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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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Yan Q, Zhang X, Chen Y, Guo B, Zhou P, Chen B, Huang Q, Wang JB. From Semirational to Rational Design: Developing a Substrate-Coupled System of Glucose Dehydrogenase for Asymmetric Synthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Qipeng Yan
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Xinhua Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Yingzhuang Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Bin Guo
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Pei Zhou
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Bo Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Qun Huang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
| | - Jian-bo Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081 Changsha, P. R. China
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Shou C, Zheng YC, Zhan JR, Li CX, Xu JH. Removing the Obstacle to (-)-Menthol Biosynthesis by Building a Microbial Cell Factory of (+)-cis-Isopulegone from (-)-Limonene. CHEMSUSCHEM 2022; 15:e202101741. [PMID: 34519416 DOI: 10.1002/cssc.202101741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Microbial synthesis of plant-based (-)-menthol is of great interest because of its high demand (≈30 kiloton per year) as well as unique odor and cooling characteristics. However, this remains a great challenge due to the yet unfilled gap between (-)-limonene and (+)-cis-isopulegone. Herein, the first artificial and effective system was developed for (+)-cis-isopulegone biosynthesis from (-)-limonene by recruiting two bacterial enzymes to replace their inefficient counterparts from Mentha piperita, limonene-3-hydroxylase, and isopiperitenol dehydrogenase. A cofactor self-regenerative recombinant Escherichia coli strain was constructed by introducing a formate dehydrogenase for nicotinamide adenine dinucleotide phosphate (NADPH) regeneration and an engineered microbial isopiperitenol dehydrogenase. The production of (+)-cis-isopulegone (up to 281.2 mg L-1 ) was improved by 36 times compared with that of the initial strain. This work lays a reliable foundation for the microbial synthesis of (-)-menthol.
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Affiliation(s)
- Chao Shou
- 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
| | - Yu-Cong 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
| | - Jing-Ru Zhan
- 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
| | - 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
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Cai Y, Wang M, Xiao X, Liang B, Fan S, Zheng Z, Cosnier S, Liu A. A membraneless starch/O 2 biofuel cell based on bacterial surface regulable displayed sequential enzymes of glucoamylase and glucose dehydrogenase. Biosens Bioelectron 2022; 207:114197. [PMID: 35358946 DOI: 10.1016/j.bios.2022.114197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/02/2022]
Abstract
Enzymatic biofuel cells (EBFCs) provide a new strategy to enable direct biomass-to-electricity conversion, posing considerable demand on sequential enzymes. However, artificial blend of multi-enzyme systems often suffer biocatalytic inefficiency due to the rambling mixture of catalytic units. In an attempt to construct a high-performance starch/O2 EBFC, herein we prepared a starch-oxidizing bioanode based on displaying a sequential enzyme system of glucoamylase (GA) and glucose dehydrogenase (GDH) on E.coli cell surfaces in a precise way using cohesin-dockerin interactions. The enzyme stoichiometry was optimized, with GA&GDH (3:1)-E.coli exhibiting the highest catalytic reaction rate. The bioanode employed polymerized methylene blue (polyMB) to collect electrons from the oxidation of NADH into NAD+, which jointly oxidized starch together with co-displayed GA and GDH. The bioanode was oxygen-insensitive, which can be combined with a laccase based biocathode, resulting in a membranless starch/O2 EBFC in a non-compartmentalized configuration. The optimal EBFC exhibited an open-circuit voltage (OCV) of 0.74 V, a maximum power density of 30.1 ± 2.8 μW cm-2, and good operational stability.
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Affiliation(s)
- Yuanyuan Cai
- Institute for Biosensing, and College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Mingyang Wang
- Institute for Biosensing, and College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xinxin Xiao
- Institute for Biosensing, and College of Life Sciences, Qingdao University, Qingdao, 266071, China; Department of Chemistry, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Bo Liang
- Qingdao Institute of Bioenergy & Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, China
| | - Shuqin Fan
- Qingdao Institute of Bioenergy & Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, China
| | - Zongmei Zheng
- Institute for Biosensing, and College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Serge Cosnier
- University Grenoble Alpes DCM UMR 5250, F-38000, Grenoble, France; Département de Chimie Moléculaire, UMR CNRS, DCM UMR 5250, F-38000, Grenoble, France
| | - Aihua Liu
- Institute for Biosensing, and College of Life Sciences, Qingdao University, Qingdao, 266071, China.
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Co-evolution of activity and thermostability of an aldo-keto reductase KmAKR for asymmetric synthesis of statin precursor dichiral diols. Bioorg Chem 2020; 103:104228. [DOI: 10.1016/j.bioorg.2020.104228] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/28/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
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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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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: 22] [Impact Index Per Article: 5.5] [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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Jia Z, Ma H, Huang Y, Huang Y, Ren P, Song S, Hu M, Tao Y. Production of (R)-3-quinuclidinol by a whole-cell biocatalyst with high efficiency. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1400019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zhenhua Jia
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Hong Ma
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Yali Huang
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Yuanyuan Huang
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Pengju Ren
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Shuishan Song
- Biology Institute, Hebei Academy of sciences, Shijiazhuang, P. R. China
| | - Meirong Hu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China
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Ding H, Gao F, Yu Y, Chen B. Biochemical and Computational Insights on a Novel Acid-Resistant and Thermal-Stable Glucose 1-Dehydrogenase. Int J Mol Sci 2017; 18:ijms18061198. [PMID: 28587256 PMCID: PMC5486021 DOI: 10.3390/ijms18061198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 11/29/2022] Open
Abstract
Due to the dual cofactor specificity, glucose 1-dehydrogenase (GDH) has been considered as a promising alternative for coenzyme regeneration in biocatalysis. To mine for potential GDHs for practical applications, several genes encoding for GDH had been heterogeneously expressed in Escherichia coli BL21 (DE3) for primary screening. Of all the candidates, GDH from Bacillus sp. ZJ (BzGDH) was one of the most robust enzymes. BzGDH was then purified to homogeneity by immobilized metal affinity chromatography and characterized biochemically. It displayed maximum activity at 45 °C and pH 9.0, and was stable at temperatures below 50 °C. BzGDH also exhibited a broad pH stability, especially in the acidic region, which could maintain around 80% of its initial activity at the pH range of 4.0–8.5 after incubating for 1 hour. Molecular dynamics simulation was conducted for better understanding the stability feature of BzGDH against the structural context. The in-silico simulation shows that BzGDH is stable and can maintain its overall structure against heat during the simulation at 323 K, which is consistent with the biochemical studies. In brief, the robust stability of BzGDH made it an attractive participant for cofactor regeneration on practical applications, especially for the catalysis implemented in acidic pH and high temperature.
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Affiliation(s)
- Haitao Ding
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China.
| | - Fen Gao
- East China Sea Fisheries Research Institute, Shanghai 200090, China.
| | - Yong Yu
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China.
| | - Bo Chen
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, China.
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10
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Sensitive detection of maltose and glucose based on dual enzyme-displayed bacteria electrochemical biosensor. Biosens Bioelectron 2017; 87:25-30. [DOI: 10.1016/j.bios.2016.07.050] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 07/04/2016] [Accepted: 07/14/2016] [Indexed: 11/23/2022]
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11
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Rational design of xylose dehydrogenase for improved thermostability and its application in development of efficient enzymatic biofuel cell. Enzyme Microb Technol 2016; 84:78-85. [DOI: 10.1016/j.enzmictec.2015.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/25/2015] [Accepted: 12/01/2015] [Indexed: 11/22/2022]
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12
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Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. PLoS One 2016; 11:e0145848. [PMID: 26741367 PMCID: PMC4704809 DOI: 10.1371/journal.pone.0145848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.
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Affiliation(s)
- Deanne W Sammond
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
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Brissos V, Gonçalves N, Melo EP, Martins LO. Improving kinetic or thermodynamic stability of an azoreductase by directed evolution. PLoS One 2014; 9:e87209. [PMID: 24475252 PMCID: PMC3903626 DOI: 10.1371/journal.pone.0087209] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/20/2013] [Indexed: 12/28/2022] Open
Abstract
Protein stability arises from a combination of factors which are often difficult to rationalise. Therefore its improvement is better addressed through directed evolution than by rational design approaches. In this study, five rounds of mutagenesis/recombination followed by high-throughput screening (≈10,000 clones) yielded the hit 1B6 showing a 300-fold higher half life at 50°C than that exhibited by the homodimeric wild type PpAzoR azoreductase from Pseudomonas putida MET94. The characterization using fluorescence, calorimetry and light scattering shows that 1B6 has a folded state slightly less stable than the wild type (with lower melting and optimal temperatures) but in contrast is more resistant to irreversible denaturation. The superior kinetic stability of 1B6 variant was therefore related to an increased resistance of the unfolded monomers to aggregation through the introduction of mutations that disturbed hydrophobic patches and increased the surface net charge of the protein. Variants 2A1 and 2A1-Y179H with increased thermodynamic stability (10 to 20°C higher melting temperature than wild type) were also examined showing the distinctive nature of mutations that lead to improved structural robustness: these occur in residues that are mostly involved in strengthening the solvent-exposed loops or the inter-dimer interactions of the folded state.
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Affiliation(s)
- Vânia Brissos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Nádia Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Eduardo P. Melo
- Institute for Biotechnology and Bioengineering, Center for Molecular and Structural Biomedicine, Universidade do Algarve, Faro, Portugal
| | - Lígia O. Martins
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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14
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Liang B, Lang Q, Tang X, Liu A. Simultaneously improving stability and specificity of cell surface displayed glucose dehydrogenase mutants to construct whole-cell biocatalyst for glucose biosensor application. BIORESOURCE TECHNOLOGY 2013; 147:492-498. [PMID: 24012845 DOI: 10.1016/j.biortech.2013.08.088] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 06/02/2023]
Abstract
The improved stability and substrate specificity of cell surface displayed glucose dehydrogenase (GDH) mutants by replacing four amino acids from Bacillus subtilis by using site-directed mutagenesis was systematically investigated. A series of mutated GDHs including E170R/Q252L, V149K/E170R/Q252L, E170R/Q252L/G259A and V149K/E170R/Q252L/G259A, were fused to the ice nucleation protein for displaying on cell surface of Eschericia coli. Q252L/E170R/V149K, Q252L/E170R/G259A and Q252L/E170R/V149K/G259A variants were found stable at a wide pH range and shown excellent thermostability. Especially, the Q252L/E170R/V149K/G259A mutant showed half-life of ~3.8days at 70 °C. Q252L/E170R/V149K/G259A variant exhibited the narrowest substrate specificity for d-glucose. The whole cell displayed GDH mutant could be cultured in a large scale with excellent enzyme activity and productivity. In addition, a sensitive and stable electrochemical glucose biosensor can be prepared using the GDH-mutant bacteria modified electrode. Thus, the whole cell biocatalysts are promising candidates for exploitation in a wide range of industrial applications.
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Affiliation(s)
- Bo Liang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Qiaolin Lang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Xiangjiang Tang
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Aihua Liu
- Laboratory for Biosensing, Qingdao Institute of Bioenergy & Bioprocess Technology, and Key Laboratory of Bioenergy, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China.
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15
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Jakoblinnert A, van den Wittenboer A, Shivange AV, Bocola M, Heffele L, Ansorge-Schumacher M, Schwaneberg U. Design of an activity and stability improved carbonyl reductase from Candida parapsilosis. J Biotechnol 2013; 165:52-62. [DOI: 10.1016/j.jbiotec.2013.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
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16
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Schallmey M, Floor RJ, Hauer B, Breuer M, Jekel PA, Wijma HJ, Dijkstra BW, Janssen DB. Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase. Chembiochem 2013; 14:870-81. [PMID: 23585096 DOI: 10.1002/cbic.201300005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Indexed: 01/30/2023]
Abstract
Two highly engineered halohydrin dehalogenase variants were characterized in terms of their performance in dehalogenation and epoxide cyanolysis reactions. Both enzyme variants outperformed the wild-type enzyme in the cyanolysis of ethyl (S)-3,4-epoxybutyrate, a conversion yielding ethyl (R)-4-cyano-3-hydroxybutyrate, an important chiral building block for statin synthesis. One of the enzyme variants, HheC2360, displayed catalytic rates for this cyanolysis reaction enhanced up to tenfold. Furthermore, the enantioselectivity of this variant was the opposite of that of the wild-type enzyme, both for dehalogenation and for cyanolysis reactions. The 37-fold mutant HheC2360 showed an increase in thermal stability of 8 °C relative to the wild-type enzyme. Crystal structures of this enzyme were elucidated with chloride and ethyl (S)-3,4-epoxybutyrate or with ethyl (R)-4-cyano-3-hydroxybutyrate bound in the active site. The observed increase in temperature stability was explained in terms of a substantial increase in buried surface area relative to the wild-type HheC, together with enhanced interfacial interactions between the subunits that form the tetramer. The structures also revealed that the substrate binding pocket was modified both by substitutions and by backbone movements in loops surrounding the active site. The observed changes in the mutant structures are partly governed by coupled mutations, some of which are necessary to remove steric clashes or to allow backbone movements to occur. The importance of interactions between substitutions suggests that efficient directed evolution strategies should allow for compensating and synergistic mutations during library design.
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Affiliation(s)
- Marcus Schallmey
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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17
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Nishioka T, Yasutake Y, Nishiya Y, Tamura T. Structure-guided mutagenesis for the improvement of substrate specificity ofBacillus megateriumglucose 1-dehydrogenase IV. FEBS J 2012; 279:3264-75. [DOI: 10.1111/j.1742-4658.2012.08713.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Güven G, Prodanovic R, Schwaneberg U. Protein Engineering - An Option for Enzymatic Biofuel Cell Design. ELECTROANAL 2010. [DOI: 10.1002/elan.200980017] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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19
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Fernandez-Lafuente R. Stabilization of multimeric enzymes: Strategies to prevent subunit dissociation. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2009.08.009] [Citation(s) in RCA: 503] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Nishioka T, Yasutake Y, Nishiya Y, Tamura N, Tamura T. C-terminal tail derived from the neighboring subunit is critical for the activity ofThermoplasma acidophilumD-aldohexose dehydrogenase. Proteins 2009; 74:801-7. [DOI: 10.1002/prot.22300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Vazquez-Figueroa E, Yeh V, Broering JM, Chaparro-Riggers JF, Bommarius AS. Thermostable variants constructed via the structure-guided consensus method also show increased stability in salts solutions and homogeneous aqueous-organic media. Protein Eng Des Sel 2008; 21:673-80. [PMID: 18799474 DOI: 10.1093/protein/gzn048] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enzyme instability is a major factor preventing widespread adoption of enzymes for catalysis. Stability at high temperatures and in the presence of high salt concentrations and organic solvents would allow enzymes to be employed for transformations of compounds not readily soluble in low temperature or in purely aqueous systems. Furthermore, many redox enzymes require costly cofactors for function and consequently a robust cofactor regeneration system. In this work, we demonstrate how thermostable variants developed via an amino acid sequence-based consensus method also showed improved stability in solutions with high concentrations of kosmotropic and chaotropic salts and water-miscible organic solvents. This is invaluable to protein engineers since deactivation in salt solutions and organic solvents is not well understood, rendering a priori design of enzyme stability in these media difficult. Variants of glucose 1-dehydrogenase (GDH) were studied in solutions of different salts along the Hofmeister series and in the presence of varying amounts of miscible organic solvent. Only the most stable variants showed little deactivation dependence on salt-type and salt concentration. Kinetic stability, expressed by the deactivation rate constant k(d,obs), did not always correlate with thermodynamic stability of variants, as measured by melting temperature T(m). However, a strong correlation (R(2) > 0.95) between temperature stability and organic solvent stability was found when plotting T(50)(60) versus C(50)(60) values. All GDH variants retained stability in homogeneous aqueous-organic solvents with >80% v/v of organic solvent.
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Affiliation(s)
- E Vazquez-Figueroa
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, Atlanta, GA 30332-0363, USA
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22
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Zhang R, Zhu G, Zhang W, Cao S, Ou X, Li X, Bartlam M, Xu Y, Zhang XC, Rao Z. Crystal structure of a carbonyl reductase from Candida parapsilosis with anti-Prelog stereospecificity. Protein Sci 2008; 17:1412-23. [PMID: 18566346 PMCID: PMC2492817 DOI: 10.1110/ps.035089.108] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2008] [Revised: 04/15/2008] [Accepted: 04/21/2008] [Indexed: 10/21/2022]
Abstract
A novel short-chain (S)-1-phenyl-1,2-ethanediol dehydrogenase (SCR) from Candida parapsilosis exhibits coenzyme specificity for NADPH over NADH. It catalyzes an anti-Prelog type reaction to reduce 2-hydroxyacetophenone into (S)-1-phenyl-1,2-ethanediol. The coding gene was overexpressed in Escherichia coli and the purified protein was crystallized. The crystal structure of the apo-form was solved to 2.7 A resolution. This protein forms a homo-tetramer with a broken 2-2-2 symmetry. The overall fold of each SCR subunit is similar to that of the known structures of other homologous alcohol dehydrogenases, although the latter usually form tetramers with perfect 2-2-2 symmetries. Additionally, in the apo-SCR structure, the entrance of the NADPH pocket is blocked by a surface loop. In order to understand the structure-function relationship of SCR, we carried out a number of mutagenesis-enzymatic analyses based on the new structural information. First, mutations of the putative catalytic Ser-Tyr-Lys triad confirmed their functional role. Second, truncation of an N-terminal 31-residue peptide indicated its role in oligomerization, but not in catalytic activity. Similarly, a V270D point mutation rendered the SCR as a dimer, rather than a tetramer, without affecting the enzymatic activity. Moreover, the S67D/H68D double-point mutation inside the coenzyme-binding pocket resulted in a nearly 10-fold increase and a 20-fold decrease in the k(cat) /K(M) value when NADH and NADPH were used as cofactors, respectively, with k(cat) remaining essentially the same. This latter result provides a new example of a protein engineering approach to modify the coenzyme specificity in SCR and short-chain dehydrogenases/reductases in general.
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Affiliation(s)
- Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
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23
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HIRATSUKA A, FUJISAWA K, MUGURUMA H. Amperometric Biosensor Based on Glucose Dehydrogenase and Plasma-polymerized Thin Films. ANAL SCI 2008; 24:483-6. [DOI: 10.2116/analsci.24.483] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Atsunori HIRATSUKA
- Research Center of Advanced Bionics, National Institute of Advanced Industrial Science and Technology (AIST), c/o Katayanagi Advanced Research Laboratories, Tokyo University of Technology
| | - Kohta FUJISAWA
- Department of Electronic Engineering, Shibaura Institute of Technology
| | - Hitoshi MUGURUMA
- Department of Electronic Engineering, Shibaura Institute of Technology
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24
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Vázquez-Figueroa E, Chaparro-Riggers J, Bommarius AS. Development of a Thermostable Glucose Dehydrogenase by a Structure-Guided Consensus Concept. Chembiochem 2007; 8:2295-301. [DOI: 10.1002/cbic.200700500] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Cloning of D-glucose dehydrogenase with a narrow substrate specificity fromBacillus thuringiensis M15. ANN MICROBIOL 2006. [DOI: 10.1007/bf03175011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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