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Xue J, Dou Z, Sun Z, Luo T, Chen X, Ni Y, Xu G. Biocatalytic Stereoselective Synthesis of Chiral Precursors for Liposoluble β 1 Receptor Blocker Nebivolol. J Org Chem 2024; 89:11043-11047. [PMID: 39042018 DOI: 10.1021/acs.joc.4c01027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Asymmetric reduction of 2-chloro-1-(6-fluorochroman-2-yl)ethan-1-one (NEB-7) into 2-chloro-1-(6-fluorochroman-2-yl)ethan-1-ol (NEB-8) is the crucial step for synthesis of liposoluble β1 receptor blocker nebivolol. Four efficient and stereoselective alcohol dehydrogenases were identified, enabling the stereoselective synthesis of all enantiomers of NEB-8 at a substrate loading of 137 g·L-1 with ee values of >99% and high space-time yields. This study provides novel biocatalysts for the efficient synthesis of nebivolol precursors and uncovers the molecular basis for enantioselectivity manipulation by parametrization of Prelog's rule.
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Affiliation(s)
- Jiayu Xue
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Zhe Dou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmacy, Zhejiang University of Technology, Hangzhou 310014, Zhejiang P. R. China
| | - Zewen Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Tianwei Luo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Xiaoyu Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Ye Ni
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Guochao Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
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2
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Bork H, Naße KE, Vorholt AJ, Gröger H. Merging High-Pressure Syngas Metal Catalysis and Biocatalysis in Tandem One-Pot Processes for the Synthesis of Nonchiral and Chiral Alcohols from Alkenes in Water. Angew Chem Int Ed Engl 2024; 63:e202401989. [PMID: 38628134 DOI: 10.1002/anie.202401989] [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: 01/28/2024] [Indexed: 06/12/2024]
Abstract
While simultaneously proceeding reactions are among the most fascinating features of biosynthesis, this concept of tandem processes also offers high potential in the chemical industry in terms of less waste production and improved process efficiency and sustainability. Although examples of one-pot chemoenzymatic syntheses exist, the combination of completely different reaction types is rare. Herein, we demonstrate that extreme "antipodes" of the "worlds of catalysis", such as syngas-based high-pressure hydroformylation and biocatalyzed reduction, can be combined within a tandem-type one-pot process in water. No significant deactivation was found for either the biocatalyst or the chemocatalyst. A proof-of-concept for the one-pot process starting from 1-octene was established with >99 % conversion and 80 % isolated yield of the desired alcohol isomers. All necessary components for hydroformylation and biocatalysis were added to the reactor from the beginning. This concept has been extended to the enantioselective synthesis of chiral products by conducting the hydroformylation of styrene and an enzymatic dynamic kinetic resolution in a tandem mode, leading to an excellent conversion of >99 % and an enantiomeric ratio of 91 : 9 for (S)-2-phenylpropanol. The overall process runs in water under mild and energy-saving conditions, without any need for intermediate isolation.
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Affiliation(s)
- Hannah Bork
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kim E Naße
- Department of Molecular Catalysis, Group Multiphase Catalysis, MPI for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Andreas J Vorholt
- Department of Molecular Catalysis, Group Multiphase Catalysis, MPI for Chemical Energy Conversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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3
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Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [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: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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4
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Teshima M, Sutiono S, Döring M, Beer B, Boden M, Schenk G, Sieber V. Development of a Highly Selective NAD + -Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell-Free Enzyme Cascades. CHEMSUSCHEM 2024; 17:e202301132. [PMID: 37872118 DOI: 10.1002/cssc.202301132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Anthropogenic climate change has been caused by over-exploitation of fossil fuels and CO2 emissions. To counteract this, the chemical industry has shifted its focus to sustainable chemical production and the valorization of renewable resources. However, the biggest challenges in biomanufacturing are technical efficiency and profitability. In our minimal cell-free enzyme cascade generating pyruvate as the central intermediate, the NAD+ -dependent, selective oxidation of D-glyceraldehyde was identified as a key reaction step to improve the overall cascade flux. Successive genome mining identified one candidate enzyme with 24-fold enhanced activity and another whose stability is unaffected in 10 % (v/v) ethanol, the final product of our model cascade. Semi-rational engineering improved the substrate selectivity of the enzyme up to 21-fold, thus minimizing side reactions in the one-pot enzyme cascade. The final biotransformation of D-glucose showed a continuous linear production of ethanol (via pyruvate) to a final titer of 4.9 % (v/v) with a molar product yield of 98.7 %. Due to the central role of pyruvate in diverse biotransformations, the optimized production module has great potential for broad biomanufacturing applications.
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Affiliation(s)
- Mariko Teshima
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
- Current address: CarboCode Germany GmbH, Byk-Gulden-Straße 2, 78467, Constance, Germany
| | - Manuel Döring
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
- Current address: CASCAT GmbH, Europaring 4, 94315, Straubing, Germany
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St. Lucia, 4072, Brisbane, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St. Lucia, 4072, Brisbane, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Corner of College and Cooper Rds, St. Lucia, 4072, Brisbane, Australia
- Sustainable Minerals Institute, The University of Queensland, Corner of College and Staff House Rds, St. Lucia, 4072, Brisbane, Australia
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Cooper Rd, St. Lucia, 4072, Brisbane, Australia
- SynBioFoundry@TUM, Technical University of Munich, Schulgasse 22, 94315, Straubing, Germany
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer Straße 1, 85748, Garching, Germany
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5
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Lagerman CE, Joe EA, Grover MA, Rousseau RW, Bommarius AS. Improvement of α-amino Ester Hydrolase Stability via Computational Protein Design. Protein J 2023; 42:675-684. [PMID: 37819423 DOI: 10.1007/s10930-023-10155-z] [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] [Accepted: 09/03/2023] [Indexed: 10/13/2023]
Abstract
Amino ester hydrolases (AEHs) are capable of rapid synthesis of cephalexin but suffer from rapid deactivation even at low temperatures. Previous efforts to engineer AEH have generated several improved variants but have been limited in scope in part due to limitations in activity assay throughput for β-lactam synthesis reactions. Rational design of 'whole variants' was explored to rapidly improve AEH thermostability by mutating between 3-15% of residues. Most variants were found to be inactive due to a mutated calcium binding site, the function of which has not previously been described. Four active variants, all with improved melting temperatures, were characterized in terms of synthesis and hydrolysis activity, melting temperature, and deactivation at 25°C. Two variants were found to have improved total turnover numbers relative to the initial AEH variant; however, a clear tradeoff exists between improved stability and overall activity of each variant.
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Affiliation(s)
- Colton E Lagerman
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - Emily A Joe
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - Martha A Grover
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - Ronald W Rousseau
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia
| | - Andreas S Bommarius
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, 30332, Georgia.
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6
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Li X, Chen B, Chen W, Pu Z, Qi X, Yang L, Wu J, Yu H. Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase. Appl Microbiol Biotechnol 2023; 107:6507-6525. [PMID: 37658164 DOI: 10.1007/s00253-023-12744-5] [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: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity was critical for its wide applications. Multiple sequence alignment (MSA) has been widely used in engineering enzymes for improved properties. Here, we first designed TaqPol mutations based on MSA of 2756 sequences from both thermophilic and non-thermophilic organisms. Two double mutations were generated including a variant H676F/R677G showing a decrease in both activity and stability, and a variant Y686R/E687K showing an improved activity, but a decreased stability. Mutations targeted on coevolutionary residues of Arg677 and Tyr686 were then applied to rescue stability or activity loss of the double mutants, which achieved a partial success. Sequence analysis revealed that the two mutations are abundant in non-thermophilic sequences but not in thermophilic homologues. Then, a small-scale MSA containing sequences from only thermophilic organisms was applied to predict 13 single variants and two of them, E507Q and E734N showed a simultaneous increase in both stability and activity, even in sensitivity. A customized MSA was hence more effective in engineering a thermophilic enzyme and could be used in engineering other enzymes. Molecular dynamics simulations revealed the impact of mutations on the protein dynamics and interactions between TaqPol and substrates. KEY POINTS: • The pool of sequence for alignment is critical to engineering Taq DNA polymerase. • The variants with low properties can be rescued by mutations in coevolving network. • Improving binding with DNA can improve DNA polymerase stability and activity.
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Affiliation(s)
- Xinjia Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Wanyi Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Xin Qi
- Building No.4, Zhongguancun Dongsheng International Science Park, No. 1 North Yongtaizhuang Road, Haidian District, Beijing, 100192, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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7
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Villa R, Ferrer-Carbonell C, Paul CE. Biocatalytic reduction of alkenes in micro-aqueous organic solvent catalysed by an immobilised ene reductase. Catal Sci Technol 2023; 13:5530-5535. [PMID: 38013840 PMCID: PMC10544049 DOI: 10.1039/d3cy00541k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/22/2023] [Indexed: 11/29/2023]
Abstract
Biocatalytic asymmetric reduction of alkenes in organic solvent is attractive for enantiopurity and product isolation, yet remains under developed. Herein we demonstrate the robustness of an ene reductase immobilised on Celite for the reduction of activated alkenes in micro-aqueous organic solvent. Full conversion was obtained in methyl t-butyl ether, avoiding hydrolysis and racemisation of products. The immobilised ene reductase showed reusability and a scale-up demonstrated its applicability.
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Affiliation(s)
- Rocio Villa
- Biocatalysis section, Department of Biotechnology, Delft University of Biotechnology van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Claudia Ferrer-Carbonell
- Biocatalysis section, Department of Biotechnology, Delft University of Biotechnology van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Caroline E Paul
- Biocatalysis section, Department of Biotechnology, Delft University of Biotechnology van der Maasweg 9 2629 HZ Delft The Netherlands
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8
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Basri RS, Rahman RNZRA, Kamarudin NHA, Ali MSM. Carboxylic acid reductases: Structure, catalytic requirements, and applications in biotechnology. Int J Biol Macromol 2023; 240:124526. [PMID: 37080403 DOI: 10.1016/j.ijbiomac.2023.124526] [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: 02/03/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/22/2023]
Abstract
Biocatalysts have been gaining extra attention in recent decades due to their industrial-relevance properties, which may hasten the transition to a cleaner environment. Carboxylic acid reductases (CARs) are large, multi-domain proteins that can catalyze the reduction of carboxylic acids to corresponding aldehydes, with the presence of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). This biocatalytic reaction is of great interest due to the abundance of carboxylic acids in nature and the ability of CAR to convert carboxylic acids to a wide range of aldehydes essentially needed as end products such as vanillin or reaction intermediates for several compounds production such as alcohols, alkanes, and amines. This modular enzyme, found in bacteria and fungi, demands an activation via post-translational modification by the phosphopantetheinyl transferase (PPTase). Recent advances in the characterization and structural studies of CARs revealed valuable information about the enzymes' dynamics, mechanisms, and unique features. In this comprehensive review, we summarize the previous findings on the phylogeny, structural and mechanistic insight of the domains, post-translational modification requirement, strategies for the cofactors regeneration, the extensively broad aldehyde-related industrial application properties of CARs, as well as their recent immobilization approaches.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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9
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Okuda-Shimazaki J, Yoshida H, Lee I, Kojima K, Suzuki N, Tsugawa W, Yamada M, Inaka K, Tanaka H, Sode K. Microgravity environment grown crystal structure information based engineering of direct electron transfer type glucose dehydrogenase. Commun Biol 2022; 5:1334. [PMID: 36473944 PMCID: PMC9727119 DOI: 10.1038/s42003-022-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The heterotrimeric flavin adenine dinucleotide dependent glucose dehydrogenase is a promising enzyme for direct electron transfer (DET) principle-based glucose sensors within continuous glucose monitoring systems. We elucidate the structure of the subunit interface of this enzyme by preparing heterotrimer complex protein crystals grown under a space microgravity environment. Based on the proposed structure, we introduce inter-subunit disulfide bonds between the small and electron transfer subunits (5 pairs), as well as the catalytic and the electron transfer subunits (9 pairs). Without compromising the enzyme's catalytic efficiency, a mutant enzyme harboring Pro205Cys in the catalytic subunit, Asp383Cys and Tyr349Cys in the electron transfer subunit, and Lys155Cys in the small subunit, is determined to be the most stable of the variants. The developed engineered enzyme demonstrate a higher catalytic activity and DET ability than the wild type. This mutant retains its full activity below 70 °C as well as after incubation at 75 °C for 15 min - much higher temperatures than the current gold standard enzyme, glucose oxidase, is capable of withstanding.
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Affiliation(s)
- Junko Okuda-Shimazaki
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
| | - Hiromi Yoshida
- grid.258331.e0000 0000 8662 309XDepartment of Basic Life Science, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793 Japan
| | - Inyoung Lee
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
| | - Katsuhiro Kojima
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Nanoha Suzuki
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Wakako Tsugawa
- grid.136594.c0000 0001 0689 5974Graduate School of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
| | - Mitsugu Yamada
- grid.62167.340000 0001 2220 7916JEM Utilization Center Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba-shi, Ibaraki 305-8505 Japan
| | - Koji Inaka
- grid.459744.fMaruwa Foods and Biosciences, 170-1 Tsutsui-cho, Yamato Koriyama-shi, Nara 639-1123 Japan
| | - Hiroaki Tanaka
- grid.459486.2Confocal Science Inc., Musashino Bldg, 5-14-15 Fukasawa, Setagaya-ku, Tokyo 158-0081 Japan
| | - Koji Sode
- grid.10698.360000000122483208Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC27599 USA
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10
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Hua L, Qianqian B, Jianfeng Z, Yinbiao X, Shengyu Y, Weishi X, Yang S, Yupeng L. Directed evolution engineering to improve activity of glucose dehydrogenase by increasing pocket hydrophobicity. Front Microbiol 2022; 13:1044226. [DOI: 10.3389/fmicb.2022.1044226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Glucose dehydrogenase (GDH) is a NAD(P)+ dependent oxidoreductase, which is useful in glucose determination kits, glucose biosensors, cofactor regeneration, and biofuel cells. However, the low efficiency of the catalysis hinders the use of GDH in industrial applications. In this study, an analysis of interactions between eight GDH mutants and NADP+ is powered by AlphaFold2 and Discovery Studio 3.0. The docking results showed that more hydrogen bonds formed between mutants, such as P45A and NADP+, which indicated that these mutants had the potential for high catalytic efficiency. Subsequently, we verified all the mutants by site-directed mutagenesis. It was notable that the enzyme activity of mutant P45A was 1829 U/mg, an improvement of 28-fold compared to wild-type GDH. We predicted the hydrophobicity of the protein-ligand complexes, which was confirmed by an 8-anilino-1-naphthalenesulphonic acid fluorescent probe. The following order of increasing hydrophobicity index was deduced: GDH < N46E < F155Y < P45A, which suggested that the enzyme activity of GDH is positively related to its pocket hydrophobicity. Furthermore, P45A still showed better catalytic ability in organic solvents, reaching 692 U/mg in 10% isopropanol, which was 19-fold that of the wild-type GDH. However, its substrate affinity was affected by organic solvents. This study provides a good theoretical foundation for further improving the catalytic efficiency of GDH.
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11
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Mansouri HR, Gracia Carmona O, Jodlbauer J, Schweiger L, Fink MJ, Breslmayr E, Laurent C, Feroz S, P. Goncalves LC, Rial DV, Mihovilovic MD, Bommarius AS, Ludwig R, Oostenbrink C, Rudroff F. Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase. ACS Catal 2022; 12:11761-11766. [PMID: 36249873 PMCID: PMC9552169 DOI: 10.1021/acscatal.2c03225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/31/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Hamid R. Mansouri
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Oriol Gracia Carmona
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Julia Jodlbauer
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Lorenz Schweiger
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Michael J. Fink
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Erik Breslmayr
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Christophe Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Saima Feroz
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
- Department of Biosciences, College of Science, University of Hafr Al Batin, PO Box 1803, Hafr Al Batin, 39524, Saudi Arabia
| | - Leticia C. P. Goncalves
- Institut de Chimie de Nice CRNS UMR7272, Université Côte d’Azur, 28 Avenue Valrose, 06108 Nice, France
| | - Daniela V. Rial
- Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Suipacha 531, S2002LRK Rosario, Argentina
| | - Marko D. Mihovilovic
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Engineered Biosystems Building (EBB), Georgia Institute of Technology, 950 Atlantic Drive, N.W., Atlanta, Georgia 30332, United States
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, BOKU−University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
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12
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Qiu S, Xu SY, Wang YJ, Zheng YG. Chemoenzymatic Catalysis of tert-Butyl 6-Cyano-(3R,5R)-dihydroxyhexanoate by Aldo-keto Reductase Coupled with Composite Fe3O4 Nanozyme Scaffold. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Zhang J, Liao D, Chen R, Zhu F, Ma Y, Gao L, Qu G, Cui C, Sun Z, Lei X, Gao SS. Tuning an Imine Reductase for the Asymmetric Synthesis of Azacycloalkylamines by Concise Structure-Guided Engineering. Angew Chem Int Ed Engl 2022; 61:e202201908. [PMID: 35322515 DOI: 10.1002/anie.202201908] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 12/27/2022]
Abstract
Although imine reductases (IREDs) are emerging as attractive reductive aminases (RedAms), their substrate scope is still narrow, and rational engineering is rare. Focusing on hydrogen bond reorganization and cavity expansion, a concise strategy combining rational cavity design, combinatorial active-site saturation test (CAST), and thermostability engineering was designed, that transformed the weakly active IR-G36 into a variant M5 with superior performance for the synthesis of (R)-3-benzylamino-1-Boc-piperidine, with a 4193-fold improvement in catalytic efficiency, a 16.2 °C improvement in Tm , and a significant increase in the e.e. value from 78 % (R) to >99 % (R). M5 exhibits broad substrate scope for the synthesis of diverse azacycloalkylamines, and the reaction was demonstrated on a hectogram-scale under industrially relevant conditions. Our study provides a compelling example of the preparation of versatile and efficient IREDs, with exciting opportunities in medicinal and process chemistry as well as synthetic biology.
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Daohong Liao
- Jiangsu JITRI Molecular Engineering Inst. Co., Ltd., Jiangsu, 215500, China
| | | | - Fangfang Zhu
- College of Biotechnology, Tianjin University of Science & Techno, Tianjin, 300457, China
| | - Yaqing Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Gao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100091, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chengsen Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100091, China
| | - Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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14
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Jia Q, Zheng YC, Li HP, Qian XL, Zhang ZJ, Xu JH. Engineering Isopropanol Dehydrogenase for Efficient Regeneration of Nicotinamide Cofactors. Appl Environ Microbiol 2022; 88:e0034122. [PMID: 35442081 PMCID: PMC9088361 DOI: 10.1128/aem.00341-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/03/2022] [Indexed: 12/18/2022] Open
Abstract
Isopropanol dehydrogenase (IPADH) is one of the most attractive options for nicotinamide cofactor regeneration due to its low cost and simple downstream processing. However, poor thermostability and strict cofactor dependency hinder its practical application for bioconversions. In this study, we simultaneously improved the thermostability (433-fold) and catalytic activity (3.3-fold) of IPADH from Brucella suis via a flexible segment engineering strategy. Meanwhile, the cofactor preference of IPADH was successfully switched from NAD(H) to NADP(H) by 1.23 × 106-fold. When these variants were employed in three typical bioredox reactions to drive the synthesis of important chiral pharmaceutical building blocks, they outperformed the commonly used cofactor regeneration systems (glucose dehydrogenase [GDH], formate dehydrogenase [FDH], and lactate dehydrogenase [LDH]) with respect to efficiency of cofactor regeneration. Overall, our study provides two promising IPADH variants with complementary cofactor specificities that have great potential for wide applications. IMPORTANCE Oxidoreductases represent one group of the most important biocatalysts for synthesis of various chiral synthons. However, their practical application was hindered by the expensive nicotinamide cofactors used. Isopropanol dehydrogenase (IPADH) is one of the most attractive biocatalysts for nicotinamide cofactor regeneration. However, poor thermostability and strict cofactor dependency hinder its practical application. In this work, the thermostability and catalytic activity of an IPADH were simultaneously improved via a flexible segment engineering strategy. Meanwhile, the cofactor preference of IPADH was successfully switched from NAD(H) to NADP(H). The resultant variants show great potential for regeneration of nicotinamide cofactors, and the engineering strategy might serve as a useful approach for future engineering of other oxidoreductases.
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Affiliation(s)
- Qiao Jia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yu-Cong Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hai-Peng Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiao-Long Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Suzhou Bioforany EnzyTech Co., Ltd., Changshu, Jiangsu, China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, School of Biotechnology, East China University of Science and Technology, Shanghai, China
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15
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Zhang J, Liao D, Chen R, Zhu F, Ma Y, Gao L, Qu G, Cui C, Sun Z, Lei X, Gao S. Tuning an Imine Reductase for the Asymmetric Synthesis of Azacycloalkylamines by Concise Structure‐Guided Engineering. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
| | - Daohong Liao
- Jiangsu JITRI Molecular Engineering Inst. Co., Ltd. Jiangsu 215500 China
| | | | - Fangfang Zhu
- College of Biotechnology Tianjin University of Science & Techno Tianjin 300457 China
| | - Yaqing Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Lei Gao
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Peking-Tsinghua Center for Life Sciences Peking University Beijing 100091 China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
| | - Chengsen Cui
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Peking-Tsinghua Center for Life Sciences Peking University Beijing 100091 China
| | - Shu‐Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin 300308 China
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16
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Thermostabilizing ketoreductase ChKRED20 by consensus mutagenesis at dimeric interfaces. Enzyme Microb Technol 2022; 158:110052. [DOI: 10.1016/j.enzmictec.2022.110052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/15/2022] [Accepted: 04/17/2022] [Indexed: 11/19/2022]
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17
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Zhang D, Zhang T, Lei Y, Lin W, Chen X, Wu M. Enantioselective Biosynthesis of L-Phenyllactic Acid From Phenylpyruvic Acid In Vitro by L-Lactate Dehydrogenase Coupling With Glucose Dehydrogenase. Front Bioeng Biotechnol 2022; 10:846489. [PMID: 35252153 PMCID: PMC8894805 DOI: 10.3389/fbioe.2022.846489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
As a valuable versatile building block, L-phenyllactic acid (L-PLA) has numerous applications in the fields of agriculture, pharmaceuticals, and biodegradable plastics. However, both normally chemically synthesized and naturally occurring PLA are racemic, and the production titer of L-PLA is not satisfactory. To improve L-PLA production and reduce the high cost of NADH, an in vitro coenzyme regeneration system of NADH was achieved using the glucose dehydrogenase variant LsGDHD255C and introduced into the L-PLA production process. Here an NADH-dependent L-lactate dehydrogenase-encoding variant gene (L-Lcldh1Q88A/I229A) was expressed in Pichia pastoris GS115. The specific activity of L-LcLDH1Q88A/I229A (Pp) was as high as 447.6 U/mg at the optimum temperature and pH of 40°C and 5.0, which was 38.26-fold higher than that of wild-type L-LcLDH1 (Pp). The catalytic efficiency (kcat/Km) of L-LcLDH1Q88A/I229A (Pp) was 94.3 mM−1 s−1, which was 67.4- and 25.5-fold higher than that of L-LcLDH1(Pp) and L-LcLDH1Q88A/I229A (Ec) expressed in Escherichia coli, respectively. Optimum reactions of L-PLA production by dual-enzyme catalysis were at 40°C and pH 5.0 with 10.0 U/ml L-LcLDH1Q88A/I229A (Pp) and 4.0 U/ml LsGDHD255C. Using 0.1 mM NAD+, 400 mM (65.66 g/L) phenylpyruvic acid was completely hydrolyzed by fed-batch process within 6 h, affording L-PLA with 90.0% yield and over 99.9% eep. This work would be a promising technical strategy for the preparation of L-PLA at an industrial scale.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Ting Zhang
- Haiyan Food and Drug Inspection and Testing Center, Haiyan, China
| | - Yuqing Lei
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wenqian Lin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xingyi Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Minchen Wu
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- *Correspondence: Minchen Wu,
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18
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Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
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19
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Zeng Y, Liu H, Zhu T, Han S, Li S. Preparation of Nanomaterial Wettable Powder Formulations of Antagonistic Bacteria from Phellodendron chinense and the Biological Control of Brown Leaf Spot Disease. THE PLANT PATHOLOGY JOURNAL 2021; 37:215-231. [PMID: 34111912 PMCID: PMC8200580 DOI: 10.5423/ppj.oa.02.2021.0020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 06/02/2023]
Abstract
Brown leaf spot disease caused by Nigrospora guilinensis on Phellodendron chinense occurs in a large area in Dayi County, Chengdu City, Sichuan Province, China each year. This outbreak has severely reduced the production of Chinese medicinal plants P. chinense and caused substantial economic losses. The bacterial isolate JKB05 was isolated from the healthy leaves of P. chinense, exhibited antagonistic effects against N. guilinensis and was identified as Bacillus megaterium. The following fermentation medium and conditions improved the inhibitory effect of B. megaterium JKB05 on N. guilinensis: 2% glucose, 0.1% soybean powder, 0.1% KCl, and 0.05% MgSO4; initial concentration 6 × 106 cfu/ml, and a 42-h optimal fermentation time. A composite of 0.1% nano-SiO2 JKB05 improved the thermal stability, acid-base stability and ultraviolet resistance by 16%, 12%, and 38.9%, respectively, and nano-SiO2 was added to the fermentation process. The best formula for the wettable powder was 35% kaolin, 4% polyethylene glycol, 8% Tween, and 2% humic acid. The following quality test results for the wettable powder were obtained: wetting time 87.0 s, suspension rate 80.33%, frequency of microbial contamination 0.08%, pH 7.2, fineness 95.8%, drying loss 1.47%, and storage stability ≥83.5%. A pot experiment revealed that the ability of JKB05 to prevent fungal infections on P. chinense increased considerably and achieved levels of control as high as 94%. The use of nanomaterials significantly improved the ability of biocontrol bacteria to control this disease.
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Affiliation(s)
- Yanling Zeng
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Han Liu
- Ganzi Institute of Forestry Research, Kangding 626001, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
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20
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Xu J, Zhou H, Yu H, Deng T, Wang Z, Zhang H, Wu J, Yang L. Computational design of highly stable and soluble alcohol dehydrogenase for NADPH regeneration. BIORESOUR BIOPROCESS 2021; 8:12. [PMID: 38650213 PMCID: PMC10992930 DOI: 10.1186/s40643-021-00362-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/19/2021] [Indexed: 11/10/2022] Open
Abstract
Nicotinamide adenine dinucleotide phosphate (NADPH), as a well-known cofactor, is widely used in the most of enzymatic redox reactions, playing an important role in industrial catalysis. However, the absence of a comparable method for efficient NADP+ to NADPH cofactor regeneration radically impairs efficient green chemical synthesis. Alcohol dehydrogenase (ADH) enzymes, allowing the in situ regeneration of the redox cofactor NADPH with high specific activity and easy by-product separation process, are provided with great industrial application potential and research attention. Accordingly, herein a NADP+-specific ADH from Clostridium beijerinckii was selected to be engineered for cofactor recycle, using an automated algorithm named Protein Repair One-stop Shop (PROSS). The mutant CbADH-6M (S24P/G182A/G196A/H222D/S250E/S254R) exhibited a favorable soluble and highly active expression with an activity of 46.3 U/mL, which was 16 times higher than the wild type (2.9 U/mL), and a more stable protein conformation with an enhanced thermal stability: Δ T 1 / 2 60 min = + 3.6 °C (temperature of 50% inactivation after incubation for 60 min). Furthermore, the activity of CbADH-6M was up-graded to 2401.8 U/mL by high cell density fermentation strategy using recombinant Escherichia coli, demonstrating its industrial potential. Finally, the superb efficiency for NADPH regeneration of the mutant enzyme was testified in the synthesis of some fine chiral aromatic alcohols coupling with another ADH from Lactobacillus kefir (LkADH).
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Affiliation(s)
- Jinling Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haisheng Zhou
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Tong Deng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ziyuan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Hongyu Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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21
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Qiu J, Yang H, Shao Y, Li L, Sun S, Wang L, Tan Y, Xin Z. Enhancing the activity and thermal stability of a phthalate-degrading hydrolase by random mutagenesis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111795. [PMID: 33341696 DOI: 10.1016/j.ecoenv.2020.111795] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Our previous work has reported that EstJ6 was a phthalate-degrading hydrolase. In the study, a random mutant library was constructed by two rounds of error-prone PCR, three mutants (ET1.1, ET2.1, and ET2.2) with enhanced hydrolytic activity against dibutyl phthalate (DBP) were obtained. The best mutant ET2.2, accumulated three amino acid substitutions (Thr91Met, Ala67Val, and Val249Ile) and exhibited 2.8-fold increase enzyme activity and 2.3-fold higher expression level. Meanwhile, compared with EstJ6, ET2.2 showed over 50% improvement in thermostability (at 50 °C for 1 h) and 1.2-fold increase in 50% methanol tolerance. Kinetic parameters analysis revealed that the Km value for ET2.2 decreased by 60% and the kcat/Km value increased by 166%. The molecular docking indicated that the shortening of hydrogen bond between Ser146-OH and DBP-CO, which may led to an increase in enzyme activity and catalytic efficiency, the enhancement of hydrophobicity of hydrophobic pocket was related to the improvement of organic solvents tolerance, and three hydrophobic amino acid substitutions Thr91Met, Ala67Val, and Val249Ile facilitated to improve the thermal stability and organic solvents tolerance. These results confirmed that random mutagenesis was an effective tool for improving enzyme properties and lay a foundation for practical applications of phthalate-degrading hydrolase in biotechnology and industrial fields.
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Affiliation(s)
- Jiarong Qiu
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Haiyan Yang
- College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, PR China
| | - Yuting Shao
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Longxiang Li
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Luyao Wang
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuzhi Tan
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Zhihong Xin
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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22
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Amalfitano E, Karlikow M, Norouzi M, Jaenes K, Cicek S, Masum F, Sadat Mousavi P, Guo Y, Tang L, Sydor A, Ma D, Pearson JD, Trcka D, Pinette M, Ambagala A, Babiuk S, Pickering B, Wrana J, Bremner R, Mazzulli T, Sinton D, Brumell JH, Green AA, Pardee K. A glucose meter interface for point-of-care gene circuit-based diagnostics. Nat Commun 2021; 12:724. [PMID: 33526784 PMCID: PMC7851131 DOI: 10.1038/s41467-020-20639-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/01/2020] [Indexed: 01/24/2023] Open
Abstract
Recent advances in cell-free synthetic biology have given rise to gene circuit-based sensors with the potential to provide decentralized and low-cost molecular diagnostics. However, it remains a challenge to deliver this sensing capacity into the hands of users in a practical manner. Here, we leverage the glucose meter, one of the most widely available point-of-care sensing devices, to serve as a universal reader for these decentralized diagnostics. We describe a molecular translator that can convert the activation of conventional gene circuit-based sensors into a glucose output that can be read by off-the-shelf glucose meters. We show the development of new glucogenic reporter systems, multiplexed reporter outputs and detection of nucleic acid targets down to the low attomolar range. Using this glucose-meter interface, we demonstrate the detection of a small-molecule analyte; sample-to-result diagnostics for typhoid, paratyphoid A/B; and show the potential for pandemic response with nucleic acid sensors for SARS-CoV-2. Getting synthetic biology circuit-based sensors into field applications is still a challenge. Here the authors combine a circuit sensor with a glucose meter for small analyte and nucleic acid detection.
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Affiliation(s)
- Evan Amalfitano
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Margot Karlikow
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Masoud Norouzi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Seray Cicek
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Fahim Masum
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | | | - Yuxiu Guo
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Laura Tang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Andrew Sydor
- Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, ON, M5G 0A4, Canada
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ, 85287, USA
| | - Joel D Pearson
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, M5T 3A9, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Daniel Trcka
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada
| | - Mathieu Pinette
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Aruna Ambagala
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Shawn Babiuk
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada
| | - Bradley Pickering
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, R3E 3M4, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, R3E 0J9, MB, Canada.,Iowa State University, College of Veterinary Medicine, Department of Veterinary Microbiology and Preventive Medicine, Ames, IA, 50011, USA
| | - Jeff Wrana
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, M5G 1X5, ON, Canada.,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, M5T 3A9, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Department of Microbiology, Sinai Health System/University Health Network, Toronto, M5G 1X5, ON, Canada
| | - David Sinton
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, ON, Canada
| | - John H Brumell
- Program in Cell Biology, Hospital for Sick Children, Peter Gilgan Center for Research and Learning, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.,Institute of Medical Science, University of Toronto, Toronto, M5S 1A8, ON, Canada.,SickKids IBD Centre, Hospital for Sick Children, Toronto, M5G 1X8, ON, Canada
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and the School of Molecular Sciences, Arizona State University, AZ, 85287, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada. .,Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, M5S 3G8, ON, Canada.
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23
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A robust and stereocomplementary panel of ene-reductase variants for gram-scale asymmetric hydrogenation. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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24
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Chen L, Yi Z, Fang Y, Jin Y, Xiao Y, Zhao D, Luo H, He H, Sun Q, Zhao H. Uncovering key residues responsible for the thermostability of a thermophilic 1,3(4)-β-d-glucanase from Nong flavor Daqu by rational design. Enzyme Microb Technol 2020; 142:109672. [PMID: 33220875 DOI: 10.1016/j.enzmictec.2020.109672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/20/2020] [Accepted: 09/16/2020] [Indexed: 11/17/2022]
Abstract
Fungal 1,3(4)-β-D-glucanases were usually applied in brewing and feedstuff industries, however, the thermostability limits the most their application. The characterized 1,3(4)-β-D-glucanase (NFEg16A) from Chinese Nong-flavor (NF) Daqu showed the highest thermostability among GH16 fungal 1,3(4)-β-D-glucanases, with half-lives of thermal inactivation (t1/2) of 44.9 min at 90 °C, so multiple rational designs were used to identify the key residues for its thermostability. Based on protein sequence and 3D structure analyses around the catalytic regions. Nine site-mutants were constructed, among which N173Y and S187A were identified as the most thermotolerant and thermolabile ones, with t1/2 values of 61 min and 14.0 min at 90 °C, respectively. Therefore, N173 and S187 were then selected as "hotspots" for site-saturation mutagenesis. Interestingly, most of the N173 and S187 variants exhibited a similar thermostability to that of N173Y and S187A, respectively, confirming their different roles in the thermostability of NFEg16A. In addition, each S187A and its surrounding substitutions (D144 N and T164 N) was independently detrimental to the thermostability of NFEg16A, since the t1/2 (90 °C) of S187A, D144 N and T164 N were 14.0 min, 20.6 min and 27.2 min, respectively. Surprisingly, combinatorial substitution of S187A with D144 N or T164 N showed positive effects on the thermostability, with the increase of t1/2 (90 °C) to 30.9 min and 63.5 min for S187A-D144 N and S187A-T164 N, respectively. More importantly, S187A-T164 N showed higher thermostability than that of wild type. In short, we successfully identified two key sites and their surrounding residues in response to the thermostability of NFEg16A and further improved its thermostability by several rational designs. These findings could be used for the protein engineering of homologous 1,3(4)-β-D-glucanases, as well as other enzyme family members with high similarities.
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Affiliation(s)
- Lanchai Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhuolin Yi
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yao Xiao
- Analytical and Testing Center, Sichuan University of Science and Engineering, Zigong 643000, PR China
| | - Dong Zhao
- Wuliangye Group, Yibin 644007, PR China
| | - Huibo Luo
- Liquor Making Bio-Technology & Application of Key Laboratory of Sichuan Province, Bioengineering College, Sichuan University of Science & Engineering, Zigong 64300, PR China
| | - Hui He
- Department of Liquor Making Engineering, Moutai College, Renhuai 564501, PR China
| | - Qun Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
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25
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Expanding the Application Range of Microbial Oxidoreductases by an Alcohol Dehydrogenase from Comamonas testosteroni with a Broad Substrate Spectrum and pH Profile. Catalysts 2020. [DOI: 10.3390/catal10111281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Alcohol dehydrogenases catalyse the conversion of a large variety of ketone substrates to the corresponding chiral products. Due to their high regio- and stereospecificity, they are key components in a wide range of industrial applications. A novel alcohol dehydrogenase from Comamonas testosteroni (CtADH) was identified in silico, recombinantly expressed and purified, enzymatically and biochemically investigated as well as structurally characterized. These studies revealed a broad pH profile and an extended substrate spectrum with the highest activity for compounds containing halogens as substituents and a moderate activity for bulky–bulky ketones. Biotransformations with selected ketones—performed with a coupled regeneration system for the co-substrate NADPH—resulted in conversions of more than 99% with all tested substrates and with excellent enantioselectivity for the corresponding S-alcohol products. CtADH/NADPH/substrate complexes modelled on the basis of crystal structures of CtADH and its closest homologue suggested preliminary hints to rationalize the enzyme’s substrate preferences
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26
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Qian WZ, Ou L, Li CX, Pan J, Xu JH, Chen Q, Zheng GW. Evolution of Glucose Dehydrogenase for Cofactor Regeneration in Bioredox Processes with Denaturing Agents. Chembiochem 2020; 21:2680-2688. [PMID: 32324965 DOI: 10.1002/cbic.202000196] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/20/2020] [Indexed: 02/04/2023]
Abstract
Glucose dehydrogenase (GDH) is a general tool for driving nicotinamide (NAD(P)H) regeneration in synthetic biochemistry. An increasing number of synthetic bioreactions are carried out in media containing high amounts of organic cosolvents or hydrophobic substrates/products, which often denature native enzymes, including those for cofactor regeneration. In this work, we attempted to improve the chemical stability of Bacillus megaterium GDH (BmGDHM0 ) in the presence of large amounts of 1-phenylethanol by directed evolution. Among the resulting mutants, BmGDHM6 (Q252L/E170K/S100P/K166R/V72I/K137R) exhibited a 9.2-fold increase in tolerance against 10 % (v/v) 1-phenylethanol. Moreover, BmGDHM6 was also more stable than BmGDHM0 when exposed to hydrophobic and enzyme-inactivating compounds such as acetophenone, ethyl 2-oxo-4-phenylbutyrate, and ethyl (R)-2-hydroxy-4-phenylbutyrate. Coupled with a Candida glabrata carbonyl reductase, BmGDHM6 was successfully used for the asymmetric reduction of deactivating ethyl 2-oxo-4-phenylbutyrate with total turnover number of 1800 for the nicotinamide cofactor, thus making it attractive for commercial application. Overall, the evolution of chemically robust GDH facilitates its wider use as a general tool for NAD(P)H regeneration in biocatalysis.
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Affiliation(s)
- Wen-Zhuo Qian
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Ling Ou
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China
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27
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Roth S, Stockinger P, Steff J, Steimle S, Sautner V, Tittmann K, Pleiss J, Müller M. Crossing the Border: From Keto- to Imine Reduction in Short-Chain Dehydrogenases/Reductases. Chembiochem 2020; 21:2615-2619. [PMID: 32315494 PMCID: PMC7540013 DOI: 10.1002/cbic.202000233] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 11/10/2022]
Abstract
The family of NAD(P)H-dependent short-chain dehydrogenases/reductases (SDRs) comprises numerous biocatalysts capable of C=O or C=C reduction. The highly homologous noroxomaritidine reductase (NR) from Narcissus sp. aff. pseudonarcissus and Zt_SDR from Zephyranthes treatiae, however, are SDRs with an extended imine substrate scope. Comparison with a similar SDR from Asparagus officinalis (Ao_SDR) exhibiting keto-reducing activity, yet negligible imine-reducing capability, and mining the Short-Chain Dehydrogenase/Reductase Engineering Database indicated that NR and Zt_SDR possess a unique active-site composition among SDRs. Adapting the active site of Ao_SDR accordingly improved its imine-reducing capability. By applying the same strategy, an unrelated SDR from Methylobacterium sp. 77 (M77_SDR) with distinct keto-reducing activity was engineered into a promiscuous enzyme with imine-reducing activity, thereby confirming that the ability to reduce imines can be rationally introduced into members of the "classical" SDR enzyme family. Thus, members of the SDR family could be a promising starting point for protein approaches to generate new imine-reducing enzymes.
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Affiliation(s)
- Sebastian Roth
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Peter Stockinger
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Jakob Steff
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Simon Steimle
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Viktor Sautner
- Department of Molecular EnzymologyUniversity of GöttingenJulia-Lermontowa-Weg 337077GöttingenGermany
| | - Kai Tittmann
- Department of Molecular EnzymologyUniversity of GöttingenJulia-Lermontowa-Weg 337077GöttingenGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstrasse 2579104FreiburgGermany
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28
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Roth S, Stockinger P, Steff J, Steimle S, Sautner V, Tittmann K, Pleiss J, Müller M. Crossing the Border: From Keto- to Imine Reduction in Short-Chain Dehydrogenases/Reductases. CHEMBIOCHEM : A EUROPEAN JOURNAL OF CHEMICAL BIOLOGY 2020. [PMID: 32315494 DOI: 10.1002/cbic.202000233.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The family of NAD(P)H-dependent short-chain dehydrogenases/reductases (SDRs) comprises numerous biocatalysts capable of C=O or C=C reduction. The highly homologous noroxomaritidine reductase (NR) from Narcissus sp. aff. pseudonarcissus and Zt_SDR from Zephyranthes treatiae, however, are SDRs with an extended imine substrate scope. Comparison with a similar SDR from Asparagus officinalis (Ao_SDR) exhibiting keto-reducing activity, yet negligible imine-reducing capability, and mining the Short-Chain Dehydrogenase/Reductase Engineering Database indicated that NR and Zt_SDR possess a unique active-site composition among SDRs. Adapting the active site of Ao_SDR accordingly improved its imine-reducing capability. By applying the same strategy, an unrelated SDR from Methylobacterium sp. 77 (M77_SDR) with distinct keto-reducing activity was engineered into a promiscuous enzyme with imine-reducing activity, thereby confirming that the ability to reduce imines can be rationally introduced into members of the "classical" SDR enzyme family. Thus, members of the SDR family could be a promising starting point for protein approaches to generate new imine-reducing enzymes.
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Affiliation(s)
- Sebastian Roth
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Peter Stockinger
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jakob Steff
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Simon Steimle
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Viktor Sautner
- Department of Molecular Enzymology, University of Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, University of Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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29
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Li C, Zhang R, Wang J, Wilson LM, Yan Y. Protein Engineering for Improving and Diversifying Natural Product Biosynthesis. Trends Biotechnol 2020; 38:729-744. [PMID: 31954530 PMCID: PMC7274900 DOI: 10.1016/j.tibtech.2019.12.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 01/26/2023]
Abstract
Proteins found in nature have traditionally been the most frequently used biocatalysts to produce numerous natural products ranging from commodity chemicals to pharmaceuticals. Protein engineering has emerged as a powerful biotechnological toolbox in the development of metabolic engineering, particularly for the biosynthesis of natural products. Recently, protein engineering has become a favored method to improve enzymatic activity, increase enzyme stability, and expand product spectra in natural product biosynthesis. This review summarizes recent advances and typical strategies in protein engineering, highlighting the paramount role of protein engineering in improving and diversifying the biosynthesis of natural products. Future prospects and research directions are also discussed.
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Affiliation(s)
- Chenyi Li
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Ruihua Zhang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jian Wang
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Lauren Marie Wilson
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials, and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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30
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Stolarczyk K, Rogalski J, Bilewicz R. NAD(P)-dependent glucose dehydrogenase: Applications for biosensors, bioelectrodes, and biofuel cells. Bioelectrochemistry 2020; 135:107574. [PMID: 32498025 DOI: 10.1016/j.bioelechem.2020.107574] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
This review discusses the physical and chemical properties of nicotinamide redox cofactor dependent glucose dehydrogenase (NAD(P) dependent GDH) and its extensive application in biosensors and bio-fuel cells. GDHs from different organisms show diverse biochemical properties (e.g., activity and stability) and preferences towards cofactors, such as nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+). The (NAD(P)+) play important roles in biological electron transfer, however, there are some difficulties related to their application in devices that originate from their chemical properties and labile binding to the GDH enzyme. This review discusses the electrode modifications aimed at immobilising NAD+ or NADP+ cofactors and GDH at electrodes. Binding of the enzyme was achieved by appropriate protein engineering techniques, including polymerisation, hydrophobisation or hydrophilisation processes. Various enzyme-modified electrodes applied in biosensors, enzymatic fuel cells, and biobatteries are compared. Importantly, GDH can operate alone or as part of an enzymatic cascade, which often improves the functional parameters of the biofuel cell or simply allows use of cheaper fuels. Overall, this review explores how NAD(P)-dependent GDH has recently demonstrated high potential for use in various systems to generate electricity from biological sources for applications in implantable biomedical devices, wireless sensors, and portable electronic devices.
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Affiliation(s)
- Krzysztof Stolarczyk
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland
| | - Jerzy Rogalski
- Department of Biochemistry and Biotechnology, Maria Curie-Sklodowska University, Akademicka Str. 19, 20-031 Lublin, Poland
| | - Renata Bilewicz
- Faculty of Chemistry, University of Warsaw, Pasteura St. 1, 02-093 Warsaw, Poland.
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31
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Meng Q, Capra N, Palacio CM, Lanfranchi E, Otzen M, van Schie LZ, Rozeboom HJ, Thunnissen AMWH, Wijma HJ, Janssen DB. Robust ω-Transaminases by Computational Stabilization of the Subunit Interface. ACS Catal 2020; 10:2915-2928. [PMID: 32953233 PMCID: PMC7493286 DOI: 10.1021/acscatal.9b05223] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/31/2020] [Indexed: 12/25/2022]
Abstract
Transaminases are attractive catalysts for the production of enantiopure amines. However, the poor stability of these enzymes often limits their application in biocatalysis. Here, we used a framework for enzyme stability engineering by computational library design (FRESCO) to stabilize the homodimeric PLP fold type I ω-transaminase from Pseudomonas jessenii. A large number of surface-located point mutations and mutations predicted to stabilize the subunit interface were examined. Experimental screening revealed that 10 surface mutations out of 172 tested were indeed stabilizing (6% success), whereas testing 34 interface mutations gave 19 hits (56% success). Both the extent of stabilization and the spatial distribution of stabilizing mutations showed that the subunit interface was critical for stability. After mutations were combined, 2 very stable variants with 4 and 6 mutations were obtained, which in comparison to wild type (T m app = 62 °C) displayed T m app values of 80 and 85 °C, respectively. These two variants were also 5-fold more active at their optimum temperatures and tolerated high concentrations of isopropylamine and cosolvents. This allowed conversion of 100 mM acetophenone to (S)-1-phenylethylamine (>99% enantiomeric excess) with high yield (92%, in comparison to 24% with the wild-type transaminase). Crystal structures mostly confirmed the expected structural changes and revealed that the most stabilizing mutation, I154V, featured a rarely described stabilization mechanism: namely, removal of steric strain. The results show that computational interface redesign can be a rapid and powerful strategy for transaminase stabilization.
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Affiliation(s)
- Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nikolas Capra
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Cyntia M. Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luc Z. van Schie
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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32
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Yao H, Cai H, Li D. Thermostabilization of Membrane Proteins by Consensus Mutation: A Case Study for a Fungal Δ8-7 Sterol Isomerase. J Mol Biol 2020; 432:5162-5183. [PMID: 32105736 DOI: 10.1016/j.jmb.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 11/15/2022]
Abstract
Membrane proteins are generally challenging to work with because of their notorious instability. Protein engineering has been used increasingly to thermostabilize labile membrane proteins such as G-protein-coupled receptors for structural and functional studies in recent years. Two major strategies exist. Scanning mutagenesis systematically eliminates destabilizing residues, whereas the consensus approach assembles mutants with the most frequent residues among selected homologs, bridging sequence conservation with stability. Here, we applied the consensus concept to stabilize a fungal homolog of the human sterol Δ8-7 isomerase, a 26.4 kDa protein with five transmembrane helices. The isomerase is also called emopamil-binding protein (EBP), as it binds this anti-ischemic drug with high affinity. The wild-type had an apparent melting temperature (Tm) of 35.9 °C as measured by the fluorescence-detection size-exclusion chromatography-based thermostability assay. A total of 87 consensus mutations sourced from 22 homologs gained expression level and thermostability, increasing the apparent Tm to 69.9 °C at the cost of partial function loss. Assessing the stability and activity of several systematic chimeric constructs identified a construct with an apparent Tm of 79.8 °C and two regions for function rescue. Further back-mutations of the chimeric construct in the two target regions yielded the final construct with similar apparent activity to the wild-type and an elevated Tm of 88.8 °C, totaling an increase of 52.9 °C. The consensus approach is effective and efficient because it involves fewer constructs compared with scanning mutagenesis. Our results should encourage more use of the consensus strategy for membrane protein thermostabilization.
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Affiliation(s)
- Hebang Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Hongmin Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.
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33
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Hu D, Wen Z, Li C, Hu B, Zhang T, Li J, Wu M. Characterization of a robust glucose 1-dehydrogenase, SyGDH, and its application in NADPH regeneration for the asymmetric reduction of haloketone by a carbonyl reductase in organic solvent/buffer system. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.09.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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34
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Chandler PG, Broendum SS, Riley BT, Spence MA, Jackson CJ, McGowan S, Buckle AM. Strategies for Increasing Protein Stability. Methods Mol Biol 2020; 2073:163-181. [PMID: 31612442 DOI: 10.1007/978-1-4939-9869-2_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The stability of wild-type proteins is often a hurdle to their practical use in research, industry, and medicine. The route to engineering stability of a protein of interest lies largely with the available data. Where high-resolution structural data is available, rational design, based on fundamental principles of protein chemistry, can improve protein stability. Recent advances in computational biology and the use of nonnatural amino acids have also provided novel rational methods for improving protein stability. Likewise, the explosion of sequence and structural data available in public databases, in combination with improvements in freely available computational tools, has produced accessible phylogenetic approaches. Trawling modern sequence databases can identify the thermostable homologs of a target protein, and evolutionary data can be quickly generated using available phylogenetic tools. Grafting features from those thermostable homologs or ancestors provides stability improvement through a semi-rational approach. Further, molecular techniques such as directed evolution have shown great promise in delivering designer proteins. These strategies are well documented and newly accessible to the molecular biologist, allowing for rapid enhancements of protein stability.
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Affiliation(s)
- Peter G Chandler
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sebastian S Broendum
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Matthew A Spence
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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35
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Tang W, Chen L, Deng J, Kuang Y, Chen C, Yin B, Wang H, Lin J, Wei D. Structure-guided evolution of carbonyl reductase for efficient biosynthesis of ethyl (R)-2-hydroxy-4-phenylbutyrate. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01411g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This study reported an attractive engineered carbonyl reductase from Gluconobacter oxydans through a structure-guided rational design to catalyze the synthesis of high concentration (R)-HPBE.
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Affiliation(s)
- Wen Tang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Lulu Chen
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Jian Deng
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Yuyao Kuang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Chao Chen
- State Key Laboratory of Bioreactor Engineering
- Biomedical Nanotechnology Center
- School of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
| | - Bo Yin
- National University of Singapore (Suzhou) Research Institute
- Suzhou 215123
- People's Republic of China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Jinping Lin
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai 200237
- People's Republic of China
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36
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Jones BJ, Kan CNE, Luo C, Kazlauskas RJ. Consensus Finder web tool to predict stabilizing substitutions in proteins. Methods Enzymol 2020; 643:129-148. [DOI: 10.1016/bs.mie.2020.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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37
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Expanding the Scope of Asinger Chemistry towards Enantiomerically Pure Secondary Amines and β-Aminothiols through Chemoenzymatic Derivatization of 3-Thiazolines. CHEMISTRY 2019. [DOI: 10.3390/chemistry1010012] [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
A proof of concept for a novel approach towards enantiomerically highly enriched acyclic secondary amines and β-aminothiols as non-cyclic target molecules when starting from 3-thiazolines as heterocycles is presented. Starting from 2,2,4,5,5-pentamethyl-3-thiazoline, we demonstrated this chemoenzymatic pathway to both of these types of amine molecules, which were isolated as urea derivatives with a non-optimized yield of up to 20%. As a substrate, 2,2,4,5,5-pentamethyl-3-thiazolidine, which was obtained with an enantiomeric excess (ee) of 99% in a biotransformation from the corresponding 3-thiazoline according to a recently developed protocol, was used. For the reductive desulfurization of this substrate leading to a sulfur-free secondary amine, in situ formed Ni2B turned out to be a suitable reducing reagent. However, when using lithium aluminum hydride as a reducing agent, β-aminothiol was obtained.
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38
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Adebar N, Gröger H. Flow Process for Ketone Reduction Using a Superabsorber-Immobilized Alcohol Dehydrogenase from Lactobacillus brevis in a Packed-Bed Reactor. Bioengineering (Basel) 2019; 6:bioengineering6040099. [PMID: 31653007 PMCID: PMC6956264 DOI: 10.3390/bioengineering6040099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 02/05/2023] Open
Abstract
Flow processes and enzyme immobilization have gained much attention over the past few years in the field of biocatalytic process design. Downstream processes and enzyme stability can be immensely simplified and improved. In this work, we report the utilization of polymer network-entrapped enzymes and their applicability in flow processes. We focused on the superabsorber-based immobilization of an alcohol dehydrogenase (ADH) from Lactobacillus brevis and its application for a reduction of acetophenone. The applicability of this immobilization technique for a biotransformation running in a packed bed reactor was then demonstrated. Towards this end, the immobilized system was intensively studied, first in a batch mode, leading to >90% conversion within 24 h under optimized conditions. A subsequent transfer of this method into a flow process was conducted, resulting in very high initial conversions of up to 67% in such a continuously running process.
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Affiliation(s)
- Niklas Adebar
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology, Faculty of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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Adebar N, Choi JE, Schober L, Miyake R, Iura T, Kawabata H, Gröger H. Overcoming Work‐Up Limitations of Biphasic Biocatalytic Reaction Mixtures Through Liquid‐Liquid Segmented Flow Processes. ChemCatChem 2019. [DOI: 10.1002/cctc.201901107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Niklas Adebar
- Chair of Industrial Organic Chemistry and Biotechnology Faculty of ChemistryBielefeld University Universitätsstr. 25 33615 Bielefeld Germany
| | - Ji Eun Choi
- Chair of Industrial Organic Chemistry and Biotechnology Faculty of ChemistryBielefeld University Universitätsstr. 25 33615 Bielefeld Germany
| | - Lukas Schober
- Chair of Industrial Organic Chemistry and Biotechnology Faculty of ChemistryBielefeld University Universitätsstr. 25 33615 Bielefeld Germany
| | - Ryoma Miyake
- Science & Innovation CenterMitsubishi Chemical Corporation 1000 Kamoshida-cho, Aoba-ku Yokohama 227-8502 Japan
| | - Takanobu Iura
- Science & Innovation CenterMitsubishi Chemical Corporation 1000 Kamoshida-cho, Aoba-ku Yokohama 227-8502 Japan
- API Corporation 13-4 Uchikanda 1-chome Chiyoda-ku Tokyo 101-0047 Japan
| | - Hiroshi Kawabata
- Science & Innovation CenterMitsubishi Chemical Corporation 1000 Kamoshida-cho, Aoba-ku Yokohama 227-8502 Japan
- API Corporation 13-4 Uchikanda 1-chome Chiyoda-ku Tokyo 101-0047 Japan
| | - Harald Gröger
- Chair of Industrial Organic Chemistry and Biotechnology Faculty of ChemistryBielefeld University Universitätsstr. 25 33615 Bielefeld Germany
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40
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Gmelch TJ, Sperl JM, Sieber V. Optimization of a reduced enzymatic reaction cascade for the production of L-alanine. Sci Rep 2019; 9:11754. [PMID: 31409820 PMCID: PMC6692406 DOI: 10.1038/s41598-019-48151-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Cell-free enzymatic reaction cascades combine the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. The absence of a regulatory cell environment enables direct process control including methods for facile bottleneck identification and process optimization. Within this work, we developed a reduced, enzymatic reaction cascade for the direct production of L-alanine from D-glucose and ammonium sulfate. An efficient, activity based enzyme selection is demonstrated for the two branches of the cascade. The resulting redox neutral cascade is composed of a glucose dehydrogenase, two dihydroxyacid dehydratases, a keto-deoxy-aldolase, an aldehyde dehydrogenase and an L-alanine dehydrogenase. This artificial combination of purified biocatalysts eliminates the need for phosphorylation and only requires NAD as cofactor. We provide insight into in detail optimization of the process parameters applying a fluorescamine based L-alanine quantification assay. An optimized enzyme ratio and the necessary enzyme load were identified and together with the optimal concentrations of cofactor (NAD), ammonium and buffer yields of >95% for the main branch and of 8% for the side branch were achieved.
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Affiliation(s)
- Tobias J Gmelch
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Josef M Sperl
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315, Straubing, Germany. .,Catalysis Research Center, Technical University of Munich, Garching, Germany. .,Fraunhofer Institute of Interfacial Biotechnology (IGB), Bio-, Electro- and Chemo Catalysis (BioCat) Branch, Straubing, Germany. .,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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41
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Zumbrägel N, Machui P, Nonnhoff J, Gröger H. Enantioselective Biocatalytic Reduction of 2 H-1,4-Benzoxazines Using Imine Reductases. J Org Chem 2019; 84:1440-1447. [PMID: 30562025 DOI: 10.1021/acs.joc.8b02867] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A biocatalytic reduction of 2 H-1,4-benzoxazines using imine reductases is reported. This process enables a smooth and enantioselective synthesis of the resulting cyclic amines under mild conditions in aqueous media by means of a catalytic amount of the cofactor NADPH as hydride source as well as glucose as the reducing agent used in stoichiometric amounts for in situ cofactor recycling. Several substrates were studied, and the 3,4-dihydro-2 H-1,4-benzoxazines were obtained with up to 99% ee. In addition, the efficiency of this reduction process based on imine reductases as catalysts has been demonstrated for one 2 H-1,4-benzoxazine on an elevated laboratory scale running at a substrate loading of 10 g L-1 in the presence of a tailor-made whole-cell catalyst.
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Affiliation(s)
- Nadine Zumbrägel
- Chair of Organic Chemistry I, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Paul Machui
- Chair of Organic Chemistry I, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Jannis Nonnhoff
- Chair of Organic Chemistry I, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , 33615 Bielefeld , Germany
| | - Harald Gröger
- Chair of Organic Chemistry I, Faculty of Chemistry , Bielefeld University , Universitätsstraße 25 , 33615 Bielefeld , Germany
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4-Hydroxyphenylpyruvate Dioxygenase Thermolability Is Responsible for Temperature-Dependent Melanogenesis in Aeromonas salmonicida subsp. salmonicida. Appl Environ Microbiol 2019; 85:AEM.01926-18. [PMID: 30341077 DOI: 10.1128/aem.01926-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022] Open
Abstract
Aeromonas salmonicida subsp. salmonicida is a major pathogen affecting fisheries worldwide and is a well-known pigmented member of the Aeromonas genus. This subspecies produces melanin at ≤22°C. However, melanogenesis decreases as the culture temperature increases and is completely suppressed at 30°C to 35°C, while bacterial growth is unaffected. The mechanism and biological significance of this temperature-dependent melanogenesis remain unclear. Heterologous expression of an A. salmonicida subsp. salmonicida 4-hydroxyphenylpyruvate dioxygenase (HppD), the most critical enzyme in the homogentisic acid (HGA)-melanin synthesis pathway, results in thermosensitive pigmentation in Escherichia coli, suggesting that HppD plays a key role in this process. In this study, we demonstrated that the thermolability of HppD is responsible for the temperature-dependent melanization of A. salmonicida subsp. salmonicida Substitutions of three residues, S18T, P103Q, and L119P, in A. salmonicida subsp. salmonicida HppD increased the thermostability of this enzyme and resulted in temperature-independent melanogenesis. Moreover, the replacement of the corresponding residues in HppD from Aeromonas media strain WS, which forms pigment independent of temperature, with those of A. salmonicida subsp. salmonicida HppD resulted in thermosensitive melanogenesis. A structural analysis suggested that mutations at these sites, especially at position P103, strengthen the secondary structure of HppD and greatly improve its thermal stability. Additionally, we found that the HppD sequences of all A. salmonicida subsp. salmonicida isolates were identical and that two of the three residues were clearly distinct from those of other Aeromonas strains.IMPORTANCE Aeromonas salmonicida subsp. salmonicida is the causative agent of furunculosis, a bacterial septicemia of cold-water fish of the Salmonidae family. Although other Aeromonas species can produce melanin, A. salmonicida subsp. salmonicida is the only member of this genus that has been reported to exhibit temperature-dependent melanization. Here, we demonstrated that thermosensitive melanogenesis in A. salmonicida subsp. salmonicida strains is due to the thermolability of 4-hydroxyphenylpyruvate dioxygenase (HppD). Additionally, we confirmed that this thermolabile HppD exhibited higher activity at low temperatures than its mesophilic homologues, suggesting this as an adaptive strategy of this enzyme to the psychrophilic lifestyle of A. salmonicida subsp. salmonicida The strictly conserved hppD sequences among A. salmonicida subsp. salmonicida isolates and the specific possession of P103 and L119 residues could be used as a reference for the identification of A. salmonicida subsp. salmonicida isolates.
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43
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Yin X, Liu Y, Meng L, Zhou H, Wu J, Yang L. Rational Molecular Engineering of Glutamate Dehydrogenases for Enhancing Asymmetric Reductive Amination of Bulky α-Keto Acids. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801251] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xinjian Yin
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Yayun Liu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Lijun Meng
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Haisheng Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
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44
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Musil M, Konegger H, Hon J, Bednar D, Damborsky J. Computational Design of Stable and Soluble Biocatalysts. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03613] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Milos Musil
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Hannes Konegger
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Hon
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment (RECETOX), and Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
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45
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Liu C, Zhao J, Liu J, Guo X, Rao D, Liu H, Zheng P, Sun J, Ma Y. Simultaneously improving the activity and thermostability of a new proline 4-hydroxylase by loop grafting and site-directed mutagenesis. Appl Microbiol Biotechnol 2018; 103:265-277. [DOI: 10.1007/s00253-018-9410-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023]
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46
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Qian H, Zhang C, Lu Z, Xia B, Bie X, Zhao H, Lu F, Yang GY. Consensus design for improved thermostability of lipoxygenase from Anabaena sp. PCC 7120. BMC Biotechnol 2018; 18:57. [PMID: 30236091 PMCID: PMC6148764 DOI: 10.1186/s12896-018-0468-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/06/2018] [Indexed: 01/21/2023] Open
Abstract
Background Lipoxygenase (LOX) from Anabaena sp. PCC 7120 (Ana-rLOX) offers important applications in the food industry, especially for improving aroma and dough rheological properties. However, industrial applications of LOXs have been limited by their poor thermostability. Herein, we report a bioinformatics-based consensus concept approach for the engineering of thermostable Ana-rLOX. Results A series of mutations (N130D, G260A, S437T, N130D/G260Q, N130D/S437Y) showed higher thermostability and activity than the wild-type enzyme. Thus, N130D/G260Q exhibited a 6.6-fold increase in half-life and 2.45 °C increase in unfolding temperature; N130D/S437Y showed a 10 °C increase in optimal temperature. The secondary structure did not change much that contributed to improved thermostability were investigated in detail using circular dichroism. Homology modeling suggested that enhanced thermostability and specific activity may result from favorable hydrophobic interactions. Conclusions A series of mutations were achieved, showing higher thermostability and activity than the wild-type enzyme by semi-rational mutagenesis with limited structure information. Our findings provide important new insights into molecular modifications aimed at improving Ana-rLOX thermostability and activity. Electronic supplementary material The online version of this article (10.1186/s12896-018-0468-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Qian
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China
| | - Bingjie Xia
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, 1st Weigang, Nanjing, 210095, People's Republic of China.
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, College of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, People's Republic of China.
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Beerens K, Mazurenko S, Kunka A, Marques SM, Hansen N, Musil M, Chaloupkova R, Waterman J, Brezovsky J, Bednar D, Prokop Z, Damborsky J. Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01677] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Koen Beerens
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Sergio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Milos Musil
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- Department of Information Systems, Faculty of Information Technology, Brno University of Technology, 612 66 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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Yin X, Wu J, Yang L. Efficient reductive amination process for enantioselective synthesis of L-phosphinothricin applying engineered glutamate dehydrogenase. Appl Microbiol Biotechnol 2018; 102:4425-4433. [DOI: 10.1007/s00253-018-8910-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 11/24/2022]
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49
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Rigoldi F, Donini S, Redaelli A, Parisini E, Gautieri A. Review: Engineering of thermostable enzymes for industrial applications. APL Bioeng 2018; 2:011501. [PMID: 31069285 PMCID: PMC6481699 DOI: 10.1063/1.4997367] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/14/2017] [Indexed: 01/19/2023] Open
Abstract
The catalytic properties of some selected enzymes have long been exploited to carry out efficient and cost-effective bioconversions in a multitude of research and industrial sectors, such as food, health, cosmetics, agriculture, chemistry, energy, and others. Nonetheless, for several applications, naturally occurring enzymes are not considered to be viable options owing to their limited stability in the required working conditions. Over the years, the quest for novel enzymes with actual potential for biotechnological applications has involved various complementary approaches such as mining enzyme variants from organisms living in extreme conditions (extremophiles), mimicking evolution in the laboratory to develop more stable enzyme variants, and more recently, using rational, computer-assisted enzyme engineering strategies. In this review, we provide an overview of the most relevant enzymes that are used for industrial applications and we discuss the strategies that are adopted to enhance enzyme stability and/or activity, along with some of the most relevant achievements. In all living species, many different enzymes catalyze fundamental chemical reactions with high substrate specificity and rate enhancements. Besides specificity, enzymes also possess many other favorable properties, such as, for instance, cost-effectiveness, good stability under mild pH and temperature conditions, generally low toxicity levels, and ease of termination of activity. As efficient natural biocatalysts, enzymes provide great opportunities to carry out important chemical reactions in several research and industrial settings, ranging from food to pharmaceutical, cosmetic, agricultural, and other crucial economic sectors.
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Affiliation(s)
- Federica Rigoldi
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Stefano Donini
- Center for Nano Science and Technology at Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133 Milano, Italy
| | - Alberto Redaelli
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology at Polimi, Istituto Italiano di Tecnologia, Via G. Pascoli 70/3, 20133 Milano, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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Pezeshgi Modarres H, Mofrad MR, Sanati-Nezhad A. ProtDataTherm: A database for thermostability analysis and engineering of proteins. PLoS One 2018; 13:e0191222. [PMID: 29377907 PMCID: PMC5788348 DOI: 10.1371/journal.pone.0191222] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 12/29/2017] [Indexed: 11/18/2022] Open
Abstract
Protein thermostability engineering is a powerful tool to improve resistance of proteins against high temperatures and thereafter broaden their applications. For efficient protein thermostability engineering, different thermostability-classified data sources including sequences and 3D structures are needed for different protein families. However, no data source is available providing such data easily. It is the first release of ProtDataTherm database for analysis and engineering of protein thermostability which contains more than 14 million protein sequences categorized based on their thermal stability and protein family. This database contains data needed for better understanding protein thermostability and stability engineering. Providing categorized protein sequences and structures as psychrophilic, mesophilic and thermophilic makes this database useful for the development of new tools in protein stability prediction. This database is available at http://profiles.bs.ipm.ir/softwares/protdatatherm. As a proof of concept, the thermostability that improves mutations were suggested for one sample protein belonging to one of protein families with more than 20 mesophilic and thermophilic sequences and with known experimentally measured ΔT of mutations available within ProTherm database.
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Affiliation(s)
- Hassan Pezeshgi Modarres
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Alberta, Canada
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, 208A Stanley Hall, Berkeley, CA, United States of America
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Mohammad R. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, 208A Stanley Hall, Berkeley, CA, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA, United States of America
| | - Amir Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, Calgary, Alberta, Canada
- Center for BioEngineering Research and Education, University of Calgary, Alberta, Canada
- * E-mail:
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