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Dong X, Zhang T, Gui C, Fei S, Xu H, Chang J, Lian C, Tang W. The critical role of residues Phe120 and Val161 of (2 R,3 R)‑2,3‑butanediol dehydrogenase from Neisseria gonorrhoeae as probed by molecular docking and site-directed mutagenesis. J Basic Microbiol 2024; 64:e2300751. [PMID: 38644586 DOI: 10.1002/jobm.202300751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
NAD+-dependent (2 R,3 R)‑2,3‑butanediol dehydrogenase (BDH) from Neisseria gonorrhoeae (NgBDH) is a representative member of the medium-chain dehydrogenase/reductase (MDR) superfamily. To date, little information is available on the substrate binding sites and catalytic residues of BDHs from this superfamily. In this work, according to molecular docking studies, we found that conserved residues Phe120 and Val161 form strong hydrophobic interactions with both (2 R,3 R)‑2,3‑butanediol (RR-BD) and meso-2,3‑butanediol (meso-BD) and that mutations of these residues to alanine or threonine impair substrate binding. To further evaluate the roles of these two residues, Phe120 and Val161 were mutated to alanine or threonine. Kinetic analysis revealed that, relative to those of wild type, the apparent KM values of the Phe120Ala mutant for RR-BD and meso-BD increased 36- and 369-fold, respectively; the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 586- and 3528-fold, respectively; and the apparent KM values of the Val161Ala mutant for RR-BD and meso-BD increased 4- and 37-fold, respectively, the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 3- and 28-fold, respectively. Additionally, the Val161Thr mutant slightly decreased catalytic efficiencies (twofold with RR-BD; 7.3-fold with meso-BD) due to an increase in KM (sixfold for RR-BD; 24-fold for meso-BD) and a slight increase (2.8-fold with RR-BD; 3.3-fold with meso-BD) in kcat. These findings validate the critical roles of Phe120 and Val161 of NgBDH in substrate binding and catalysis. Overall, the current study provides a better understanding of the substrate binding and catalysis of BDHs within the MDR superfamily.
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Affiliation(s)
- Xue Dong
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Tingting Zhang
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Chuanyue Gui
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Shuping Fei
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Haonan Xu
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Jianrong Chang
- Scientific Research Center, Bengbu Medical University, Bengbu, China
| | - Chaoqun Lian
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
| | - Wanggang Tang
- Bengbu Medical University Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
- Department of Biochemistry and Molecular Biology, School of Laboratory Medicine, Bengbu Medical University, Bengbu, China
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Li Y, Zhao X, Yao M, Yang W, Han Y, Liu L, Zhang J, Liu J. Mechanism of microbial production of acetoin and 2,3-butanediol optical isomers and substrate specificity of butanediol dehydrogenase. Microb Cell Fact 2023; 22:165. [PMID: 37644496 PMCID: PMC10466699 DOI: 10.1186/s12934-023-02163-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
3-Hydroxybutanone (Acetoin, AC) and 2,3-butanediol (BD) are two essential four-carbon platform compounds with numerous pharmaceutical and chemical synthesis applications. AC and BD have two and three stereoisomers, respectively, while the application of the single isomer product in chemical synthesis is superior. AC and BD are glucose overflow metabolites produced by biological fermentation from a variety of microorganisms. However, the AC or BD produced by microorganisms using glucose is typically a mixture of various stereoisomers. This was discovered to be due to the simultaneous presence of multiple butanediol dehydrogenases (BDHs) in microorganisms, and AC and BD can be interconverted under BDH catalysis. In this paper, beginning with the synthesis pathways of microbial AC and BD, we review in detail the studies on the formation mechanisms of different stereoisomers of AC and BD, summarize the properties of different types of BDH that have been tabulated, and analyze the structural characteristics and affinities of different types of BDH by comparing them using literature and biological database data. Using microorganisms, recent research on the production of optically pure AC or BD was also reviewed. Limiting factors and possible solutions for chiral AC and BD production are discussed.
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Affiliation(s)
- Yuchen Li
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiangying Zhao
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China.
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Mingjing Yao
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
| | - Wenli Yang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Yanlei Han
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
| | - Liping Liu
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Jiaxiang Zhang
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Jianjun Liu
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology, Shandong Academy of Sciences), Jinan, 250013, China
- School of Food Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
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Wang X, Jia L, Ji F. Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase. Biochim Biophys Acta Gen Subj 2023; 1867:130326. [PMID: 36781054 DOI: 10.1016/j.bbagen.2023.130326] [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: 09/11/2022] [Revised: 12/22/2022] [Accepted: 02/07/2023] [Indexed: 02/13/2023]
Abstract
2,3-butanediol dehydrogenase (BDH, EC 1.1.1.76) also known as acetoin reductase (AR, EC 1.1.1.4) is the key enzyme converting acetoin (AC) into 2,3-butanediol (BD) and undertaking the irreversible conversion of diacetyl to acetoin in various microorganisms. The existence of three BDHs (R,R-, meso-, and S,S-BDH) product different BD isomers. Catalyzing mechanisms of meso- and S,S-BDH have been understood with the assistance of their X-ray crystal structures. However, the lack of structural data for R,R-BDH restricts the integral understanding of the catalytic mechanism of BDHs. In this study, we successfully crystallized and solved the X-ray crystal structure of Bacillus subtilis R,R-BDH. A zinc ion was found locating in the catalytic center and coordinated by Cys37, His70 and Glu152, helping to stabilize the chiral substrates observed in the predicted molecular docking model. The interaction patterns of different chiral substrates in the molecular docking model explained the react priority measured by the enzyme activity assay of R,R-BDH. Site-directed mutation experiments determined that the amino acids Cys37, Thr244, Ile268 and Lys340 are important in the catalytically active center. The structural information of R,R-BDH presented in this study accomplished the understanding of BDHs catalytic mechanism and more importantly provides useful guidance for the directional engineering of R,R-BDH to obtain high-purity monochiral BD and AC.
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Affiliation(s)
- Xiaofei Wang
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, PR China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, PR China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, PR China.
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Shanbhag AP. Stairway to Stereoisomers: Engineering Short- and Medium-Chain Ketoreductases To Produce Chiral Alcohols. Chembiochem 2023; 24:e202200687. [PMID: 36640298 DOI: 10.1002/cbic.202200687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/15/2023]
Abstract
The short- and medium-chain dehydrogenase/reductase superfamilies are responsible for most chiral alcohol production in laboratories and industries. In nature, they participate in diverse roles such as detoxification, housekeeping, secondary metabolite production, and catalysis of several chemicals with commercial and environmental significance. As a result, they are used in industries to create biopolymers, active pharmaceutical intermediates (APIs), and are also used as components of modular enzymes like polyketide synthases for fabricating bioactive molecules. Consequently, random, semi-rational and rational engineering have helped transform these enzymes into product-oriented efficient catalysts. The rise of newer synthetic chemicals and their enantiopure counterparts has proved challenging, and engineering them has been the subject of numerous studies. However, they are frequently limited to the synthesis of a single chiral alcohol. The study attempts to defragment and describe hotspots of engineering short- and medium-chain dehydrogenases/reductases for the production of chiral synthons.
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Affiliation(s)
- Anirudh P Shanbhag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, India.,Bugworks Research India Pvt. Ltd., C-CAMP, National Centre for Biological Sciences (NCBS-TIFR), Bellary Road, Bangalore, 560003, India
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5
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Characterization of four diol dehydrogenases for enantioselective synthesis of chiral vicinal diols. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Choi Y, Kim YH. Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13. J Microbiol 2022; 60:411-418. [DOI: 10.1007/s12275-022-2018-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
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Jiang L, Lee MH, Kim CY, Kim SW, Kim PI, Min SR, Lee J. Plant Growth Promotion by Two Volatile Organic Compounds Emitted From the Fungus Cladosporium halotolerans NGPF1. FRONTIERS IN PLANT SCIENCE 2021; 12:794349. [PMID: 34925431 PMCID: PMC8678569 DOI: 10.3389/fpls.2021.794349] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Microbial volatiles have beneficial roles in the agricultural ecological system, enhancing plant growth and inducing systemic resistance against plant pathogens without being hazardous to the environment. The interactions of plant and fungal volatiles have been extensively studied, but there is limited research specifically elucidating the effects of distinct volatile organic compounds (VOCs) on plant growth promotion. The current study was conducted to investigate the impact of VOCs from Cladosporium halotolerans NGPF1 on plant growth, and to elucidate the mechanisms for the plant growth-promoting (PGP) activity of these VOCs. The VOCs from C. halotolerans NGPF1 significantly promoted plant growth compared with the control, and this PGP activity of the VOCs was culture medium-dependent. Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) identified two VOC structures with profiles that differed depending on the culture medium. The two compounds that were only produced in potato dextrose (PD) medium were identified as 2-methyl-butanal and 3-methyl-butanal, and both modulated plant growth promotion and root system development. The PGP effects of the identified synthetic compounds were analyzed individually and in blends using N. benthamiana plants. A blend of the two VOCs enhanced growth promotion and root system development compared with the individual compounds. Furthermore, real-time PCR revealed markedly increased expression of genes involved in auxin, expansin, and gibberellin biosynthesis and metabolism in plant leaves exposed to the two volatile blends, while cytokinin and ethylene expression levels were decreased or similar in comparison with the control. These findings demonstrate that naturally occurring fungal VOCs can induce plant growth promotion and provide new insights into the mechanism of PGP activity. The application of stimulatory volatiles for growth enhancement could be used in the agricultural industry to increase crop yield.
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Affiliation(s)
- Lingmin Jiang
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
| | - Myoung Hui Lee
- Wheat Research team, National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
| | - Pyoung Il Kim
- Center for Industrialization of Agricultural and Livestock Microorganisms (CIALM), Jeongeup, South Korea
| | - Sung Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jiyoung Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, South Korea
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Maina S, Prabhu AA, Vivek N, Vlysidis A, Koutinas A, Kumar V. Prospects on bio-based 2,3-butanediol and acetoin production: Recent progress and advances. Biotechnol Adv 2021; 54:107783. [PMID: 34098005 DOI: 10.1016/j.biotechadv.2021.107783] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/19/2022]
Abstract
The bio-based platform chemicals 2,3-butanediol (BDO) and acetoin have various applications in chemical, cosmetics, food, agriculture, and pharmaceutical industries, whereas the derivatives of BDO could be used as fuel additives, polymer and synthetic rubber production. This review summarizes the novel technological developments in adapting genetic and metabolic engineering strategies for selection and construction of chassis strains for BDO and acetoin production. The valorization of renewable feedstocks and bioprocess development for the upstream and downstream stages of bio-based BDO and acetoin production are discussed. The techno-economic aspects evaluating the viability and industrial potential of bio-based BDO production are presented. The commercialization of bio-based BDO and acetoin production requires the utilization of crude renewable resources, the chassis strains with high fermentation production efficiencies and development of sustainable purification or conversion technologies.
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Affiliation(s)
- Sofia Maina
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos, 75, 11855 Athens, Greece
| | - Ashish A Prabhu
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Narisetty Vivek
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Anestis Vlysidis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos, 75, 11855 Athens, Greece
| | - Apostolis Koutinas
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos, 75, 11855 Athens, Greece.
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
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Purification and Characterization of (2R,3R)-2,3-Butanediol Dehydrogenase of the Human Pathogen Neisseria gonorrhoeae FA1090 Produced in Escherichia coli. Mol Biotechnol 2021; 63:491-501. [PMID: 33763825 DOI: 10.1007/s12033-021-00308-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
2,3-Butanediol dehydrogenase (BDH), also known as acetoin/diacetyl reductase, is a pivotal enzyme for the formation of 2,3-butanediol (2,3-BD), a chiral compound with potential roles in the virulence of certain pathogens. Here, a NAD(H)-dependent (2R,3R)-BDH from Neisseria gonorrhoeae FA1090 (NgBDH), the causative agent of gonorrhoea, was functionally characterized. Sequence analysis indicated that it belongs to zinc-containing medium-chain dehydrogenase/reductase family. The recombinant NgBDH migrated as a single band with a size of around 45 kDa on SDS-PAGE and could be confirmed by Western blotting and mass spectrometry. For the oxidation of either (2R,3R)-2,3-BD or meso-2,3-BD, the enzyme exhibited a broad pH optimum between pH 9.5 to 11.5. For the reduction of (3R/3S)-acetoin, the pH optimum was around 6.5. The enzyme could catalyze the stereospecific oxidation of (2R,3R)-2,3-BD (Km = 0.16 mM, kcat/Km = 673 s-1 · mM-1) and meso-BD (Km = 0.72 mM, kcat/Km = 165 s-1 · mM-1). Moreover, it could also reduce (3R/3S)-acetoin with a Km of 0.14 mM and a kcat/Km of 885 s-1 · mM-1. The results presented here contribute to understand the 2,3-BD metabolism in N. gonorrhoeae and pave the way for studying the influence of 2,3-BD metabolism on the virulence of this pathogen in the future.
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Qiao Y, Wang C, Zeng Y, Wang T, Qiao J, Lu C, Wang Z, Ying X. Efficient whole-cell oxidation of α,β-unsaturated alcohols to α,β-unsaturated aldehydes through the cascade biocatalysis of alcohol dehydrogenase, NADPH oxidase and hemoglobin. Microb Cell Fact 2021; 20:17. [PMID: 33468136 PMCID: PMC7816460 DOI: 10.1186/s12934-021-01511-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Background α,β-Unsaturated aldehydes are widely used in the organic synthesis of fine chemicals for application in products such as flavoring agents, fragrances and pharmaceuticals. In the selective oxidation of α,β-unsaturated alcohols to the corresponding α,β-unsaturated aldehydes, it remains challenging to overcome poor selectivity, overoxidation and a low atom efficiency in chemical routes. Results An E. coli strain coexpressing the NADP+-specific alcohol dehydrogenase YsADH and the oxygen-dependent NADPH oxidase TkNOX was constructed; these components enabled the NADP+ regeneration and catalyzed the oxidation of 100 mM 3-methyl-2-buten-1-ol to 3-methyl-2-butenal with a yield of 21.3%. The oxygen supply was strengthened by introducing the hemoglobin protein VsHGB into recombinant E. coli cells and replacing the atmosphere of the reactor with pure oxygen, which increased the yield to 51.3%. To further improve catalytic performance, the E. coli cells expressing the multifunctional fusion enzyme YsADH-(GSG)-TkNOX-(GSG)-VsHGB were generated, which completely converted 250 mM 3-methyl-2-buten-1-ol to 3-methyl-2-butenal after 8 h of whole-cell oxidation. The reaction conditions for the cascade biocatalysis were optimized, in which supplementation with 0.2 mM FAD and 0.4 mM NADP+ was essential for maintaining high catalytic activity. Finally, the established whole-cell system could serve as a platform for the synthesis of valuable α,β-unsaturated aldehydes through the selective oxidation of various α,β-unsaturated alcohols. Conclusions The construction of a strain expressing the fusion enzyme YsADH-(GSG)-TkNOX-(GSG)-VsHGB achieved efficient NADP+ regeneration and the selective oxidation of various α,β-unsaturated alcohols to the corresponding α,β-unsaturated aldehydes. Among the available redox enzymes, the fusion enzyme YsADH-(GSG)-TkNOX-(GSG)-VsHGB has become the most recent successful example to improve catalytic performance in comparison with its separate components.
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Affiliation(s)
- Yan Qiao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Can Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yin Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Tairan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jingjing Qiao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Chenze Lu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiangxian Ying
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
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Elmahmoudy M, Elfeky N, Zhongji P, Zhang Y, Bao Y. Identification and characterization of a novel 2R,3R-Butanediol dehydrogenase from Bacillus sp. DL01. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Subramanian V, Lunin VV, Farmer SJ, Alahuhta M, Moore KT, Ho A, Chaudhari YB, Zhang M, Himmel ME, Decker SR. Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:186. [PMID: 33292448 PMCID: PMC7656694 DOI: 10.1186/s13068-020-01820-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/21/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. RESULTS Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh (SmBdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34-2.87 µmol/min/mg). The SmBdh crystal structure was determined through crystallization with cofactor (NAD+) and substrate (acetoin) molecules bound in the active site. Active SmBdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. SmBdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae (EcBdh) enzyme resulted in reduction of SmBdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the EcBdh to mimic the SmBdh structure resulted in ~ 70% increase in its activity. CONCLUSIONS This study has demonstrated that SmBdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. SmBdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.
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Affiliation(s)
- Venkataramanan Subramanian
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA.
| | - Samuel J Farmer
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Kyle T Moore
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Angela Ho
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Yogesh B Chaudhari
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
- Biodiversity and Ecosystem Research, Institute of Advanced Study in Science and Technology (IASST), Guwahati, Assam, India
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
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Kuang X, Ouyang Y, Guo Y, Li Q, Wang H, Abrha GT, Ayepa E, Gu Y, Li X, Chen Q, Ma M. New insights into two yeast BDHs from the PDH subfamily as aldehyde reductases in context of detoxification of lignocellulosic aldehyde inhibitors. Appl Microbiol Biotechnol 2020; 104:6679-6692. [PMID: 32556414 DOI: 10.1007/s00253-020-10722-9] [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: 01/16/2020] [Revised: 05/25/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022]
Abstract
At least 24 aldehyde reductases from Saccharomyces cerevisiae have been characterized and most function in in situ detoxification of lignocellulosic aldehyde inhibitors, but none is classified into the polyol dehydrogenase (PDH) subfamily of the medium-chain dehydrogenase/reductase (MDR) superfamily. This study confirmed that two (2R,3R)-2,3-butanediol dehydrogenases (BDHs) from industrial (denoted Y)/laboratory (denoted B) strains of S. cerevisiae, Bdh1p(Y)/Bdh1p(B) and Bdh2p(Y)/Bdh2p(B), were members of the PDH subfamily with an NAD(P)H binding domain and a catalytic zinc binding domain, and exhibited reductive activities towards lignocellulosic aldehyde inhibitors, such as acetaldehyde, glycolaldehyde, and furfural. Especially, the highest enzyme activity towards acetaldehyde by Bdh2p(Y) was 117.95 U/mg with cofactor nicotinamide adenine dinucleotide reduced (NADH). Based on the comparative kinetic property analysis, Bdh2p(Y)/Bdh2p(B) possessed higher specific activity, substrate affinity, and catalytic efficiency towards glycolaldehyde than Bdh1p(Y)/Bdh1p(B). This was speculated to be related to their 49% sequence differences and five nonsynonymous substitutions (Ser41Thr, Glu173Gln, Ile270Leu, Ile316Met, and Gly317Cys) occurred in their conserved NAD(P)H binding domains. Compared with BDHs from a laboratory strain, Bdh1p(Y) and Bdh2p(Y) from an industrial strain displayed five nonsynonymous mutations (Thr12, Asn61, Glu168, Val222, and Ala235) and three nonsynonymous mutations (Ala34, Ile96, and Ala369), respectively. From a first analysis with selected aldehydes, their reductase activities were different from BDHs of laboratory strain, and their catalytic efficiency was higher towards glycolaldehyde and lower towards acetaldehyde. Comparative investigation of kinetic properties of BDHs from S. cerevisiae as aldehyde reductases provides a guideline for their practical applications in in situ detoxification of aldehyde inhibitors during lignocellulose bioconversion.Key Points• Two yeast BDHs have enzyme activities for reduction of aldehydes.• Overexpression of BDHs slightly improves yeast tolerance to acetaldehyde and glycolaldehyde.• Bdh1p and Bdh2p differ in enzyme kinetic properties.• BDHs from strains with different genetic backgrounds differ in enzyme kinetic properties.
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Affiliation(s)
- Xiaolin Kuang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yidan Ouyang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yaping Guo
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.,Patent Examination Cooperation Sichuan Center of the Patent Office, SIPO, Chengdu, 610213, Sichuan, People's Republic of China
| | - Qian Li
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Hanyu Wang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Getachew Tafere Abrha
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Ellen Ayepa
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Yunfu Gu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Qiang Chen
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China
| | - Menggen Ma
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, No. 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China. .,Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, People's Republic of China.
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14
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Muschallik L, Molinnus D, Jablonski M, Kipp CR, Bongaerts J, Pohl M, Wagner T, Schöning MJ, Selmer T, Siegert P. Synthesis of α-hydroxy ketones and vicinal (R,R)-diols by Bacillus clausii DSM 8716T butanediol dehydrogenase. RSC Adv 2020; 10:12206-12216. [PMID: 35497574 PMCID: PMC9050739 DOI: 10.1039/d0ra02066d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/05/2020] [Indexed: 12/04/2022] Open
Abstract
α-hydroxy ketones (HK) and 1,2-diols are important building blocks for fine chemical synthesis. Here, we describe the R-selective 2,3-butanediol dehydrogenase from B. clausii DSM 8716T (BcBDH) that belongs to the metal-dependent medium chain dehydrogenases/reductases family (MDR) and catalyzes the selective asymmetric reduction of prochiral 1,2-diketones to the corresponding HK and, in some cases, the reduction of the same to the corresponding 1,2-diols. Aliphatic diketones, like 2,3-pentanedione, 2,3-hexanedione, 5-methyl-2,3-hexanedione, 3,4-hexanedione and 2,3-heptanedione are well transformed. In addition, surprisingly alkyl phenyl dicarbonyls, like 2-hydroxy-1-phenylpropan-1-one and phenylglyoxal are accepted, whereas their derivatives with two phenyl groups are not substrates. Supplementation of Mn2+ (1 mM) increases BcBDH's activity in biotransformations. Furthermore, the biocatalytic reduction of 5-methyl-2,3-hexanedione to mainly 5-methyl-3-hydroxy-2-hexanone with only small amounts of 5-methyl-2-hydroxy-3-hexanone within an enzyme membrane reactor is demonstrated. Reduction of symmetric or asymmetric vicinal diketones with BcBDH leads to the synthesis of either α-hydroxyketones or vicinal diols.![]()
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Affiliation(s)
- Lukas Muschallik
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Denise Molinnus
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Melanie Jablonski
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Carina Ronja Kipp
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Martina Pohl
- IBG-1: Biotechnology
- Forschungszentrum Jülich
- 52425 Jülich
- Germany
| | - Torsten Wagner
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Michael J. Schöning
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Thorsten Selmer
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies
- Aachen University of Applied Sciences
- 52428 Jülich
- Germany
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15
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Fernández-Gutierrez D, Veillette M, Ávalos Ramirez A, Giroir-Fendler A, Faucheux N, Heitz M. Biovalorization of glucose in four culture media and effect of the nitrogen source on fermentative alcohols production by Escherichia coli. ENVIRONMENTAL TECHNOLOGY 2020; 41:211-221. [PMID: 29969951 DOI: 10.1080/09593330.2018.1494751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/22/2018] [Indexed: 06/08/2023]
Abstract
Glucose is one of the most abundant monosaccharides and the easiest carbon source to be consumed by bacteria. In this study, four culture media (LB, M9, M63 and MOPS) were supplemented with glucose at three different concentrations (4, 12.5 and 25 g/L) in the presence of a genetically modified strain of Escherichia coli with the purpose of selecting the most suitable culture medium to obtain ABD (acetoin (A) and 2,3-butanediol (2,3-BD)). The selected medium was M9, the cheapest culture medium, since the ABD yields obtained fermenting 12.5 and 25 g/L of glucose in M9 culture medium at 37°C, atmospheric pressure, initial pH 6.5, 100 rpm and 10% (v/v) of inoculum were similar compared to the ABD yields obtained using M63 and LB culture media. The influence of nitrogen on ABD yield was tested adding sodium nitrate (NaNO3) or urea ((NH2)2CO) to M9 culture medium at three different nitrogen concentrations (2.5, 5.0 and 7.0 g N/L). Adding urea (7.0 g N/L) to M9 supplemented with 25 g/L of glucose improved by 23% the ABD yield at 96 h compared to M9 without urea, reaching a value of 27.2% (g ABD/g glucose). In contrast, the use of NaNO3 had no significant effect on the ABD yield.
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Affiliation(s)
- David Fernández-Gutierrez
- Department of Chemical and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, Sherbrooke, Canada
- Université Lyon 1, CNRS, UMR 5256, IRCELYON, Institut de Recherches sur la Catalyse et l'Environnement de Lyon, Villeurbanne Cedex, France
| | - Marc Veillette
- Department of Chemical and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, Sherbrooke, Canada
| | - Antonio Ávalos Ramirez
- Centre National en Électrochimie et en Technologies Environnementales, Shawinigan, Canada
| | - Anne Giroir-Fendler
- Université Lyon 1, CNRS, UMR 5256, IRCELYON, Institut de Recherches sur la Catalyse et l'Environnement de Lyon, Villeurbanne Cedex, France
| | - Nathalie Faucheux
- Department of Chemical and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, Sherbrooke, Canada
| | - Michèle Heitz
- Department of Chemical and Biotechnological Engineering, Faculty of Engineering, Université de Sherbrooke, Sherbrooke, Canada
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16
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Gong FQ, Liu QS, Tan HD, Li T, Tan CY, Yin H. Cloning, expression and characterization of a novel (2R,3R) -2,3-butanediol dehydrogenase from Bacillus thuringiensis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Ying X, Yu S, Huang M, Wei R, Meng S, Cheng F, Yu M, Ying M, Zhao M, Wang Z. Engineering the Enantioselectivity of Yeast Old Yellow Enzyme OYE2y in Asymmetric Reduction of ( E/ Z)-Citral to ( R)-Citronellal. Molecules 2019; 24:E1057. [PMID: 30889828 PMCID: PMC6470962 DOI: 10.3390/molecules24061057] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 11/25/2022] Open
Abstract
The members of the Old Yellow Enzyme (OYE) family are capable of catalyzing the asymmetric reduction of (E/Z)-citral to (R)-citronellal-a key intermediate in the synthesis of L-menthol. The applications of OYE-mediated biotransformation are usually hampered by its insufficient enantioselectivity and low activity. Here, the (R)-enantioselectivity of Old Yellow Enzyme from Saccharomyces cerevisiae CICC1060 (OYE2y) was enhanced through protein engineering. The single mutations of OYE2y revealed that the sites R330 and P76 could act as the enantioselectivity switch of OYE2y. Site-saturation mutagenesis was conducted to generate all possible replacements for the sites R330 and P76, yielding 17 and five variants with improved (R)-enantioselectivity in the (E/Z)-citral reduction, respectively. Among them, the variants R330H and P76C partly reversed the neral derived enantioselectivity from 32.66% e.e. (S) to 71.92% e.e. (R) and 37.50% e.e. (R), respectively. The docking analysis of OYE2y and its variants revealed that the substitutions R330H and P76C enabled neral to bind with a flipped orientation in the active site and thus reverse the enantioselectivity. Remarkably, the double substitutions of R330H/P76M, P76G/R330H, or P76S/R330H further improved (R)-enantioselectivity to >99% e.e. in the reduction of (E)-citral or (E/Z)-citral. The results demonstrated that it was feasible to alter the enantioselectivity of OYEs through engineering key residue distant from active sites, e.g., R330 in OYE2y.
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Affiliation(s)
- Xiangxian Ying
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Shihua Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meijuan Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Ran Wei
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Shumin Meng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meilan Yu
- College of Life Sciences, Zhejiang Sci-Tech Univeristy, Hangzhou 310018, China.
| | - Meirong Ying
- Grain and Oil Products Quality Inspection Center of Zhejiang Province, Hangzhou 310012, China.
| | - Man Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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18
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Jia X, Kelly RM, Han Y. Simultaneous biosynthesis of ( R)-acetoin and ethylene glycol from D-xylose through in vitro metabolic engineering. Metab Eng Commun 2018; 7:e00074. [PMID: 30197863 PMCID: PMC6127078 DOI: 10.1016/j.mec.2018.e00074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/18/2018] [Accepted: 06/24/2018] [Indexed: 11/28/2022] Open
Abstract
(R)-acetoin is a four-carbon platform compound used as the precursor for synthesizing novel optically active materials. Ethylene glycol (EG) is a large-volume two-carbon commodity chemical used as the anti-freezing agent and building-block molecule for various polymers. Currently established microbial fermentation processes for converting monosaccharides to either (R)-acetoin or EG are plagued by the formation of undesirable by-products. We show here that a cell-free bioreaction scheme can generate enantiomerically pure acetoin and EG as co-products from biomass-derived D-xylose. The seven-step, ATP-free system included in situ cofactor regeneration and recruited enzymes from Escherichia coli W3110, Bacillus subtilis shaijiu 32 and Caulobacter crescentus CB 2. Optimized in vitro biocatalytic conditions generated 3.2 mM (R)-acetoin with stereoisomeric purity of 99.5% from 10 mM D-xylose at 30 °C and pH 7.5 after 24 h, with an initial (R)-acetoin productivity of 1.0 mM/h. Concomitantly, EG was produced at 5.5 mM, with an initial productivity of 1.7 mM/h. This in vitro biocatalytic platform illustrates the potential for production of multiple value-added biomolecules from biomass-based sugars with no ATP requirement.
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Key Words
- (R)-acetoin
- BSA, bovine serum albumin
- Cofactor regeneration
- D-xylose
- EG, ethylene glycol
- EMP, Embden-Meyerhoff-Parnas
- Ethylene glycol
- FAD, flavin adenine dinucleotide
- GC, gas chromatography
- HPLC, high-pressure liquid chromatography
- IPTG, isopropyl-β-D-thiogalactopyranoside
- In vitro metabolic engineering
- LB, lysogeny broth
- NAD+, oxidized nicotinamide adenine dinucleotide
- NADH, reduced nicotinamide adenine dinucleotide
- PET, polyethylene terephthalate
- PP, pentose phosphate
- SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis
- ThDP, Thiamine diphosphate
- ee, enantiomeric excess
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Affiliation(s)
- Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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19
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Ying X, Zhang J, Wang C, Huang M, Ji Y, Cheng F, Yu M, Wang Z, Ying M. Characterization of a Carbonyl Reductase from Rhodococcus erythropolis WZ010 and Its Variant Y54F for Asymmetric Synthesis of ( S)- N-Boc-3-Hydroxypiperidine. Molecules 2018; 23:molecules23123117. [PMID: 30487432 PMCID: PMC6321125 DOI: 10.3390/molecules23123117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 11/25/2018] [Accepted: 11/27/2018] [Indexed: 11/16/2022] Open
Abstract
The recombinant carbonyl reductase from Rhodococcus erythropolis WZ010 (ReCR) demonstrated strict (S)-stereoselectivity and catalyzed the irreversible reduction of N-Boc-3-piperidone (NBPO) to (S)-N-Boc-3-hydroxypiperidine [(S)-NBHP], a key chiral intermediate in the synthesis of ibrutinib. The NAD(H)-specific enzyme was active within broad ranges of pH and temperature and had remarkable activity in the presence of higher concentration of organic solvents. The amino acid residue at position 54 was critical for the activity and the substitution of Tyr54 to Phe significantly enhanced the catalytic efficiency of ReCR. The kcat/Km values of ReCR Y54F for NBPO, (R/S)-2-octanol, and 2-propanol were 49.17 s−1 mM−1, 56.56 s−1 mM−1, and 20.69 s−1 mM−1, respectively. In addition, the (S)-NBHP yield was as high as 95.92% when whole cells of E. coli overexpressing ReCR variant Y54F catalyzed the asymmetric reduction of 1.5 M NBPO for 12 h in the aqueous/(R/S)-2-octanol biphasic system, demonstrating the great potential of ReCR variant Y54F for practical applications.
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Affiliation(s)
- Xiangxian Ying
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Jie Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Can Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meijuan Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yuting Ji
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meilan Yu
- College of Life Sciences, Zhejiang Sci-Tech Univeristy, Hangzhou 310018, China.
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Meirong Ying
- Grain and Oil Products Quality Inspection Center of Zhejiang Province, Hangzhou 310012, China.
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20
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Yang Z, Zhang Z. Recent advances on production of 2, 3-butanediol using engineered microbes. Biotechnol Adv 2018; 37:569-578. [PMID: 29608949 DOI: 10.1016/j.biotechadv.2018.03.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/17/2018] [Accepted: 03/23/2018] [Indexed: 12/31/2022]
Abstract
As a significant platform chemical, 2, 3-butanediol (2, 3-BD) has found wide applications in industry. The success of microbial 2, 3-BD production was limited by the use of pathogenic microorganisms and low titer in engineered hosts. The utilization of cheaply available feedstock such as lignocellulose was another major challenge to achieve economic production of 2, 3-BD. To address those issues, engineering strategies including both genetic modifications and process optimization have been employed. In this review, we summarized the state-of-the-art progress in the biotechnological production of 2, 3-BD. Metabolic engineering and process engineering strategies were discussed.
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Affiliation(s)
- Zhiliang Yang
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur Private, Ottawa, ON K1N 6N5, Canada.
| | - Zisheng Zhang
- Department of Chemical and Biological Engineering, University of Ottawa, 161 Louis Pasteur Private, Ottawa, ON K1N 6N5, Canada.
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21
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Efficient (3S)-Acetoin and (2S,3S)-2,3-Butanediol Production from meso-2,3-Butanediol Using Whole-Cell Biocatalysis. Molecules 2018; 23:molecules23030691. [PMID: 29562693 PMCID: PMC6017632 DOI: 10.3390/molecules23030691] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/06/2018] [Accepted: 03/12/2018] [Indexed: 11/17/2022] Open
Abstract
(3S)-Acetoin and (2S,3S)-2,3-butanediol are important platform chemicals widely applied in the asymmetric synthesis of valuable chiral chemicals. However, their production by fermentative methods is difficult to perform. This study aimed to develop a whole-cell biocatalysis strategy for the production of (3S)-acetoin and (2S,3S)-2,3-butanediol from meso-2,3-butanediol. First, E. coli co-expressing (2R,3R)-2,3-butanediol dehydrogenase, NADH oxidase and Vitreoscilla hemoglobin was developed for (3S)-acetoin production from meso-2,3-butanediol. Maximum (3S)-acetoin concentration of 72.38 g/L with the stereoisomeric purity of 94.65% was achieved at 24 h under optimal conditions. Subsequently, we developed another biocatalyst co-expressing (2S,3S)-2,3-butanediol dehydrogenase and formate dehydrogenase for (2S,3S)-2,3-butanediol production from (3S)-acetoin. Synchronous catalysis together with two biocatalysts afforded 38.41 g/L of (2S,3S)-butanediol with stereoisomeric purity of 98.03% from 40 g/L meso-2,3-butanediol. These results exhibited the potential for (3S)-acetoin and (2S,3S)-butanediol production from meso-2,3-butanediol as a substrate via whole-cell biocatalysis.
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22
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Muschallik L, Molinnus D, Bongaerts J, Pohl M, Wagner T, Schöning MJ, Siegert P, Selmer T. (R,R)-Butane-2,3-diol dehydrogenase from Bacillus clausii DSM 8716 T: Cloning and expression of the bdhA-gene, and initial characterization of enzyme. J Biotechnol 2017; 258:41-50. [PMID: 28793235 DOI: 10.1016/j.jbiotec.2017.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/09/2017] [Accepted: 07/21/2017] [Indexed: 12/01/2022]
Abstract
The gene encoding a putative (R,R)-butane-2,3-diol dehydrogenase (bdhA) from Bacillus clausii DSM 8716T was isolated, sequenced and expressed in Escherichia coli. The amino acid sequence of the encoded protein is only distantly related to previously studied enzymes (identity 33-43%) and exhibited some uncharted peculiarities. An N-terminally StrepII-tagged enzyme variant was purified and initially characterized. The isolated enzyme catalyzed the (R)-specific oxidation of (R,R)- and meso-butane-2,3-diol to (R)- and (S)-acetoin with specific activities of 12U/mg and 23U/mg, respectively. Likewise, racemic acetoin was reduced with a specific activity of up to 115U/mg yielding a mixture of (R,R)- and meso-butane-2,3-diol, while the enzyme reduced butane-2,3-dione (Vmax 74U/mg) solely to (R,R)-butane-2,3-diol via (R)-acetoin. For these reactions only activity with the co-substrates NADH/NAD+ was observed. The enzyme accepted a selection of vicinal diketones, α-hydroxy ketones and vicinal diols as alternative substrates. Although the physiological function of the enzyme in B. clausii remains elusive, the data presented herein clearly demonstrates that the encoded enzyme is a genuine (R,R)-butane-2,3-diol dehydrogenase with potential for applications in biocatalysis and sensor development.
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Affiliation(s)
- Lukas Muschallik
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Denise Molinnus
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Johannes Bongaerts
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Torsten Wagner
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Michael J Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Petra Siegert
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany
| | - Thorsten Selmer
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, 52428 Jülich, Germany.
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Stereospecificity of Corynebacterium glutamicum 2,3-butanediol dehydrogenase and implications for the stereochemical purity of bioproduced 2,3-butanediol. Appl Microbiol Biotechnol 2016; 100:10573-10583. [DOI: 10.1007/s00253-016-7860-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 08/22/2016] [Accepted: 09/13/2016] [Indexed: 10/20/2022]
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24
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Takeda M, Matsumura AT, Kurosaki K, Chhetri RT, Motomatsu S, Suzuki I, Sahabi DM. An enantioselective NADP+-dependent alcohol dehydrogenase responsible for cooxidative production of (3S)-5-hydroxy-3-methyl-pentanoic acid. Biosci Biotechnol Biochem 2016; 80:1155-63. [DOI: 10.1080/09168451.2016.1148578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
A soil bacterium, Mycobacterium sp. B-009, is able to grow on racemic 1,2-propanediol (PD). The strain was revealed to oxidize 3-methyl-1,5-pentanediol (MPD) to 5-hydroxy-3-methyl-pentanoic acid (HMPA) during growth on PD. MPD was converted into an almost equimolar amount of the S-form of HMPA (S-HMPA) at 72%ee, suggesting the presence of an enantioselective MPD dehydrogenase (MPD-DH). As expected, an NADP+-dependent alcohol dehydrogenase, which catalyzes the initial step of MPD oxidation, was detected and purified from the cell-free extract. This enzyme was suggested to be a homodimeric medium-chain alcohol dehydrogenase/reductase (MDR). The catalytic and kinetic parameters indicated that MPD is the most suitable substrate for the enzyme. The enzyme was encoded by a 1047-bp gene (mpd1) and several mycobacterial strains were found to have putative MDR genes similar to mpd1. In a phylogenetic tree, MPD-DH formed an independent clade together with the putative MDR of Mycobacterium neoaurum, which produces opportunistic infections.
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Affiliation(s)
- Minoru Takeda
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | | | - Kaishi Kurosaki
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Rajan Thapa Chhetri
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Shigekazu Motomatsu
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Ichiro Suzuki
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Danladi Mahuta Sahabi
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
- Department of Biochemistry, Usmanu Danfodiyo University, Sokoto, Nigeria
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25
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Redesigning alcohol dehydrogenases/reductases for more efficient biosynthesis of enantiopure isomers. Biotechnol Adv 2015; 33:1671-84. [DOI: 10.1016/j.biotechadv.2015.08.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/11/2015] [Accepted: 08/12/2015] [Indexed: 11/20/2022]
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26
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Jawed M, Pi J, Xu L, Zhang H, Hakeem A, Yan Y. Enhanced H2 Production and Redirected Metabolic Flux via Overexpression of fhlA and pncB in Klebsiella HQ-3 Strain. Appl Biochem Biotechnol 2015; 178:1113-28. [PMID: 26590848 DOI: 10.1007/s12010-015-1932-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 11/16/2015] [Indexed: 11/26/2022]
Abstract
Genetic modifications are considered as one of the most important technologies for improving fermentative hydrogen yield. Herein, we overexpress fhlA and pncB genes from Klebsiella HQ-3 independently to enhance hydrogen molar yield. HQ-3-fhlA/pncB strain is developed by manipulation of pET28-Pkan/fhlA Kan(r) and pBBR1-MCS5/pncB Gm(r) as expression vectors to examine the synchronous effects of fhlA and pncB. Optimization of anaerobic batch fermentations is achieved and the maximum yield of biohydrogen (1.42 mol H2/mol of glucose) is produced in the range of pH 6.5-7.0 at 33-37 °C. Whole cell H2 yield is increased up to 40 % from HQ-3-fhlA/pncB, as compared with HQ-3-fhlA 20 % and HQ-3-pncB 12 % keeping HQ-3-C as a control. Mechanism of improved H2 yield is studied in combination with metabolic flux analysis by measuring glucose consumption and other metabolites including formate, succinate, 2,3 butanediol, lactate, acetate, ethanol, and hydrogen. The results suggest that under transient conditions, the increase in the total level of NAD by NAPRTase can enhance the rate of NADH-dependent pathways, and therefore, final distribution of metabolites is changed. Combined overexpression of fhlA and pncB eventually modifies the energy and carbon balance leading to enhanced H2 production from FHL as well as by NADH pathway.
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Affiliation(s)
- Muhammad Jawed
- Key Laboratory of Molecular Biophysics, the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Jian Pi
- Key Laboratory of Molecular Biophysics, the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Li Xu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Houjin Zhang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Abdul Hakeem
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
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