154817 DOI: 10.1016/j.abb.2024.110126] [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: 01/30/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Nattokinase (NK) is an enzyme that has been recognized as a new potential thrombolytic drug due to its strong thrombolytic activity. However, it is difficult to maintain the enzyme activity of NK during high temperature environment of industrial production. In this study, we constructed six NK mutants with potential for higher thermostability using a rational protein engineering strategy integrating free energy-based methods and molecular dynamics (MD) simulation. Then, wild-type NK and NK mutants were expressed in Escherichia coli (E. coli), and their thermostability and thrombolytic activity were tested. The results showed that, compared with wild-type NK, the mutants Y256P, Q206L and E156F all had improved thermostability. The optimal mutant Y256P showed a higher melting temperature (Tm) of 77.4 °C, an increase of 4 °C in maximum heat-resistant temperature and an increase of 51.8 % in activity at 37 °C compared with wild-type NK. Moreover, we also explored the mechanism of the increased thermostability of these mutants by analysing the MD trajectories under different simulation temperatures.
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Affiliation(s)
- Lianxin Wang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Jinhui Meng
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Xiaomiao Yu
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Jie Wang
- School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Yuying Zhang
- School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Man Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Yuxi Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Hengyi Wang
- School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Huawei Feng
- Liaoning Provincial Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China; School of Pharmacy, Liaoning University, Shenyang, 110036, China
| | - Qifeng Tian
- School of Life Science, Liaoning University, Shenyang, 110036, China
| | - Li Zhang
- School of Life Science, Liaoning University, Shenyang, 110036, China; Liaoning Provincial Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China.
| | - Hongsheng Liu
- Liaoning Provincial Key Laboratory of Computational Simulation and Information Processing of Biomacromolecules, Shenyang, 110036, China; Engineering Laboratory for Molecular Simulation and Designing of Drug Molecules of Liaoning, Shenyang, 110036, China; School of Pharmacy, Liaoning University, Shenyang, 110036, China.
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2
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Wan X, Shahrear S, Chew SW, Vilaplana F, Mäkelä MR. Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:120. [PMID: 39261970 PMCID: PMC11391777 DOI: 10.1186/s13068-024-02566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods. RESULTS This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method. CONCLUSIONS This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.
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Affiliation(s)
- Xing Wan
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Sazzad Shahrear
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Shea Wen Chew
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullbacken 21, 11421, Stockholm, Sweden
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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3
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Zhu J, Liu M, Kang J, Wang S, Zha Z, Zhan Y, Wang Z, Li J, Cai D, Chen S. Engineering Bacillus licheniformis as industrial chassis for efficient bioproduction from starch. BIORESOURCE TECHNOLOGY 2024; 406:131061. [PMID: 38960005 DOI: 10.1016/j.biortech.2024.131061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/11/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Starch is an attractive feedstock in biorefinery processes, while the low natural conversion rate of most microorganisms limits its applications. Herein, starch metabolic pathway was systematically investigated using Bacillus licheniformis DW2 as the host organism. Initially, the effects of overexpressing amylolytic enzymes on starch hydrolysis were evaluated. Subsequently, the transmembrane transport system and intracellular degradation module were modified to accelerate the uptake of hydrolysates and their further conversion to glucose-6-phosphate. The DW2-derived strains exhibited robust growth in starch medium, and productivity of bacitracin and subtilisin were improved by 38.5% and 32.6%, with an 32.3% and 22.9% increase of starch conversion rate, respectively. Lastly, the employment of engineering strategies enabled another B. licheniformis WX-02 to produce poly-γ-glutamic acid from starch with a 2.1-fold increase of starch conversion rate. This study not only provided excellent B. licheniformis chassis for sustainable bioproduction from starch, but shed light on researches of substrate utilization.
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Affiliation(s)
- Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Min Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jianling Kang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Shiyi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Ziyan Zha
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Zhi Wang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan 430068, Hubei, PR China
| | - Junhui Li
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, 430062, PR China.
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4
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Shalem A, Yehezkeli O, Fishman A. Enzymatic degradation of polylactic acid (PLA). Appl Microbiol Biotechnol 2024; 108:413. [PMID: 38985324 PMCID: PMC11236915 DOI: 10.1007/s00253-024-13212-4] [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: 04/03/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/11/2024]
Abstract
Environmental concerns arising from the increasing use of polluting plastics highlight polylactic acid (PLA) as a promising eco-friendly alternative. PLA is a biodegradable polyester that can be produced through the fermentation of renewable resources. Together with its excellent properties, suitable for a wide range of applications, the use of PLA has increased significantly over the years and is expected to further grow. However, insufficient degradability under natural conditions emphasizes the need for the exploration of biodegradation mechanisms, intending to develop more efficient techniques for waste disposal and recycling or upcycling. Biodegradation occurs through the secretion of depolymerizing enzymes, mainly proteases, lipases, cutinases, and esterases, by various microorganisms. This review focuses on the enzymatic degradation of PLA and presents different enzymes that were isolated and purified from natural PLA-degrading microorganisms, or recombinantly expressed. The review depicts the main characteristics of the enzymes, including recent advances and analytical methods used to evaluate enantiopurity and depolymerizing activity. While complete degradation of solid PLA particles is still difficult to achieve, future research and improvement of enzyme properties may provide an avenue for the development of advanced procedures for PLA degradation and upcycling, utilizing its building blocks for further applications as envisaged by circular economy principles. KEY POINTS: • Enzymes can be promisingly utilized for PLA upcycling. • Natural and recombinant PLA depolymerases and methods for activity evaluation are summarized. • Approaches to improve enzymatic degradation of PLA are discussed.
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Affiliation(s)
- Adi Shalem
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Omer Yehezkeli
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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5
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Xu L, Nawaz MZ, Khalid HR, Waqar-Ul-Haq, Alghamdi HA, Sun J, Zhu D. Modulating the pH profile of vanillin dehydrogenase enzyme from extremophile Bacillus ligniniphilus L1 through computational guided site-directed mutagenesis. Int J Biol Macromol 2024; 263:130359. [PMID: 38387643 DOI: 10.1016/j.ijbiomac.2024.130359] [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: 11/22/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Vanillin dehydrogenase (VDH) has recently come forward as an important enzyme for the commercial production of vanillic acid from vanillin in a one-step enzymatic process. However, VDH with high alkaline tolerance and efficiency is desirable to meet the biorefinery requirements. In this study, computationally guided site-directed mutagenesis was performed by increasing the positive and negative charges on the surface and near the active site of the VDH from the alkaliphilic marine bacterium Bacillus ligniniphilus L1, respectively. In total, 20 residues including 15 from surface amino acids and 5 near active sites were selected based on computational analysis and were subjected to site-directed mutations. The optimum pH of the two screened mutants including I132R, and T235E from surface residue and near active site mutant was shifted to 9, and 8.6, with a 2.82- and 2.95-fold increase in their activity compared to wild enzyme at pH 9, respectively. A double mutant containing both these mutations i.e., I132R/T235E was produced which showed a shift in optimum pH of VDH from 7.4 to 9, with an increase of 74.91 % in enzyme activity. Therefore, the double mutant of VDH from the L1 strain (I132R/T235E) produced in this study represents a potential candidate for industrial applications.
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Affiliation(s)
- Lingxia Xu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Muhammad Zohaib Nawaz
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Hafiz Rameez Khalid
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Waqar-Ul-Haq
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha 61413, Saudi Arabia
| | - Jianzhong Sun
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Daochen Zhu
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; International Joint Laboratory on Synthetic Biology and Biomass Biorefinery, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, PR China.
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6
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Zhang L, Dai W, Rong S, Schwaneberg U, Xu G, Ni Y. Engineering diaryl alcohol dehydrogenase KpADH reveals importance of retaining hydration shell in organic solvent tolerance. Protein Sci 2024; 33:e4933. [PMID: 38501647 PMCID: PMC10949390 DOI: 10.1002/pro.4933] [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: 12/21/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 03/20/2024]
Abstract
Alcohol dehydrogenases (ADHs) are synthetically important biocatalysts for the asymmetric synthesis of chiral alcohols. The catalytic performance of ADHs in the presence of organic solvents is often important since most prochiral ketones are highly hydrophobic. Here, the organic solvent tolerance of KpADH from Kluyveromyces polyspora was semi-rationally evolved. Using tolerant variants obtained, meticulous experiments and computational studies were conducted to explore properties including stability, activity and kinetics in the presence of various organic solvents. Compared with WT, variant V231D exhibited 1.9-fold improvement in ethanol tolerance, while S237G showed a 6-fold increase in catalytic efficiency, a higherT 50 15 $$ {\mathrm{T}}_{50}^{15} $$ , as well as 15% higher tolerance in 7.5% (v/v) ethanol. Based on 3 × 100 ns MD simulations, the increased tolerance of V231D and S237G against ethanol may be ascribed to their enhanced ability in retaining water molecules and repelling ethanol molecules. Moreover, 6.3-fold decreased KM value of V231D toward hydrophilic ketone substrate confirmed its capability of retaining hydration shell. Our results suggest that retaining hydration shell surrounding KpADH is critical for its tolerance to organic solvents, as well as catalytic performance. This study provides useful guidance for engineering organic solvent tolerance of KpADH and other ADHs.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Wei Dai
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Shuo Rong
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | | | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of EducationSchool of Biotechnology, Jiangnan UniversityWuxiChina
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7
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Chatterjee A, Puri S, Sharma PK, Deepa PR, Chowdhury S. Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles. Front Bioeng Biotechnol 2023; 11:1229300. [PMID: 37409164 PMCID: PMC10318364 DOI: 10.3389/fbioe.2023.1229300] [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: 05/26/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
The use of enzymes to accelerate chemical reactions for the synthesis of industrially important products is rapidly gaining popularity. Biocatalysis is an environment-friendly approach as it not only uses non-toxic, biodegradable, and renewable raw materials but also helps to reduce waste generation. In this context, enzymes from organisms living in extreme conditions (extremozymes) have been studied extensively and used in industries (food and pharmaceutical), agriculture, and molecular biology, as they are adapted to catalyze reactions withstanding harsh environmental conditions. Enzyme engineering plays a key role in integrating the structure-function insights from reference enzymes and their utilization for developing improvised catalysts. It helps to transform the enzymes to enhance their activity, stability, substrates-specificity, and substrate-versatility by suitably modifying enzyme structure, thereby creating new variants of the enzyme with improved physical and chemical properties. Here, we have illustrated the relatively less-tapped potentials of plant enzymes in general and their sub-class of extremozymes for industrial applications. Plants are exposed to a wide range of abiotic and biotic stresses due to their sessile nature, for which they have developed various mechanisms, including the production of stress-response enzymes. While extremozymes from microorganisms have been extensively studied, there are clear indications that plants and algae also produce extremophilic enzymes as their survival strategy, which may find industrial applications. Typical plant enzymes, such as ascorbate peroxidase, papain, carbonic anhydrase, glycoside hydrolases and others have been examined in this review with respect to their stress-tolerant features and further improvement via enzyme engineering. Some rare instances of plant-derived enzymes that point to greater exploration for industrial use have also been presented here. The overall implication is to utilize biochemical clues from the plant-based enzymes for robust, efficient, and substrate/reaction conditions-versatile scaffolds or reference leads for enzyme engineering.
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Affiliation(s)
| | | | | | - P. R. Deepa
- *Correspondence: P. R. Deepa, ; Shibasish Chowdhury,
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8
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Li SF, Cheng F, Wang YJ, Zheng YG. Strategies for tailoring pH performances of glycoside hydrolases. Crit Rev Biotechnol 2023; 43:121-141. [PMID: 34865578 DOI: 10.1080/07388551.2021.2004084] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glycoside hydrolases (GHs) exhibit high activity and stability under harsh conditions, such as high temperatures and extreme pHs, given their wide use in industrial biotechnology. However, strategies for improving the acidophilic and alkalophilic adaptations of GHs are poorly summarized due to the complexity of the mechanisms of these adaptations. This review not only highlights the adaptation mechanisms of acidophilic and alkalophilic GHs under extreme pH conditions, but also summarizes the recent advances in engineering the pH performances of GHs with a focus on four strategies of protein engineering, enzyme immobilization, chemical modification, and medium engineering (additives). The examples described here summarize the methods used in modulating the pH performances of GHs and indicate that methods integrated in different protein engineering techniques or methods are efficient to generate industrial biocatalysts with the desired pH performance and other adapted enzyme properties.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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9
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Xie T, Zhou L, Han L, Cui W, Liu Z, Cheng Z, Guo J, Zhou Z. Modulating the pH profile of the pullulanase from Pyrococcus yayanosii CH1 by synergistically engineering the active center and surface. Int J Biol Macromol 2022; 216:132-139. [PMID: 35777517 DOI: 10.1016/j.ijbiomac.2022.06.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/14/2022] [Accepted: 06/23/2022] [Indexed: 11/24/2022]
Abstract
A preferable pullulanase with high thermostability and catalytic activity at pH 4.5-5 is desired to match with glucoamylase in the starch-saccharification process. However, most of them exhibit low activity under such low pH conditions. Here, the optimal pH of the hyperthermostable pullulanase from Pyrococcus yayanosii (PulPY2) was successfully shifted from 6.4 to 5 with a 2-fold increase in the specific activity based on synergistic engineering of the active center and surface. Synergistic engineering was performed by introducing histidine within 6 Å of the active sites, and by enhancing negative charges on the enzymatic surface. Two single-site mutants of PulPY2-Q13H and PulPY2-I25E with higher hydrolytic activity were obtained, the optimal pH of which was shifted to pH 5 and 5.4, respectively; the combined mutant PulPY2-Q13H/I25E exhibited the optimal pH of 5, 3.2-fold increasing catalytic efficiency at pH 5, and high thermostability compared to PulPY2. These results not only obtained an applicable pullulanase for industrial application, but also provided a strategy for shifting the optimal pH of the enzyme based on synergistic engineering of the active center and surface.
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Affiliation(s)
- Ting Xie
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Li Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Laichuang Han
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Wenjing Cui
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhongmei Liu
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhongyi Cheng
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Junling Guo
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhemin Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China.
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10
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Tang L, Bao M, Wang Y, Fu Z, Han F, Yu W. Effects of Module Truncation of a New Alginate Lyase VxAly7C from Marine Vibrio xiamenensis QY104 on Biochemical Characteristics and Product Distribution. Int J Mol Sci 2022; 23:ijms23094795. [PMID: 35563187 PMCID: PMC9102848 DOI: 10.3390/ijms23094795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alginate lyase has received extensive attention as an important tool for oligosaccharide preparation, pharmaceutical production, and energy biotransformation. Noncatalytic module carbohydrate-binding modules (CBM) have a major impact on the function of alginate lyases. Although the effects of two different families of CBMs on enzyme characteristics have been reported, the effect of two combined CBM32s on enzyme function has not been elucidated. Herein, we cloned and expressed a new multimodular alginate lyase, VxAly7C, from Vibrioxiamenensis QY104, consisting of two CBM32s at N-terminus and a polysaccharide lyase family 7 (PL7) at C-terminus. To explore the function of CBM32s in VxAly7C, full-length (VxAly7C-FL) and two truncated mutants, VxAly7C-TM1 (with the first CBM32 deleted) and VxAly7C-TM2 (with both CBM32s deleted), were characterized. The catalytic efficiency of recombinant VxAly7C-TM2 was 1.82 and 4.25 times higher than that of VxAly7C-TM1 and VxAly7C-FL, respectively, indicating that CBM32s had an antagonistic effect. However, CBM32s improved the temperature stability, the adaptability in an alkaline environment, and the preference for polyG. Moreover, CBM32s contributed to the production of tri- and tetrasaccharides, significantly affecting the end-product distribution. This study advances the understanding of module function and provides a reference for broader enzymatic applications and further enzymatic improvement and assembly.
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Affiliation(s)
- Luyao Tang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (L.T.); (M.B.); (Y.W.); (Z.F.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Bao
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (L.T.); (M.B.); (Y.W.); (Z.F.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
| | - Ying Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (L.T.); (M.B.); (Y.W.); (Z.F.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
| | - Zheng Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (L.T.); (M.B.); (Y.W.); (Z.F.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (L.T.); (M.B.); (Y.W.); (Z.F.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
- Correspondence: (F.H.); (W.Y.); Tel.: +86-532-82032067 (F.H.); +86-532-82031680 (W.Y.)
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (L.T.); (M.B.); (Y.W.); (Z.F.)
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Qingdao 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Qingdao 266003, China
- Correspondence: (F.H.); (W.Y.); Tel.: +86-532-82032067 (F.H.); +86-532-82031680 (W.Y.)
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11
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Molecular Identification of Keratinase DgokerA from Deinococcus gobiensis for Feather Degradation. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12010464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Keratin is a tough fibrous structural protein that is difficult to digest with pepsin and trypsin because of the presence of a large number of disulfide bonds. Keratin is widely found in agricultural waste. In recent years, especially, the development of the poultry industry has resulted in a large accumulation of feather keratin resources, which seriously pollute the environment. Keratinase can specifically attack disulfide bridges in keratin, converting them from complex to simplified forms. The keratinase thermal stability has drawn attention to various biotechnological industries. It is significant to identify keratinases and improve their thermostability from microorganism in extreme environments. In this study, the keratinases DgoKerA was identified in Deinococcus gobiensis I-0 from the Gobi desert. The amino acid sequence analysis revealed that DgoKerA was 58.68% identical to the keratinase MtaKerA from M. thermophila WR-220 and 40.94% identical to the classical BliKerA sequence from B. licheniformis PWD-1. In vitro enzyme activity analysis showed that DgoKerA exhibited an optimum temperature of 60 °C, an optimum pH of 7 and a specific enzyme activity of 51147 U/mg. DgoKerA can degrade intact feathers at 60 °C and has good potential for industrial applications. The molecular modification of DgoKerA was also carried out using site-directed mutagenesis, in which the mutant A350S enzyme activity was increased by nearly 30%, and the results provide a theoretical basis for the development and optimization of keratinase applications.
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12
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Hao M, Cui R, Zhu X, Han L, Zhou Z, Liu Z. Improving the activity and synergistic catalysis of l-aspartate β-decarboxylase by arginine introduction on the surface. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00700b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction of arginine on the surface relieved the pH-dependent inactivation of l-aspartate-β-decarboxylase, which promoted its application in synthetic biology and biocatalysis.
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Affiliation(s)
- Mingzhu Hao
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Ruizhi Cui
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Xiaoqing Zhu
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, China
| | - Zhongmei Liu
- School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Binhu-qu, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, China
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13
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Takenaka S, Takada A, Kimura Y, Watanabe M, Kuntiya A. Improvement of the halotolerance of a Bacillus serine protease by protein surface engineering. J Basic Microbiol 2021; 62:174-184. [PMID: 34811778 DOI: 10.1002/jobm.202100335] [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: 07/16/2021] [Revised: 10/24/2021] [Accepted: 11/06/2021] [Indexed: 11/07/2022]
Abstract
A moderately halotolerant serine protease was previously isolated from Bacillus subtilis from salted, fermented food. Eight mutation sites on the protein surface were selected for protein engineering based on sequence and structural comparisons with moderately halotolerant proteases and homologous non-halotolerant proteases. The newly constructed multiple mutants with substituted Asp and Arg residues were compared with the recombinant wild type (rApr) and the previously constructed mAla-8 substituted with Ala to analyze the contribution of protein surface charge to the salt adaptation of the protease. The three mutants showed >1.2-fold greater halotolerance than rApr. In addition, the mutants showed a broader range of pH stability than rApr, retaining >80% of their maximum activity in the pH range 5.0-11. The mutants also retained >75% of their activity after incubation for 1 h at pH 8.0 and 55°C or at pH 11.5 and 25°C. The Asp and Arg residues exchanged by multiple substitution probably played a role in increasing protein surface hydration and solubility in high salt conditions. This study illustrated that increasing a high proportion of the negative or positive charge on the surface of the Bacillus serine protease stably improved the protein's salt adaptation.
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Affiliation(s)
- Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Airi Takada
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masanori Watanabe
- Department of Food, Life, and Environmental Science, Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Ampin Kuntiya
- Bioprocess Research Cluster, School of Agro-Industry, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai, Thailand
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14
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Victorino da Silva Amatto I, Gonsales da Rosa-Garzon N, Antônio de Oliveira Simões F, Santiago F, Pereira da Silva Leite N, Raspante Martins J, Cabral H. Enzyme engineering and its industrial applications. Biotechnol Appl Biochem 2021; 69:389-409. [PMID: 33555054 DOI: 10.1002/bab.2117] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 01/03/2023]
Abstract
Recently, there has been an increase in the demand for enzymes with modified activity, specificity, and stability. Enzyme engineering is an important tool to meet the demand for enzymes adjusted to different industrial processes. Knowledge of the structure and function of enzymes guides the choice of the best strategy for engineering enzymes. Each enzyme engineering strategy, such as rational design, directed evolution, and semi-rational design, has specific applications, as well as limitations, which must be considered when choosing a suitable strategy. Engineered enzymes can be optimized for different industrial applications by choosing the appropriate strategy. This review features engineered enzymes that have been applied in food, animal feed, pharmaceuticals, medical applications, bioremediation, biofuels, and detergents.
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Affiliation(s)
- Isabela Victorino da Silva Amatto
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathalia Gonsales da Rosa-Garzon
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Flávio Antônio de Oliveira Simões
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Pharmaceutical Sciences Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Fernanda Santiago
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Nathália Pereira da Silva Leite
- Pharmaceutical Sciences Program, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, XUniversity of São Paulo, Ribeirão Preto, SP, Brazil
| | - Júlia Raspante Martins
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Biosciences and Biotechnology Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil.,Pharmaceutical Sciences Program, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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15
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Surface charge-based rational design of aspartase modifies the optimal pH for efficient β-aminobutyric acid production. Int J Biol Macromol 2020; 164:4165-4172. [DOI: 10.1016/j.ijbiomac.2020.08.229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022]
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16
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The hydrophobicity of an amino acid residue in a flexible loop of KP-43 protease alters activity toward a macromolecule substrate. Appl Microbiol Biotechnol 2020; 104:8339-8349. [PMID: 32840642 PMCID: PMC7471176 DOI: 10.1007/s00253-020-10826-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 08/02/2020] [Accepted: 08/11/2020] [Indexed: 12/02/2022]
Abstract
Abstract KP-43, a 43-kDa alkaline serine protease, is resistant to chemical oxidants and surfactants, making it suitable for use in laundry detergents. An amino acid residue at position 195, in a unique flexible loop that binds a Ca2+ ion, dramatically affects the proteolytic activity and thermal stability of KP-43. In the present study, we obtained 20 variants with substitutions at position 195 and investigated how these residues affect hydrolytic activity toward a macromolecular substrate (casein) and a synthetic tetra-peptide (AAPL). At pH 10, the variant with the highest caseinolytic activity, Tyr195Gln, exhibited 4.4-fold higher activity than the variant with the lowest caseinolytic activity, Tyr195Trp. A significant negative correlation was observed between the hydrophobicity of the residue at position 195 and caseinolytic activity at pH 8–10. At pH 7, the correlation became weak; at pH 6, the correlation reversed to positive. Unlike casein, in the case of hydrolysis of AAPL, no correlation was observed at pH 10 or pH 6. Because the amino acid residue at position 195 is located on the protein surface and considered sufficiently far from the active cleft, the variation in caseinolytic activity between the 20 variants was attributed to changes in interaction efficiency with different states of casein at different pH values. To improve the enzymatic activity, we propose substituting amino acid residues on the protein surface to change the efficiency of interaction with the macromolecular substrates. Key points • A single amino acid residue on the protein surface markedly changed enzyme activity. • The hydrophobicity of the amino acid residue and enzyme activity had a correlation. • The key amino acid residue for substrate recognition exists on the protein surface. Electronic supplementary material The online version of this article (10.1007/s00253-020-10826-2) contains supplementary material, which is available to authorized users.
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17
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Wang H, Zhang L, Wang Y, Li J, Du G, Kang Z. Engineering the heparin-binding pocket to enhance the catalytic efficiency of a thermostable heparinase III from Bacteroides thetaiotaomicron. Enzyme Microb Technol 2020; 137:109549. [DOI: 10.1016/j.enzmictec.2020.109549] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 02/06/2023]
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18
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Al-Ghanayem AA, Joseph B. Current prospective in using cold-active enzymes as eco-friendly detergent additive. Appl Microbiol Biotechnol 2020; 104:2871-2882. [PMID: 32037467 DOI: 10.1007/s00253-020-10429-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 12/13/2022]
Abstract
Advanced developments in the field of enzyme technology have increased the use of enzymes in industrial applications, especially in detergents. Enzymes as detergent additives have been extensively studied and the demand is considerably increasing due to its distinct properties and potential applications. Enzymes from microorganisms colonized at various geographical locations ranging from extreme hot to cold are explored for compatibility studies as detergent additives. Especially psychrophiles growing at cold conditions have cold-active enzymes with high catalytic activity and their stability under extreme conditions makes it as an appropriate eco-friendly and cost-effective additive in detergents. Adequate number of reports are available on cold-active enzymes such as proteases, lipases, amylases, and cellulases with high efficiency and exceptional features. These enzymes with increased thermostability and alkaline stability have become the premier choice as detergent additives. Modern approaches in genomics and proteomics paved the way to understand the compatibility of cold-active enzymes as detergent additives in broader dimensions. The molecular techniques such as gene coding, amino acid sequencing, and protein engineering studies helped to solve the mysteries related to alkaline stability of these enzymes and their chemical compatibility with oxidizing agents. The present review provides an overview of cold-active enzymes used as detergent additives and molecular approaches that resulted in development of these enzymes as commercial hit in detergent industries. The scope and challenges in using cold-active enzymes as eco-friendly and sustainable detergent additive are also discussed.
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Affiliation(s)
- Abdullah A Al-Ghanayem
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra, 11961, Kingdom of Saudi Arabia
| | - Babu Joseph
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Shaqra, 11961, Kingdom of Saudi Arabia.
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19
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Zeng Y, Xu J, Fu X, Tan M, Liu F, Zheng H, Song H. Effects of different carbohydrate-binding modules on the enzymatic properties of pullulanase. Int J Biol Macromol 2019; 137:973-981. [DOI: 10.1016/j.ijbiomac.2019.07.054] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/29/2022]
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20
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Han C, Liu S, Liu C, Xie X, Fang L, Min W. The mutant T379L of novel aspartokinase from Corynebacterium pekinense: A combined experimental and molecular dynamics simulation study. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Cai D, Zhang B, Rao Y, Li L, Zhu J, Li J, Ma X, Chen S. Improving the utilization rate of soybean meal for efficient production of bacitracin and heterologous proteins in the aprA-deficient strain of Bacillus licheniformis. Appl Microbiol Biotechnol 2019; 103:4789-4799. [PMID: 31025072 DOI: 10.1007/s00253-019-09804-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/20/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
Soybean meal is commonly applied as the raw material in the bio-fermentation industry, and bacitracin is a widely used feed additive in the feed industry. In this study, we investigated the influence of subtilisin enhancement on soybean meal utilization and bacitracin production in Bacillus licheniformis DW2, an industrial strain for bacitracin production. Firstly, blocking sRNA aprA expression benefited bacitracin synthesis, and the bacitracin yield produced by aprA-deficient strain DW2△PaprA reached 931.43 U/mL, 18.92% higher than that of DW2 (783.25 U/mL). The bacitracin yield was reduced by 14.27% in the aprA overexpression strain. Furthermore, our results showed that deficiency of aprA led to a 6.54-fold increase of the aprE transcriptional level and a 1.84-fold increase of subtilisin activity, respectively, which led to the increases of soybean meal utilization rate (28.86%) and precursor amino acid supplies for bacitracin synthesis. Additionally, strengthening the utilization rate of soybean meal also benefited heterologous protein production, and the α-amylase and nattokinase activities were respectively enhanced by 59.81% and 50.53% in aprA-deficient strains. Collectively, this research demonstrated that strengthening subtilisin production could improve the utilization rate of soybean meal and thereby enhance bacitracin and target protein production; also, this strategy would be useful for the improvement of protein/peptide production using soybean meal as the main nitrogen source in the fermentation process.
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Affiliation(s)
- Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Bowen Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Yi Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Lingfeng Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Jiang Zhu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Junhui Li
- Lifecome Biochemistry Co. Ltd, Nanping, 353400, People's Republic of China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China.
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22
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Tuning the pH profile of β-glucuronidase by rational site-directed mutagenesis for efficient transformation of glycyrrhizin. Appl Microbiol Biotechnol 2019; 103:4813-4823. [PMID: 31055652 DOI: 10.1007/s00253-019-09790-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/16/2019] [Accepted: 03/20/2019] [Indexed: 02/05/2023]
Abstract
In this study, we aimed to shift the optimal pH of acidic β-glucuronidase from Aspergillus oryzae Li-3 (PGUS) to the neutral region by site-directed mutagenesis, thus allowing high efficient biotransformation of glycyrrhizin (GL) into glycyrrhetinic acid (GA) under higher pH where the solubility of GL could be greatly enhanced. Based on PGUS structure analysis, five critical aspartic acid and glutamic acid residues were replaced with arginine on the surface to generate a variant 5Rs with optimal pH shifting from 4.5 to 6.5. The catalytic efficiency (kcat /Km) value of 5Rs at pH 6.5 was 10.7-fold higher than that of PGUS wild-type at pH 6.5, even 1.4-fold higher than that of wild-type at pH 4.5. Molecular dynamics simulation was performed to explore the molecular mechanism for the shifted pH profile and enhanced pH stability of 5Rs.
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23
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Pedersen JN, Zhou Y, Guo Z, Pérez B. Genetic and chemical approaches for surface charge engineering of enzymes and their applicability in biocatalysis: A review. Biotechnol Bioeng 2019; 116:1795-1812. [DOI: 10.1002/bit.26979] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/10/2019] [Accepted: 03/28/2019] [Indexed: 12/25/2022]
Affiliation(s)
| | - Ye Zhou
- Department of EngineeringAarhus UniversityAarhus Denmark
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life ScienceJilin UniversityChangchun China
| | - Zheng Guo
- Department of EngineeringAarhus UniversityAarhus Denmark
| | - Bianca Pérez
- AgrotechDanish Technological InstituteAarhus Denmark
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24
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Tian J, Long X, Tian Y, Shi B. Enhanced extracellular recombinant keratinase activity in Bacillus subtilis SCK6 through signal peptide optimization and site-directed mutagenesis. RSC Adv 2019; 9:33337-33344. [PMID: 35529123 PMCID: PMC9073338 DOI: 10.1039/c9ra07866e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 11/21/2022] Open
Abstract
The extracellular recombinant keratinase activity in Bacillus subtilis SCK6 was enhanced by signal peptide optimization and site-directed mutagenesis.
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Affiliation(s)
- Jiewei Tian
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
| | - Xiufeng Long
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
| | - Yongqiang Tian
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
| | - Bi Shi
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University)
- Department of Biomass and Leather Engineering
- Ministry of Education
- College of Biomass Science and Engineering (Sichuan University)
- Sichuan University
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25
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J. Thiele M, Davari MD, König M, Hofmann I, Junker NO, Mirzaei Garakani T, Vojcic L, Fitter J, Schwaneberg U. Enzyme–Polyelectrolyte Complexes Boost the Catalytic Performance of Enzymes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02935] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Martin J. Thiele
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Melanie König
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Isabell Hofmann
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Niklas O. Junker
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
| | | | - Ljubica Vojcic
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- Codexis, Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Jörg Fitter
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse 14, 52074 Aachen, Germany
- Institute of Complex Systems (ICS-5): Molecular Biophysics, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstraße 50, 52056 Aachen, Germany
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26
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Integrating enzyme immobilization and protein engineering: An alternative path for the development of novel and improved industrial biocatalysts. Biotechnol Adv 2018; 36:1470-1480. [DOI: 10.1016/j.biotechadv.2018.06.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/02/2018] [Accepted: 06/04/2018] [Indexed: 12/15/2022]
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Körfer G, Novoa C, Kern J, Balla E, Grütering C, Davari MD, Martinez R, Vojcic L, Schwaneberg U. Directed evolution of an acid Yersinia mollaretii phytase for broadened activity at neutral pH. Appl Microbiol Biotechnol 2018; 102:9607-9620. [DOI: 10.1007/s00253-018-9308-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 01/25/2023]
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Belsare KD, Horn T, Ruff AJ, Martinez R, Magnusson A, Holtmann D, Schrader J, Schwaneberg U. Directed evolution of P450cin for mediated electron transfer. Protein Eng Des Sel 2016; 30:119-127. [PMID: 28007937 DOI: 10.1093/protein/gzw072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 11/28/2016] [Accepted: 12/05/2016] [Indexed: 11/13/2022] Open
Abstract
Directed evolution is a powerful method to optimize enzyme properties for application demands. Interesting targets are P450 monooxygenases which catalyze the stereo- and regiospecific hydroxylation of chemically inert C-H bonds. Synthesis employing P450s under cell-free reaction conditions is limited by low total turnover numbers, enzyme instability, low product yields and the requirement of the expensive co-factor NADPH. Bioelectrocatalysis is an alternative to replace NADPH in cell-free P450-catalyzed reactions. However, natural enzymes are often not suitable for using non-natural electron delivery systems. Here we report the directed evolution of a previously engineered P450 CinA-10aa-CinC fusion protein (named P450cin-ADD-CinC) to use zinc/cobalt(III)sepulchrate as electron delivery system for an increased hydroxylation activity of 1,8-cineole. Two rounds of Sequence Saturation Mutagenesis (SeSaM) each followed by one round of multiple site-saturation mutagenesis of the P450 CinA-10aa-CinC fusion protein generated a variant (Gln385His, Val386Ser, Thr77Asn, Leu88Arg; named KB8) with a 3.8-fold increase in catalytic efficiency (28 µM-1 min-1) compared to P450cin-ADD-CinC (7 µM-1 min-1). Furthermore, variant KB8 exhibited a 1.5-fold higher product formation (500 µM µM-1 P450) compared to the equimolar mixture of CinA, CinC and Fpr using NADPH as co-factor (315 µM µM-1 P450). In addition, electrochemical experiments with the electron delivery system platinum/cobalt(III)sepulchrate showed that the KB8 variant had a 4-fold higher product formation rate (0.16 nmol (nmol) P450-1 min-1 cm-2) than the P450cin-ADD-CinC (0.04 nmol (nmol) P450-1 min-1 cm-2). In summary, the current work shows prospects of using directed evolution to generate P450 enzymes suitable for use with alternative electron delivery systems.
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Affiliation(s)
- Ketaki D Belsare
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Thomas Horn
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Ronny Martinez
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Anders Magnusson
- Biochemical Engineering Group, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Dirk Holtmann
- Biochemical Engineering Group, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Jens Schrader
- Biochemical Engineering Group, DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany .,DWI-Leibniz-Institut für Interaktive Materialien e. V., Forckenbeckstraße 50, 52074 Aachen, Germany
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Wang X, Lin H, Zheng Y, Feng J, Yang Z, Tang L. MDC-Analyzer-facilitated combinatorial strategy for improving the activity and stability of halohydrin dehalogenase from Agrobacterium radiobacter AD1. J Biotechnol 2015; 206:1-7. [PMID: 25896949 DOI: 10.1016/j.jbiotec.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/05/2023]
Abstract
Halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) displays a broad substrate range with high regio- and enantioselectivity of both ring-closure and ring-opening reactions, making the enzyme a useful catalyst for the production of optically pure epoxides and β-substituted alcohols. In this study, we report a novel method using an MDC-Analyzer-facilitated combinatorial strategy to improve the activity and stability of HheC by simultaneously randomizing multiple contiguous residues. Six contiguous active-site residues, which are the hotspots for improving the activity of HheC, were simultaneously selected and randomized using the MDC-Analyzer-facilitated combinatorial strategy, resulting in a high-quality mutagenesis library. After screening a total of 1152 clones, three positive mutants were obtained, which exhibited approximately 3.5-5.9-fold higher kcat values than the wild-type HheC toward 1,3-dichloro-2-propanol (1,3-DCP). However, the inactivation half-life of the best mutant (DG9) at 55 °C decreased 9-fold compared with that of the wild-type HheC. To improve the stability of mutant DG9, seven contiguous potential surface amino acids were revealed by using the B-FITTER tool. Two charged amino acids, Glu and Lys, which are more abundant in thermophilic proteins than in their mesophilic counterparts, were selected to substitute those seven amino acids and were combined together via an MDC-Analyzer-facilitated combinatorial strategy. Two mutants displaying 1.6- and 2.3-fold higher half-life τ1/2 (55 °C) values than their DG9 template were obtained after screening only 384 clones. The results indicated that an MDC-Analyzer-facilitated combinatorial strategy represents an efficient tool for the directed evolution of functional enzymes with multiple contiguous targeting sites.
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Affiliation(s)
- Xiong Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Yu Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Juan Feng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
| | - Lixia Tang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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Huang R, Yang Q, Feng H. Single amino acid mutation alters thermostability of the alkaline protease from Bacillus pumilus: thermodynamics and temperature dependence. Acta Biochim Biophys Sin (Shanghai) 2015; 47:98-105. [PMID: 25534779 DOI: 10.1093/abbs/gmu120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dehairing alkaline protease (DHAP) from Bacillus pumilus BA06 has been demonstrated to have high catalytic efficiency and good thermostability, with potential application in leather processing. In order to get insights into its catalytic mechanism, two mutants with single amino acid substitution according to the homology modeling and multiple sequence alignment were characterized in thermodynamics of thermal denaturation and temperature dependence of substrate hydrolysis. The results showed that both mutants of V149I and R249E have a systematic increase in catalytic efficiency (kcat/Km) in a wide range of temperatures, mainly due to an increase of k1 (substrate diffusion) and k2 (acylation) for V149I and of k2 and k3 (deacylation) for R249E. In comparison with the wild-type DHAP, the thermostability is increased for V149I and decreased for R249E. Thermodynamic analysis indicated that the free energy (ΔGa°) of activation for thermal denaturation may govern the thermostability. The value of ΔGa° is increased for V149I and decreased for R249E. Based on these data and the structural modeling, it is suggested that substitution of Val149 with Ile may disturb the local flexibility in the substrate-binding pocket, leading to enhancement of binding affinity for the substrate. In contrast, substitution of Arg249 with Glu leads to interruption of interaction with the C-terminal of enzyme, thus resulting in less thermostability. This study indicates that amino acid residues in the active center or in the substrate-binding pocket may disturb the catalytic process and can be selected as the target for protein engineering in the bacterial alkaline proteases.
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Affiliation(s)
- Rong Huang
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Qingjun Yang
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Hong Feng
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
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Vojcic L, Pitzler C, Körfer G, Jakob F, Ronny Martinez, Maurer KH, Schwaneberg U. Advances in protease engineering for laundry detergents. N Biotechnol 2015; 32:629-34. [PMID: 25579194 DOI: 10.1016/j.nbt.2014.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/02/2014] [Accepted: 12/31/2014] [Indexed: 02/03/2023]
Abstract
Proteases are essential ingredients in modern laundry detergents. Over the past 30 years, subtilisin proteases employed in the laundry detergent industry have been engineered by directed evolution and rational design to tailor their properties towards industrial demands. This comprehensive review discusses recent success stories in subtilisin protease engineering. Advances in protease engineering for laundry detergents comprise simultaneous improvement of thermal resistance and activity at low temperatures, a rational strategy to modulate pH profiles, and a general hypothesis for how to increase promiscuous activity towards the production of peroxycarboxylic acids as mild bleaching agents. The three protease engineering campaigns presented provide in-depth analysis of protease properties and have identified principles that can be applied to improve or generate enzyme variants for industrial applications beyond laundry detergents.
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Affiliation(s)
- Ljubica Vojcic
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | | | | | - Felix Jakob
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Ronny Martinez
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany; EW-Nutrition GmbH, Enzyme Technology, Nattermannallee 1, D-50829 Köln, Germany
| | | | - Ulrich Schwaneberg
- RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany; DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, D-52074 Aachen, Germany.
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Cheng F, Zhu L, Schwaneberg U. Directed evolution 2.0: improving and deciphering enzyme properties. Chem Commun (Camb) 2015; 51:9760-72. [DOI: 10.1039/c5cc01594d] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A KnowVolution: knowledge gaining directed evolution including four phases is proposed in this feature article, which generates improved enzyme variants and molecular understanding.
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Affiliation(s)
- Feng Cheng
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Leilei Zhu
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie
- RWTH Aachen University
- 52074 Aachen
- Germany
- DWI-Leibniz Institute for Interactive Materials
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Sakaguchi M, Osaku K, Maejima S, Ohno N, Sugahara Y, Oyama F, Kawakita M. Highly conserved salt bridge stabilizes a proteinase K subfamily enzyme, Aqualysin I, from Thermus aquaticus YT-1. AMB Express 2014; 4:59. [PMID: 25136511 PMCID: PMC4131155 DOI: 10.1186/s13568-014-0059-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/02/2014] [Indexed: 11/10/2022] Open
Abstract
The proteinase K subfamily enzymes, thermophilic Aqualysin I (AQN) from Thermus aquaticus YT-1 and psychrophilic serine protease (VPR) from Vibrio sp. PA-44, have six and seven salt bridges, respectively. To understand the possible significance of salt bridges in the thermal stability of AQN, we prepared mutant proteins in which amino acid residues participating in salt bridges common to proteinase K subfamily members and intrinsic to AQN were replaced to disrupt the bridges one at a time. Disruption of a salt bridge common to proteinase K subfamily enzymes in the D183N mutant resulted in a significant reduction in thermal stability, and a massive change in the content of the secondary structure was observed, even at 70°C, in the circular dichroism (CD) analysis. These results indicate that the common salt bridge Asp183-Arg12 is important in maintaining the conformation of proteinase K subfamily enzymes and suggest the importance of proximity between the regions around Asp183 and the N-terminal region around Arg12. Of the three mutants that lack an AQN intrinsic salt bridge, D212N was more prone to unfolding at 80°C than the wild-type enzyme. Similarly, D17N and E237Q were less thermostable than the wild-type enzyme, although this may be partially due to increased autolysis. The AQN intrinsic salt bridges appear to confer additional thermal stability to this enzyme. These findings will further our understanding of the factors involved in stabilizing protein structure.
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